Iowa State University

Iowa State University
Bioinformatics & Computational Biology Bioinformatics & Computational Biology


Faculty Research


Faculty in the BCB Graduate Program conduct research in all major research areas of computational molecular biology, including genomics, structural genomics, functional genomics, and computational systems biology, with access to some of the most modern experimental platforms. Many interdisciplinary research projects take place at Iowa State.

Below are brief descriptions of the research interests of the BCB faculty. Our faculty come from many backgrounds and provide opportunities for research in a wide variety of areas.



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* Asterisked Faculty currently serve as major or co-major professors for BCB Students.


Dean Adams

BCB Faculty Member in the EEOB Department

Education: Ph.D., SUNY at Stony Brook, 1999

Research Interests:

  • Comparative evolutionary biology; micro- and macroevolutionary morphology; theory and analytical methods in evolution; herpetology; morphometrics (statistical shape analysis).
  • Mathematical Biology, Computational Modeling, Computational Systems Biology

Description: Our research focuses on the evolution of the multivariate phenotype. We are interested in understanding micro- and macroevolutionary patterns of phenotypic diversification, and the historical and ecological processes that are responsible for them. We use a comparative evolutionary framework to attain these goals, directing our empirical work towards vertebrates, with an emphasis on plethodontid salamanders. We also develop new theoretical and analytical approaches for quantifying the multivariate phenotype, and for elucidating patterns of phenotypic evolution and change.

Select Recent Publications:

  • Adams, D.C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution. 68: doi: 10.1111/evo.12463.
  • Adams, D.C. 2014. A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data. Systematic Biology. 63: 10.1093/sysbio/syu030.
  • Caruso, N.M., M. Sears, D.C. Adams, and K.R. Lips. 2014. Widespread rapid reductions in body size of Appalachian salamanders in response to climate change. Global Change Biology. 20:1751-1759. ** Featured commentary in 1) Nature News, 2) Science Now ** Media coverage: 1) Scientific American, 2) National Geographic, 3) BBC Nature, 4) NBC News, 5) Nature World News, 6) International Business Times, 7) Headlines and Global News, 8) The Weather Channel, 9) Austrian Tribune, 10) Huffington Post, 11) University Herald, 12) Der Standard, 13) EcoWatch, 14) Environmental Protection Online, 15) United Press International, 16) RedOrbit, 17) Des Moines Register, 18) Futurity, 19) RadioIowa, 20) Ames Tribune
  • Adams, D.C. and R. Felice. 2014. Assessing phylogenetic morphological integration and trait covariation in morphometric data using evolutionary covariance matrices. PLoS ONE. 9(4):e94335.
  • Kraemer, A.C.*, and D.C. Adams. 2014. Predator perception of Batesian mimicry in a salamander. Evolution. 68:1197-1206.
  • Condon, M.A., S.J. Scheffer, M. Lewis, R. Wharton, D.C. Adams, and A.A. Forbes. Lethal interactions between parasites and prey increase niche diversity in a tropical community. Science. 343:1240-1244. ** Featured Commentary in Science 343:1213-1214.
  • Rivera, G., J.N. Davis*, J.C. Godwin, and D.C. Adams. 2014. Parallel evolution of habitat-associated divergence in shell shape of turtles. Evolutionary Biology. 41:29-37.
  • Adams, D.C. 2014. Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Systematic Biology. 63:166-177.
  • Adams, D.C. 2013. Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood. Systematic Biology . 62:181-192.
  • Adams, D.C., F. J. Rohlf, and D.E. Slice. 2013. A field comes of age: Geometric morphometrics in the 21st century. Hystrix. 24:7-14.
  • Adams, D.C., and E. Otarola-Castillo. 2013. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution . 4:393-399.
  • Ceballos, C., D.C. Adams, J. Iverson, and N. Valenzuela. 2013. Phylogenetic patterns of sexual size dimorphism in turtles and their implications for Rensch's rule. Evolutionary Biology . 40:194-208.

Vita: Click here to download

Website: Dean Adams

Amy Andreotti

BCB Faculty Member in the BBMB Department

Education: Ph.D., Princeton, 1994

Research Interests: Macromolecular structure-function, NMR spectroscopy

  • Macromolecular Structure and Function--Macromolecular structure/function relationships; protein structure determination using nuclear magnetic resonance; molecular recognition


Finely tuned signal transduction cascades control all aspects of cell renewal and cell death in normal, healthy cells. Altered gene products introduce the possibility of imbalance within the tightly controlled signaling networks that regulate cell growth and proliferation. This is evident in the malignant form of the src tyrosine kinase, the viral oncogene v-src. For this protein it has been shown (both biochemically and structurally) that a single amino acid mutation disrupts the intramolecular interactions responsible for inactivating the enzyme, thus rendering the protein constitutively active(1). Aberrant signaling due to excess phosphorylation ensues, leading to dire consequences for the cell and, ultimately, for the organism. While the molecular details of the regulation of some families of kinases (i.e. Src) have now been clarified, it is not understood how the substrate binding and catalytic activity of other families of protein tyrosine kinases are controlled. We are particularly interested in a family of intracellular signaling molecules that is exclusively expressed in hematopoeitic cells, and we have focused our attention on the IL2-inducible tyrosine kinase (Itk), a member of the Tec family of tyrosine kinases that is restricted to the T-cell lineage.

Structurally, Itk and related tyrosine kinases (Btk, Tec, Bmx and Rlk) are quite distinct from the well-studied Src kinase family and are most likely regulated by an alternative mechanism given the nature of the differences in domain structure (2). The Andreotti laboratory makes use of nuclear magnetic resonance (NMR) spectroscopy to determine the three-dimensional structures of various domains of Itk and related family members. Additionally, NMR is used to examine interactions between domains to ultimately understand the regulatory apparatus of the Tec kinases in molecular detail.

The overreaching goal of the research program is to gain a better understanding of hematopoeitic cell signaling at the molecular level. Eventually, the complex pathways that control signaling through cell surface receptors such as the T cell receptor should be completely understood. Our knowledge of such events will allow more complete under-standing of how malfunction of the immune response can lead to autoimmune diseases and cancer.

Selected Publications:

  • Xie Q, Joseph RE, Fulton DB, Andreotti AH. Substrate recognition of PLCγ1 via a specific docking surface on Itk. J Mol Biol. 2013 Feb 22;425(4):683-96. doi: 10.1016/j.jmb.2012.10.023. Epub 2012 Dec 3. PubMed PMID: 23219468.
  • Boyken SE, Fulton DB, Andreotti AH. Rescue of the aggregation prone Itk Pleckstrin Homology domain by two mutations derived from the related kinases, Btk and Tec. Protein Sci. 2012 Sep;21(9):1288-97. doi: 10.1002/pro.2114. Epub 2012 Jul 16. PubMed PMID: 22761113; PubMed Central PMCID: PMC3631358.
  • Levytskyy RM, Hirve N, Guimond DM, Min L, Andreotti AH, Tsoukas CD. In Vivo Consequences of Disrupting SH3-Mediated Interactions of the Inducible T-Cell Kinase. J Signal Transduct. 2012;2012:694386. doi: 10.1155/2012/694386. Epub 2012 May 9. PubMed PMID: 22649724; PubMed Central PMCID: PMC3357558.
  • Joseph RE, Ginder ND, Hoy JA, Nix JC, Fulton DB, Honzatko RB, Andreotti AH. Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Feb 1;68(Pt 2):145-53. doi: 10.1107/S1744309111049761. Epub 2012 Jan 25. PubMed PMID: 22297986; PubMed Central PMCID: PMC3274390.
  • Joseph RE, Ginder ND, Hoy JA, Nix JC, Honzatko RB, Andreotti AH. Purification, crystallization and preliminary crystallographic analysis of the SH2 domain of IL-2-inducible T-cell kinase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt 2):269-73. doi: 10.1107/S1744309110052346. Epub 2011 Jan 27. PubMed PMID: 21301103; PubMed Central PMCID: PMC3034625.
  • Joseph RE, Andreotti AH. Controlling the activity of the Tec kinase Itk by mutation of the phenylalanine gatekeeper residue. Biochemistry. 2011 Jan
    18;50(2):221-9. Epub 2010 Dec 16. PubMed PMID: 21138328; PubMed Central PMCID: PMC3083488.

Vita: Click here to download

Website: Amy Andreotti

*William Beavis

BCB Faculty Member in the Agronomy Department

Education: Ph.D., 1986, Plant Breeding, Iowa State University, Ames, IA

Research Interests:

  • Theoretically, the impact of genetic bottlenecks is through selection, drift and disequilibrium which limit genetic potential of a crop to sub-optimal levels (Robertson, 1960; Hill and Robertson, 1968; Bulmer, 1971). Despite theoretical considerations of limits to genetic potential, we do not know: 1) whether desirable allelic variants have been eliminated during the adaptation and breeding processes, 2) how to distinguish desirable and undesirable allelic variants in unadapted germplasm, and 3) if desirable alleles can be identified, how do we recover them without sacrificing genetic gains made by previous generations of breeders?
  • Until the emergence of genomics and high throughput genotyping technologies, these types of questions could not be addressed on an experimental basis. Thus, theories developed over 50 years ago have not been tested and modified. We use the tools of genomics, bioinformatics, population genetics, quantitative genetics and modeling to address these questions.  Explicitly, we are developing: 1) experimental strategies for identifying desirable alleles in unadapted germplasm 2) methods to predict the value of desirable alleles, 3) optimal breeding strategies for migrating desirable alleles from unadapted germplasm into elite breeding populations without sacrificing established genetic gains and 4)computational tools to recognize genomic signatures of breeding populations with sub-optimal limits to selection. The impact of addressing these challenges experimentally and analytically will assure that the full genetic potential of maize can be realized using the most effective genetic resources and efficient breeding methods.  From an academic perspective this project also will begin the process of integrating discoveries from genomics with theoretical models of population and quantitative genetics.

Selected Publications:

  • Xu, P., L. Wang, W.D. Beavis (2011). An optimization approach to gene stacking. European Journal of Operational Research 214: 168-178.

  • Asoro F.G., M.A. Newell, W.D. Beavis, M.P. Scott and J.-L. Jannink. (2011). Accuracy and training population design for genomic selection in elite North American oats. Plant Genome 4:132-144.

  • Kingsmore, SF, IE Lindquist, J Mudge WD Beavis (2007) Genome-Wide Association Studies: Progress in Identifying Genetic Biomarkers in Common, Complex Diseases. Biomarker Insights 2007:2 1–10.

  • Beavis, WD , FD Schilkey, SM Baxter (2007). Translational Bioinformatics: At the Interface of Genomics and Quantitative Genetics. Crop Science 47(s3): 32-43

  • Gonzales, MD, K Gajendran, AD Farmer, E Archuleta, WD Beavis (2007) Leveraging model legume information to find candidate genes for soybean Sudden Death Syndrome using the Legume Information System (LIS). In Ed. Edwards D. Methods in Molecular Biology , Humana Press ( USA), pp. 245-260

  • Stein, L, DD Gessler, D Rokshar, D Main, L Mueller, E Huala, C Lawrence, S Rhee, WD Beavis (2006) Save our Data. The Scientist April 24-25.

  • Beavis, WD . (2005) Architectures for Integration of Data and Applications: Lessons from Integration Projects. In Genome Exploration:Data Mining and the Genome. The Stadler Genetics Symposia XXII:.Springer (eds. P. Gustafson, R. Shoemaker and J.W. Snape) pp. 31-46

  • Gepts, P. WD Beavis, EC Brummer, RC Shoemaker, HT Stalker, NF Weeden, ND Young. (2005) Legumes as a Model Plant Family: Genomics for Food and Feed. Report of the Cross Legume Advances through Genomics Conference. Plant Physiology 137: 1228-1235.

Vita: Click here to download

Website: William Beavis

Madan Bhattacharyya

BCB Faculty Member in the Agronomy Department

Education: Ph.D., Western Ontario, 1987

Research Interests: Functional genomic and proteomic approaches to disease resistance and susceptibility

  • Functional and Structural Genomics: Functional genomic and proteomic approaches to disease resistance and susceptibility
  • Genome Evolution: Evolution of disease resistance genes

Description: My current research program has been on understanding the molecular basis of host-pathogen interaction. The soybean-Phytophthora sojae interaction has been the main model system investigated extensively in our lab to understand the molecular basis of plant disease resistance. We are also investigating the soybean-Fusarium virguliformae interaction to understand the mechanism used by a phytotoxin to cause plant disease. In addressing the above biological questions we are applying both functional genomics and proteomics approaches that require bioinformatics tools.

Selected Publications:

  • Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Hyten, D., Song, Q., Mitros, T., Nelson, W., May, G.D., Gill, N., Peto, M., Goodstein, D., Thelen, J.J., Cheng, J., Sakurai, T., Umezawa, T., Du, J., Bhattacharyya, M.K., Sandhu, D., Grant, D., Joshi, T., Libault, M., Zhang, X-C., Xu, D., Futrell-Griggs, M., Abernathy, B., Hellsten, U., Berry, K., Grimwood, J., Wing, R.A., Cregan, P., Stacey, G., Specht, J., Rokhsar, D. Shoemaker, R.C, & Jackson S.A. (2010). Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature: 463, 178-83.

  • Xu, M., Brar, H., Grosic, S., Palmer, R., & Bhattacharyya, M.K. (2010). Excision of an active CACTA-like transposable element from DFR2 led to variegated flowers in soybean .  Genetics: 184, 53-63.

  • Sandhu, D., Tasma, M.I., Frasch, R., & Bhattacharyya, M.K. (2009). Systemic Acquired Resistance in Soybean is regulated by Two Proteins, Orthologous to Arabidopsis NPR1- Phytopthora sojae interaction. BMC Plant Biology: 9, 105.

  • Narayanan, N.N., Tasma, I.M., Grant, D., Shoemaker, R., & Bhattacharyya, M.K. (2009). Identification of candidate signaling genes including regulators of chromosome condensation 1 proteins family differentially expressed in the soybean-Phytopthora sojae interaction. Theoretical and Applied Genetics: 118, 399-412. 

Vita: Click here to download

Website: Madan Bhattacharyya

Anne Bronikowski

BCB Faculty Member in the EEOB Department

Education: Ph.D., University of Chicago, 1997

Research Interests: Evolution of life history variation with an emphasis on the evolution of senescence

  • Bioinformatics-- Our research focuses on the evolution of life history variation with an emphasis on the evolution of senescence (the functional decline in biochemical and physiological processes with age). We address fundamental questions in life history evolution using field studies, laboratory experiments (physiological and molecular), and mathematical modeling. Current research focuses on the evolution and ecology of senescence in 1) natural reptile populations; 2) laboratory populations of mice and 3) semi-natural populations of baboons
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking—Same as above

Description: We address fundamental questions in life history evolution using field studies, laboratory experiments (physiological and molecular), and mathematical modeling

Selected Publications:

  • Robert, K. & Bronikowski, A.M. (2010). Evolution of senescence: Physiological evolution in natural populations of the garter snake with divergent life history ecotypes. The American Naturalist: 175, 147-159.

  • Sparkman, A.M., Vleck, C., & Bronikowski, A.M. (2009). Evolutionary ecology of endocrine-mediated life history variation in the garter snake, Thamnophis elegans. Ecology: 90, 720–728. Featured in Faculty of 1000 Biology, 16 April 2009 (selected by Tim Coulson)

  • Robert, K., Vleck, C., & Bronikowski, A.M. (2009). The effects of maternal corticosterone levels on offspring behavior in fast and slow growth garter snakes (Thamnophis elegans). Hormones & Behavior: 55, 24-32.

Vita: Click here to download

Website: Anne Bronikowski

Ludovico Cademartiri

BCB Faculty Member in the Materials Science and Engineering Department

Education: Ph.D., University of Toronto, 2008

Research Interests: We have recently been awarded a Beckman Young Investigator Award by the Arnold and Mabel Beckman Foundation to explore collective behaviors in plants that might be originating from root-root connections that would enable plants to form communities capable of exchanging effectively small amounts of signaling molecules over large distances. Interestingly, the behavior of this community should then depend on the topology of the network formed by the root systems. Our proposal detailed the construction of experimental setups for the creation of such communities of plants and their investigation.

This study is highly interdisciplinary and would require expertise that extend far beyond pure engineering. We are therefore interested in candidates that would understand biology but also have the mathematical capabilities to handle network theory, without being afraid of the highly disciplined type of experimental work that is required.

Selected Publications:

  • Nanowires and Nonostructures that grow like Polymers, S. Shaw, L. Cademartiri, Advanced Materials, 2013, 25(35),4829-4844 featured on frontspiece
  • Recent Advances in the Synthesis of Colloidal Nanowires, A. Repko, L. Cademartiri, Cannadian Journal of Chemistry, 2012, 90(12), 1015-1031
  • Polymer-Like Conformation and Growth Kinetics of Bi2S3 Nanowires, L. Cademartiri, G. Guerin, K. J. M. Bishop, M.A. Winnik*, G.A. Ozin*, Journal of the American Chemical Society 2012, 134(22), 9327-9334
  • A Simple and Versatile 2-Dimensional Platform to Study Plant Germination and Growth under Controlled Humidity (paper) T. Sizmur, K. R. Lind, S. Benomar, H. VanEvery, L. Cademartiri* PLoS ONE, 2014 9(5), e96730
  • LEGO Bricks as Building Blocks for Centimeter Scale Biological Environments (paper) K. R. Lind, T. Sizmur, S. Benomar, A. I. Miller, L. Cademartiri* PLoS ONE, 2014, 9(6), e100867 - Featured on Popular Science, Wired, Smithsonian Mag.

Vita: Click here to download.


Steven Cannon

BCB Faculty Member in the Agronomy Department

Education: Ph.D., University of Minnesota, 2003

Research Interests: Plant genome and gene family evolution, comparative genomics, bioinformatic methods for gene and genome sequence analysis.

BCB Research Areas:

  • Bioinformatics-- methods for gene and genome sequence analysis, including genome comparisons, phylogenetics, and high-throughput transcript profiling.
  • Genome evolution-- patterns and rates of genome rearrangement; effects of polyploidy and transposon activity.

Description: I am a USDA-ARS Research Geneticist, and an adjunct assistant professor in the Agronomy Department.
My ARS research group focuses on bioinformatics for crop improvement, particularly in soybean and other crop legumes. We do this by developing software for analyzing and transferring information between crop and model species - including sequence, genetic, functional, and phenotype data. We study the evolution of disease resistance and nitrogen fixation, and the responses of genomes to polyploidy. We also provide support for two genome sequencing efforts: soybean, and a relative of alfalfa called Medicago truncatula. This support includes development of genetic markers, development of web-based tools for genomic data access and visualization.

Selected Publications:

  • A reference genome for common bean and genome-wide analysis of dual domestications. (2014) Schmutz, J., McClean, P., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S.M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M.A., Chovatia, M., Gepts, P., Goodstein, D.M., Gonzales, M., Hellsten, U., Hyten, D.L., Jia, G., Kelly, J.D., Kudrna, D., Lee, R., Richard, M.M.S., Miklas, P.N., Osorno, J.M., Rodrigues, J., Thareau, V., Urrea, C.A., Wang, M., Yu, Y., Zhang, M., Wing, R.A., Cregan, P.B., Rokhsar, D.S., Jackson, S.A. Nature Genetics June 8, 2014, doi:10.1038/ng.3008
  • A roadmap for functional and structural variants in the soybean genome. (2014). Anderson, J.E., Kantar, M.B., Kono, T.Y., Fu, F., Stec, A.O., Song, Q., Cregan, P.B., Specht, J.E., Diers, B.W., Cannon, S.B., McHale, L.H., Stupar, R.M. Genes Genomes Genetics (G3), May 22, 2014, 10.1534/g3.114.011551
  • Keeping an Eye on the Biology: A Guided Genomics Exploration. Singer, S.R., Schwarz, J.A., Manduca, C.A., Fox, S.P., Iverson, E.R., Taylor, B., Cannon, S.B., May, G.D. 2013. Keeping an Eye on the Biology: A Guided Genomics Exploration. Science. 339(6118):408-409.
  • Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S.B., Rosen, B., Tar'An, B., Millan, T. 2013. Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. Nature Genetics. DOI:10.1038/nbt.2491.
  • Genome-Wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Tian, Z., She, M., Zhao, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Lam, H., Ma, J. 2012. The Plant Cell. 24(11): 4422-4436.
  • The medicago genome provides insight into evolution of rhizobial symbiosis. (2011). Young, N.D., Debelle, F., Oldroyd, G., Geurts, R., Cannon, S.B., Mayer, K.F., Gouzy, J., Van De Peer, Y., Schoof, H., Udvardi, M.K., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Proost, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Benedito, V.A., Murray, J.D., Naoumkin, M.A., Rosen, B., Silverstein, K.A., Tang, H., Rombauts, S., Zhao, P.X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Doyle, J.J., Dudez, A., Farmer, A.D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Gonzalez, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jocker, A., Kenton, S.M., Kim, D., Klee, K., Lai, H., Lang, C., Lin, S., Macmill, S.L., Magdelenat, G., Matthews, L., Mccorrison, J., Monaghan, E.L., Mun, J., Najar, F.Z., Nicholson, C., Noirot, C., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E.F., Riddle, C., Sallet, E., Samain, S., Samson, N., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Seigfried, M., Severin, A., Sherrier, J.D., Shi, R., Sims, S., Sinharoy, S., Sterck, L., Vasylenko, I., Viollet, A., Wang, K., Wang, B., Wang, X. 2011. Nature. doi:10.1038/nature10625.
  • Cannon, E.K., Cannon, S.B. (2011) CViT: Chromosome Visualization Tool - A whole-genome viewer. International Journal of Plant Genomics. doi:10.1155/2011/373875.
  • Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P.B., Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Palaeopolyploid Soybean (glycine max (l.). The Plant Cell. 24(1):21-32.
  • Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Mulaosmanovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K., Varshney, R.K. (2012) A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms. Molecular Plant. doi:10.1093/mp/ssr111.
  • Severin, A.J., Cannon, S.B., Graham, M.A., Grant, D.M., Shoemaker, R.C. (2011) Changes in twelve conserved soybean genomic regions following three rounds of polyploidy.  The Plant Cell. 23(9):3129-3136.
  • Cannon, S.B., Shoemaker, R.C. 2012. Evolutionary and comparative analyses of the soybean genome. Journal of Breeding Science. 61(5):437-444.


Vita: Click here to download

Website: Steven Cannon

Michael Cho

BCB Faculty Member in the BMS Department

Education: Ph.D., University of Utah, 1994

Research Interests: Bioinformatics, computational and molecular biology

Description: Research focuses on development of an HIV-1 vaccine. We are interested in designing antigens that can elicit protective humoral immune responses against the virus. AIDs vaccine development does require significant involvement with bioinformatics because of the significant genetic/antigenic diversity of the virus. My research also heavily involves computational biology as a part of my work deals with prediction of antigen structures and antigen design.

Selected Publications:

  • Hioe, C. E., M. Tuen, G. Vasiliver-Shamis, Y. Alvarez, K. C. Prins, S. Banerjee, A. Nadas, M. W. Cho, M. L. Dustin, S. C. Kachlany (2011).  HIV Envelope gp120 Activates LFA-1 on CD4 T-Lymphocytes and Increases Cell Susceptibility to LFA-1-Targeting Leukotoxin (LtxA). 6(8):e23202.  PMCID: PMC3151267.
  • Lederman, M.M., G. Alter, D. C. Daskalaskis, B. Rodrigues, S. F. Sieg, G. Hardy, M. Cho, D. Anthony, C. Harding, A. Weinberg, R. H. Silverman, D. C. Douek, L. Margolis, D. B. Goldstein, M. Carrington, and J. J. Goedert. (2010).  Determinants of protection among HIV-exposed seronegative persons:  An overview.  Journal of Infectious Diseases202:  S333-338.  PMCID: PMC3184646.
  • Nara, P. L., G. J. Tobin, A. R. Chaudhuri, J. D. Trujillo, G. Lin, M. W. Cho, S. A. Levin, W. Ndifon, N. S. Wingreen (2010).  How can vaccines against influenza and other viral diseases be made more effective?  PLoS Biology8:  e1000571.  PMCID: PMC3006352.
  • Wang, L., Y. Qin, S. Ilchenko, J. Bohon, W. Shi, M.W. Cho, K. Takamoto, M. R. Chance (2010). Structural analysis of a highly glycosylated and unliganded gp120-based antigen using mass spectrometry. Biochemistry. 49: 9032-9045.
  • Shi, W., J. Bohon, D. Han, H. Habte, Y. Qin, M. W. Cho, M.R. Chance (2010). Structural characterization of HIV gp41 with the membrane proximal external region. J. Biol. Chem. 285: 24290- 24298. PMCID: PMC2911339.
  • Penn-Nicholson, A., D. P. Han, S. J. Kim, H. Park, R. Ansari, D. C. Montefiori, and M. W. Cho (2008). Assessment of antibody responses against gp41 in HIV-1-infected patients using soluble gp41 fusion proteins and peptides derived from M group consensus envelope. Virology. 372: 442-56. PMCID: PMC2293309.
  • Han, D. P., M. Lohani and M. W. Cho (2007). Specific asparagine-linked glycosylation sites are critical for DC-SIGN- and L-SIGN-mediated SARS-CoV entry. J. Virol. 81:12029-12039. PMCID: PMC2168787.
  • Han, D. P., A. Penn-Nicholson and M. W. Cho (2006). Identification of critical determinants on ACE2 for SARS-CoV entry and development of a potent entry inhibitor. Virology 350: 15-25.
  • Han, D. P., H. G. Kim, Y. B. Kim, L. L. M. Poon, M. W. Cho (2004). Development of a safe neutralization assay for SARS-CoV and Characterization of S glycoprotein. Virology. 326: 140-149.
  • Cho, M. W. (2003). Subunit protein vaccines: Theoretical and practical considerations for HIV-1. Curr. Mol. Med. 3:243-263.

Vita: Click here to download

Department Website:

*Hui-Hsien Chou

BCB Faculty Member in the GDCB and Computer Science Departments

Education: Ph.D., University of Maryland at College Park, 1996

Research Interests: Bioinformatics, computational biology and computer-aided biological research

Description: My research interest has been the development of sophisticated computer algorithms to efficiently solve large scale biological research problems. For example, I have developed the automatic DNA sequence clean up programs (LUCY1 & 2) for genomic research, the efficient whole-genome oligo microarray design tool (PICKY) for post-genomic research, and the automatic Perl programming tool (VECT) for biologists. My software tools usually employ novel approaches to computing and provide better results than previous solutions. For example, while most microarray design tools are still based on sequence-level comparison (e.g., BLAST) to screen out nontargets, my PICKY program has embedded a complete suite of thermodynamic equations in its calculations to infer the best oligo candidates based on physics, and it does so orders of magnitude faster than any other comparable microarray design tools with comparable computation depth. My recent research focus is on the computer-aided biological research area. This area differs from computational biology in that the end goals are still the successes in molecular biology, but the approach are greatly improved (both in efficiency and chance of success) by using computer analyses. A good example of this new type of research is the whole-genome siRNA design approach we have conducted using Picky and we have validated (in actual bench experiments) that our computer-aided siRNA design indeed greatly reduces the off-target effects of the experiments.

Ongoing projects: National Science Foundation (NSF) has awarded a grant for the research project entitled "Optimal siRNA Design Based on Whole Genome Thermodynamic Analysis" to start in September 2009. RNA interference (RNAi) is a natural phenomenon in cells where siRNAs guide the recognition, inhibition and potential degradation of target messenger RNAs (mRNAs), resulting in the loss of their gene functions. RNAi is an important molecular biology technology that can be used to perform functional genomic studies. It is also suggested that siRNAs can be used as drugs to stop oncogenes in cancer cells or to fight off viruses. The two main goals of this project are to create novel siRNA design software that can select high quality, gene-specific siRNAs based on the comprehensive thermodynamic analysis of an entire genome and to validate the quality of the designed siRNAs with RNAi experiments.

Selected Publications:

  • Xi Chen, Lu Shen, and Hui-Hsien Chou. MicroRNA-Target Binding Structures Mimic MicroRNA Duplex Structures in Humans. PLoS ONE, 2014;9(2):e88806. doi: 10.1371/journal.pone.0088806. eCollection 2014.

  • Xi Chen, Peng Liu and Hui-Hsien Chou. Whole-Genome Thermodynamic Analysis Reduces siRNA Off-target Effects. PLoS ONE, 2013;8(3):e58326.
  • Hui-Hsien Chou. Shared probe design and existing microarray reanalysis using Picky. BMC Bioinformatics, 11:196, April 20, 2010.
  • Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C. Hsing, Pamela C. Ronald and Patrick S. Schnable. Direct calibration of PICKY-designed microarrays. BMC Bioinformatics, 10:347, Oct. 23, 2009.
  • Hui-Hsien Chou. Computational Methods for Microarray Design. In Srinivas Aluru, editor, Handbook of Computational Molecular Biology. ISBN 1584884061. CRC Press, Boca Raton, FL, Dec. 21, 2005.
  • Hui-Hsien Chou. Vect: an automatic visual Perl programming tool for nonprogrammers. BioTechniques, 38:615-621, April 2005.
  • Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable. Picky: Oligo Microarray Design for Large Genomes. Bioinformatics, 20:2893-2902, Nov. 2004.
  • Song Li and Hui-Hsien Chou. Lucy2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics, 20:2865-2866, Nov. 2004.
  • Hui-Hsien Chou and Michael H. Holmes. DNA Sequence Quality Trimming and Vector Removal. Bioinformatics, 17:1093-1104, Dec. 2001.
Vita: Click here to download

Lab Website: Hui-Hsien Chou

Department Website: Hui-Hsien Chou

Dianne Cook

BCB Faculty Member in the Statistics Department

Education: Ph.D., Rutgers, 1993

Research Interests: Visualization of high-dimensional data, linking data views with other visualization of biological phenomenon

  • Bioinformatics-- Visualization of multivariate, high-dimensional data, in particular gene expression data, and metabolic networks. Interested developing methods for linking data views with other informative visualization of biological phenomenon
  • Mathematical Biology, Computational Modeling, Metabolic and Developmental Networking—Same as above

Description: My research is in methods for visualizing high-dimensional data using interactive and dynamic methods. This includes data arising from biological experiments such as microarray data, metabolomics and proteomics. We're developing software to assist in this, called GeneGobi, which builds functionality in the data analysis language R and the data visualization software GeneGobi

Selected Publications:

  • Hobbs , J., Wickham, H., Hofmann, H. and Cook, D. (2008) Glaciers Melt as Mountains Warm: A Graphical Case Study Computational Statistics, To appear.
  • Lawrence, M., Cook, D., Lee, E.-K., Babka, H. and Wurtele, E. (2008) explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology, Journal of Statistical Software, 25(9):
  • Cook, D., Hofmann, H., Lee, E.-K., Yang, H., Nikolau, B., and Wurtele, E. (2007) Exploring Gene Expression Data, Using Plots, Journal of Data Science, 5(2):151{182.
  • Lee, E.-K., Cook, D., Klinke, S., and Lumley, T. (2005). Projection Pursuit for Exploratory Supervised Classification. Journal of Computational and Graphical Statistics, bf 14(4):831{846.
  • Swayne, D. F., Temple Lang, D., Buja, A. and Cook, D. (2003) GGobi: Evolving from XGobi into an Extensible Framework for Interactive Data Visualization, Journal of Computational Statistics and Data Analysis, 43(4):423{444.
  • Wurtele, E., Li, J., Diao, L., Zhang, H., Foster, C., Fatland, B., Dickerson, J., Brown, A., Cox, Z., Cook, D., Lee, E. K., Hofmann, H. (2003) MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis, Comparative and Functional Genomics, 4:239{245.


Vita: Click here to download

Website: Dianne Cook

Jack Dekkers

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Wisconsin, Madison, 1989

Research Interests: Integrating molecular and quantitative genetics for animal breeding programs

  • Biological statistics -- Statistical methods for QTL detection and for estimating relationships between QTL and phenotype; identifying genes of economic importance in swine and poultry; systems analysis approaches to optimize the use of molecular genetic information in genetic improvement programs.

Description: Quantitative genetics and animal breeding with application to swine and poultry genetics, including design and optimization of breeding strategies, use of molecular genetic information, QTL detection, and economic aspects of breeding programs.

Selected Publications:

  • Lkhagvadorj, S., Qu, L,, Cai, W., Couture, O.,P., Barb, C.R., Hausman, G.J., Nettleton, D., Anderson, L.L., Dekkers, J.C.M., & Tuggle, C.K. (2010). Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. Am J Physiol Regul Integr Comp Physiol: 298, R494-R507.
  • Barb, C.R., Hausman, G.J., Rekaya, R., Lents, C.A., Lkhagvadorj, S., Qu, L., Cai, W., Couture, O.P., Anderson, L.L., Dekkers, J.C.M., Tuggle, C.K. (2010). Gene expression in hypothalamus, liver and adipose tissues and food intake response to melanocortin-4 receptor (MC4R) agonist in pigs expressing MC4R mutations. Physiol. Genomics . doi:10.1152/physiolgenomics.00006.2010
  • Lkhagvadorj, S., Qu, L., Cai, W., Couture, O.P, Barb, C.R., Hausman, G.J., Nettleton, D., Anderson, L.L., Dekkers, J.C.M., & Tuggle, C.K. (2009). Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology: 298, R494-R507.
  • Toosi, A., Fernando, R.L., & Dekkers, J.C.M. (2010). Genomic Selection in admixed and crossbred populations. Journal of Animal Science: 88, 32-46.
  • Alexander, L.S., Qu, A., Cutler, S.A., Mahajan, A., Rothschild, M.F., Cai, W., Dekkers, J.C.M., & Stahl, C.H. (2009). A calcitonin receptor (CALCR) single nucleotide polymorphism is associated with growth performance and bone integrity in response to dietary phosphorus deficiency. Journal of Animal Science: 87, 868-875.
  • Pyiasatian, N., Fernando, R.L., & Dekkers, J.C.M. (2009). Models for marker-assisted genetic evaluation with multiple QTL in a crossbred population. Livestock Science: 125, 141-148.
  • Lkhagvadorj, S., Qu, L., Cai, W., O.P. Couture, C.R. Barb, G.J. Hausman, D. Nettleton, L.L. Anderson, Dekkers, J.C.M., & Tuggle, C.K. (2009). Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiological Genomics: 38, 98.

Vita: Click here to download

Website: Jack Dekkers

*Julie Dickerson

BCB Faculty Member in the ECPE Department

Education: Ph.D., USC, 1993

Research Interests: Fuzzy expert systems, metabolic networks, macromolecular structure-function relationships. Systems biology and modeling of metabolic networks, analysis of microarray and
metabolomic data using pattern recognition methods, and data visualization in virtual reality

  • Bioinformatics--Systems biology and modeling of metabolic networks, analysis of microarray and metabolomic data using pattern recognition methods, and data visualization in virtual reality
  • Macromolecular Structure and Function-- Same as above

Selected Publications:

  • El Kaissi, M., Jia, M., Dickerson, J., Wurtele, E., & Reiners, D. (2009). Reaction centric layout for metabolic networks. Lecture Notes in Computer Science: 5876, Advances in Visual Computing, 81-91.

  • El Kaissi, M., Jia, M., Reiners, D., Dickerson, J., & Wurtele, E. (2009). Visualization of Gene Regulatory Networks Lecture Notes in Computer Science, 5876, Advances in Visual Computing, 909-918.

  • Grimplet, J., Cramer, G.R., Dickerson, J.A., Mathiason, K., Van Hemert, J., & Fennell, A.Y. (2009). VitisNet: "Omics" Integration through Grapevine Molecular Networks. PLoS One: 4, 12, e8365.

  • Mao, L., Van Hemert, J., Dash, S., & Dickerson, J. (2009). Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics: 10, 1, 346.

  • Bais, P., Moon, S., He, K., Leitao, R., Dreher, K., Walk, T., et al. (2010). A Web Portal for Plant Metabolomics Experiments. Plant Physiology: 109.

Vita: Click here to download

Website: Julie Dickerson

*Philip Dixon

BCB Faculty Member in the Statistics Department

Education: Ph.D., Cornell, 1986

Research Interests: Modeling virus sequence evolution and immune system response, ecological and environmental statistics

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Modeling virus sequence evolution and immune system response, ecological and environmental statistics

Description: develops and evaluates statistical methods to answer interesting biological questions.  A lot of this work is collaborative.  The themes are using likelihood inference in non-standard situations and using computer-intensive methods

Selected Publications:

  • Kapler, E.J., Widrlechner, M.P., Dixon, P.M., and Thompson, J.R. 2012. Performance of five models to predict the naturalization of non-native woody plants in Iowa. Journal of Environmental Horticulture. 30:35-41.
  • Fletcher, D., and Dixon, P.M. 2012. Modelling data from different sites, times or studies: weighted vs. unweighted regression. Methods in Ecology and Evolution 3:168-176.
  • Dzul, M.C., Quist, M.C., Dinsmore, S.J., Dixon, P.M., Bower, M.R., Wilson, K.P., and Gaines, D.B. 2012. Identifying sources of error in surveys of Devils Hole Pupfish (Cyprinodon diabolis). Southwestern Naturalist 57:44-50.
  • Khanal, S., Anex, R.P., Gelder, B.K,., Dixon, P., and Caragea, P. 2012. Cropping pattern choice with proximity to ethanol production and animal feeding operations. Biofuels, Bioproducts, and Biorefining. Published online, Jan 30 2012, DOI: 10.1002/bbb.1337;
  • Weirich, J.W., Shaw, D.R., Owen, M.D.K, Dixon, P.M., Weller, S.C., Young, B.G, Wilson, R.G., and Jordan, D.L. 2011. Benchmark study on glyphosate-resistant cropping systems in the United States. Part 5: Effects of glyphosate-based weed management programs on farm-level profitability. Pest Management Science. 67:781-4
  • Weirich, J.W., Shaw, D.R., Coble, K.H., Owen, M.D.K, Dixon, P.M., Weller, S.C., Young, B.G, Wilson, R.G., and Jordan, D.L. 2011. Benchmark study on glyphosate-resistant cropping systems in the United States. Part 6: Timeliness of economic decision-making in implementing weed resistance management strategies. Pest Management Science. 67:785-9.
  • Picasso, V.D., Brummer, E.C., Liebman, M, Dixon, P.M., and Wilsey, B.J. 2011. Diverse perennial crop mixtures sustain higher productivity over time based on ecological complementarity. Renewable Agriculture and Food Systems 26:317-327.
  • Trapp, A. Dixon, P.M., Widrlechner, M.P. and Kovach, D. 2012. Scheduling viability tests for seeds in long-term storage based on a Bayesian multi-level model. Journal of Agricultural, Biological and Ecological Statistics. 17:192-208.
  • Picasso, V.D., Brummer, E.C., Liebman, M., Dixon, P.M. and Wilsey, B.J. 2008. Crop species diversity affects productivity and weed suppression in perennial polycultures under two management strategies. Crop Science 48:331-342.
  • Prasifka, J.R., Hellmich, R.L. Dively, G.P., Higgins, L.S., Dixon, P.M., and Duan, J.J. 2008. Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power. Environmental Entomology 37:1-10
  • Schmidt, N.P., O’Neal, M.E., and Dixon, P.M. 2008. Aphidophagous predators in Iowa soybean: a community comparison across multiple years and sampling methods. Annals Ent. Soc. Amer. 101:341-350.
  • Xu, Z., Gleason, M.L, Mueller, D.S., Esker, P.D., Bradley, C.A., Buck, J.W., Dixon, P.M., and Monteiro, J.E.B.A. 2008. Overwintering of Sclerotium rolfsii and S. rolfsii var. delphinii in different latitudes of the United States. Plant Disease 92:719-724.
  • Esker, P.D, Gibb KS, and Dixon, P.M., Survival Analysis and Space-Time Point Pattern Analysis to Improve the Epidemiological Understanding of the Papaya-Papaya Yellow Crinkle Pathosystem. Plant Health Progress, in press.
  • Scott, E.M. and Dixon, P.M. Statistical Sampling Designs for Radionuclides. book chapter, in review
  • Westerrnan, P.R., Dixon, P.M., and Liebman, M. Burial rates of surrogate seeds in arable fields. Weed Research, submitted.
  • Schleuter, J.A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J.J., and Shoemaker, R.C. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47:868-876

Vita: Click here to download

Website: Philip Dixon

*Drena Dobbs

BCB Faculty Member in the GDCB Department

Education: Ph.D. Oregon, 1983

Research Interests: Computational biology; predicting protein and nucleic acid structure, function, and interactions

  • Macromolecular Structure and Function-- Analysis and prediction of macromolecular structure and function; protein-protein, protein-nucleic acid interactions, determinants of molecular recognition.

Description: Our group’s long-term research goals are:  i) to understand how proteins and nucleic acids achieve their functional 3-D structures, and ii) to elucidate mechanisms that regulate interactions among proteins, nucleic acids and other molecules in cells. Our laboratory uses both computational and wet-lab experimental approaches to explore the structure and function of important macromolecular complexes and interaction networks. Current areas of focus include: development of novel RNA-based antiviral therapies against HIV-1 and other lentiviruses; improved rational design of zinc finger proteins (ZFPs) as tools for genome modification and gene therapy; prediction of epitopes and nucleic acid binding residues in proteins; and prediction and experimental validation of regulatory RNA-protein networks that function in development and disease.

For details, please visit the Dobbs Lab website:

Selected Publications:

  • Walia RR, Xue LC, Wilkins K, EL-Manzalawy Y, Dobbs D, Honavar V (2014) RNABindRPlus: A predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins. PLoS ONE 20; 9(5):e97725.
  • Muppirala UK, Lewis BA, Dobbs D (2013) Computational tools for investigating RNA-protein interaction partners. J Comput Sci Syst Biol 6:182-187
  • Xue, LC, Jordan, R, El-Manzalawy Y, Dobbs D, and Honavar V. (2013) DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction. Proteins 82:250-67
  • Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V. (2012) Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics13:41.

  • Xue LC, Dobbs D, Honavar V. (2011). HomPPI: a class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics.12:244.
  • Steczkiewicz K, Zimmermann MT, Kurcinski M, Lewis BA, Dobbs D, Kloczkowski A, Jernigan RL, Kolinski A, Ginalski K. (2011). Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. Proc Natl Acad Sci U S A. 108:9443-8.
  • Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR. (2011). ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. BMC Genomics.12:83.
  • Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK. (2011). Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8:67-9.
  • Lewis BA, Walia RR, Terribilini M, Ferguson J, Zheng C, Honavar V, Dobbs D. (2011). PRIDB: a Protein-RNA Interface Database. Nucleic Acids Res.39:D277-82.
  • Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D. (2010). Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics. 11:543.
  • Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D. (2010). ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res. 2010 Jul; 38 (Web Server issue) :W462-8. PubMed PMID:20435679; PubMed Central PMCID: PMC2896148.
  • Carpenter S, Dobbs D. (2010). Molecular and biological characterization of equine infectious anemia virus Rev. Curr HIV Res. 8:87-93.

Vita: Click here to download

Website: Drena Dobbs

*Karin Dorman

BCB Faculty Member in the Statistics Department

Education: Ph.D., UCLA, 2001

Research Interests: Mathematical modeling, virus evolution, phylogenetics

  • Genome Evolution-- I employ mathematical models and computational tools to capture the essential aspects of biological systems. I am interested in the role of pathogen diversity in diseases caused by rapidly evolving organisms (HIV-1, EIAV, HCV), statistical techniques for the detection of recombination or gene conversion, and stochastic models for explaining the uncertainty in biological outcomes
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Same as above

Description: I am interested in the genomic changes occurring in fast-evolving viruses and how these changes can be used to better understand how they cause disease. I have developed methods to detect recombination and selection in the hundreds and thousands of genomic sequences available for viruses like HIV, HBV, and EIAV. I am currently developing new methods to detect and quantitate selection in overlapping reading frames, a genomic structure common in viruses and heretofor largely unstudied. I am also developing computational models of virus/host interactions and the accompanying statistical methods for data analysis and tting. In the future, I will continue to develop new methods for genetic analysis, for example a model to estimate transposon birth and death rates, and explore extended models of host/pathogen interactions, for example to test the hypothesis that changes in EIAV during disease are helping the virus evade a maturing immune response.

Selected Publications:

  • Towfic, G., Graziano, F., Towfic, F., Dorman, K. S., Cook, D., Kettoola, S. & Neal, L. (2013). HIV dynamics impacting the efficacy of HIV/AIDS treatments. Journal of Proteomics and Bioinformatics, 6, 51-57.
  • Krishnan, S., Strasburg, C. S., Lutz, R. R., Goseva-Popstojanova, K. & Dorman, K. S. (2013). Predicting failure-proneness in an evolving software product line. Information and Software Technology, 55, 1479-1495.
  • Blitvich, B. J., Loro~no-Pino, M. A., Garcia-Rejon, J. E., Farfan-Ale, J. A. & Dorman, K. S. (2012). Nucleotide sequencing and serologic analysis of Cache Valley virus isolates from the Yucatan Peninsula of Mexico. Virus Genes, 45, 176-180.
  • Blitvich, B. J., Saiyasombat, R., Dorman, K. S., Garcia-Rejon, J. E., Farfan-Ale, J. A. & Lorono-Pino, M. A. (2012). Sequence and phylogenetic data indicate that an Orthobunyavirus recently detected in the Yucatan Peninsula of Mexico is a novel reassortant of Potosi and Cache Valley viruses. Archives of Virology, 157, 1199-1204.
  • Blitvich, B. J., Staley, M., Lorono-Pino, M. A., Garcia-Rejon, J. E., Farfan-Ale, J. A. & Dorman, K. S. (2012). Identification of a novel subtype of South River virus (family Bunyaviridae). Archives of Virology, 157, 1205-1209.
  • Wu, W., Blythe, D. C., Loyd, H., Mealey, R. H., Tallmadge, R. L., Dorman, K. S. & Carpenter, S. (2011). Decreased infectivity of a neutralization-resistant equine infectious anemia virus variant can be overcome by efficient cell-to-cell spread. Journal of Virology, 85, 10421-10424.
  • Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M.-A., Ryan, R. P., Meyer, D. F., Han, S.-W., Aparna, G., Rajaram, M. L., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S.-W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V., Rabinowicz, P. D., Leach, J. E., White, F. F. & Salzberg, S. L. (2011). Two new complete genome sequences o er insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193, 5450-5464.
  • Yang, X., Aluru, S. & Dorman, K. S. (2011). Repeat-aware modeling and detection of short read errors. BMC Bioinformatics, 12, S52.
  • Carpenter, S., Chen, W.-C.& Dorman, K. S. (2011). Rev variation during persistent lentivirus infection. Viruses, 3, 1-11.
  • Yang, X., Dorman, K. S. & Aluru, S. (2010). Reptile: representative tiling for short read error correction. Bioinformatics, 26, 2526-2533.
  • Staley, M., Dorman, K. S., Fernandez-Salas, I., Farfan-Ale, J. A., Lorono-Pino, M. A., Garcia-Rejon, J. E., Ibarra-Juarez, L. & Blitvich, B. J. (2010). Universal primers for the amplification and sequence analysis of actin-1 from diverse mosquito species. Journal of the American Mosquito Control Association, 26, 214-218.
  • Saiyasombat, R., Dorman, K. S., Garcia-Rejon, J. E., Lorono-Pino, M. A., Farfan Ale, J. A. & Blitvich, B. J. (2010). Isolation and sequence analysis of Culex flavivirus from Culex interrogator and Culex quinquefasciatus in the Yucatan Peninsula of Mexico. Archives of Virology, 155, 983-986.
  • Dancik, G. M., Jones, D. E. & Dorman, K. S. (2010). Parameter estimation and sensitivity analysis in an agent-based model of Leishmania major infection. Journal of Theoretical Biology, 262, 398-412.
  • Farfan-Ale, J. A., Lorono-Pino, M. A., Garcia-Rejon, J. E., Soto, V., Lin, M., Staley, M., Dorman, K. S., Bartholomay, L. C., Hovav, E. & Blitvich, B. J. (2010). Detection of flaviviruses and orthobunyaviruses in mosquitoes in the Yucatan Peninsula of Mexico in 2008. Vector Borne and Zoonotic Diseases, 10, 777-783.

Vita: Click here to download

Website: Karin Dorman

Oliver Eulenstein

BCB Faculty Member in the Computer Science Department

Education: Ph.D., Bonn, 1998

Research Interests: Design and analysis of algorithms for molecular biology

  • Bioinformatics-- Design and analysis of algorithms in computational biology: phylogenetic trees, protein folding, physical mapping, genome rearrangements, sequence alignment, fragment assembly
  • Genome Evolution-- Same as above

Description: Development of algorithms to solve problems in molecular biology

Selected Publications:

Vita: Click here to download

Website: Oliver Eulenstein

Rohan Fernando

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Illinois, Urbana-Champaign, 1984

Research Interests: Methods for mapping QTL and for marker-assisted selection

  • Functional and Structural Genomics-- Mapping and characterizing quantitative trait loci; use of genetic data in animal breeding

Description: Statistical methodology for mapping QTL; marker assisted selection; and genetic evaluation and parameter estimation in crossbred populations

Selected Publications:

  • Toosi, A., Fernando, R. L., & Dekkers, J. C. M. (2010). Genomic selection in admixed and crossbred populations. J Anim. Sci.: 88, 32-46.

  • Kizilkaya, K., Fernando, R. L., & Garrick D. J. (2010). Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J. Anim. Science: 88, 544-551.

  • Zhong, S., Dekkers, J. C. M., Fernando, R. L., & Jannink, J. (2009). Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a Barley case study. Genetics: 182, 355-364.

  • Gianola, D., de los Campos, G., Hill, W. G., Manfredi, E., & Fernando, R. L. (2009). Additive Genetic Variability and the Bayesian Alphabet. Genetics: 183, 347-363.

  • Koltes, J. E., Mishra, B. P., Kumar, D., Kataria, R. S., Totir, L. R., Fernando, R. L., Cobbold, R., Steffen, D., Coppieters, W., Georges, M., & Reecy, J. M. (2009). A nonsense mutation in cGMP-dependent type II protein kinase (PRKG2) causes dwarfism in American Angus cattle. Proceedings of the National Academy of Sciences, USA: 106, 19250-19255.

  • Coster, A., Heuven, H. C., Fernando, R. L., & Dekkers, J. C. (2009). Haplotype inference in crossbred populations without pedigree information. Genet. Sel. Evolution: 41, 40.

  • Legarra, A. & Fernando, R. L. (2009). Linear models for joint association and linkage QTL mapping. GSE: 41, 43.

  • Gianola, D., R. L. Fernando, and A. Stella. 2006. Genomic assisted prediction of genetic value with semi-parametric procedures. Genetics 173:1761-1776.

  • Minick, J.A., L. R. Totir, D. E. Wilson, R. L. Fernando. 2006. Conception rate in Angus heifers. J. Anim. Sci. 84:2022-2025.

  • Abraham, K. J., L. R. Totir, and R. L. Fernando. 2007. Improved techniques for sampling complex pedigrees with the Gibbs sampler. GSE 39: 27-38.

  • Zhao, H.H., R.L. Fernando, and J.C.M. Dekkers. 2007. Power and precision of alternate methods for linkage disequilibrium mapping of QTL. Genetics 175: 1975-1986.

Vita: Click here to download

Website: Rohan Fernando

Iddo Friedberg

BCB Faculty Member in the VMPM Department

Education: Ph.D., Hebrew University, Jerusalem

Research Interests: The evolution of operons and gene blocks The evolution of gene blocks and co- transcribed genes (operons) is an important subject in microbial evolution. My laboratory is implementing a computational model whose goal is to detect which events lead to the formation of operons, and what do the ancestral, pre-operon genomic sections may have looked like. This research is funded by a grant from the National Science Foundation (ABI- 1146960).

Metagenomics of the infant gut microbiome, and the relationship to the host gut transcriptome. This work is in collaboration with Robert Chapkin from Texas A&M University and Sharon Donovan from the University of Illinois, Urbana-Champaign. This study has direct applications to our understanding of infant health, specifically on how infant gut microbes and, in turn, infant health are affected by diet.

Critical Assessment of Function Annotation. A community-driven effort which I am leading to assess how well protein function prediction algorithms perform. The main focus of this research effort is assessing algorithms used for prediction of protein function from sequence. The development and implementation of assessment algorithms, and their use and endorsement by the bioinformatics community are of great interest in my laboratory. This is a community effort I have been leading since 2005. CAFA currently includes 54 participating groups from America, Europe, Asia and Australia. We have published the results of the first CAFA experiment in Nature Methods.

Biological Database of Images and Genomes. BioDIG is a database and website that links phenotype and genotype data. This project, BioDIG, is now in advanced stages, and has been published in Database.

Selected Publications:

  • Jiang Y, Clark W, Friedberg I, Radivojac P The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective (2014) Bioinformatics (accepted)
  • Radivojac P, Clark WT,.., Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction methods (2013) Nature Methods 10, 221-227 doi:10.1038/nmeth.2340
  • Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space . PLoS Computational Biology 9(5): e1003063.
  • Rodrigues APC, Grant BE, Godzik A and Friedberg I : The AFP 2006 Meeting BMC Bioinformatics (2007) 8(Suppl 4):S1
  • Friedberg I. and Godzik A. Functional Differentiation of Proteins: Implications for Structural Genomics Structure (2007) 15(4):405-415

Vita: Click here to download.


M. H. West Greenlee

BCB Faculty Member in the VMPM Department

Education: Ph.D., Iowa State, 1999

Research Interests: The molecular basis of neural differentiation


My laboratory is focused on cell fate determination in the developing retina. Within this context we have generated protein expression datasets, and utilized previously reported gene expression data to identify genes and gene networks involved in this process. My intent is to develop the developing retina as a model for Systems Biology research. Bioinformatics and collaboration in Computational Biology are integral to my agenda.

Selected Publications:

  • Towfic, F., West Greenlee, M.H., & Honavar, V.G. (2009). Aligning Biomolecular Networks Using Modular Graph Kernels. WABI: LNBI, 5724, 345–361.

  • Smith, J.D., Greenlee, J.J., Hamir, A.N., Richt, J.A., & West Greenlee, M.H. (2009). Retinal function and morphology are altered in cattle experimentally infected with transmissible mink encephalopathy. Veterinary Pathology: 46, 810-818.

  • Smith, J. D., Greenlee, J. J., Hamir, A. N., West Greenlee, M. H. (2009). Altered electroretinogram b-wave in a scrapie-affected Suffolk sheep. Veterinary Record: 165, 179-81.

  • Laura A. Hecker, Tim C. Alcon, Vasant G. Honavar, M. H. West Greenlee (2008) Using a seed-network to query large scale gene expression data from the developing retina. Bioinformatics and Biology Insights, 2008:2 91-102.

  • Samantha Van Hoffelen, M. Heather W Greenlee, Matthew M Harper, Daniel T Au. (2008) Cell birth and death in the developing retina of the Brazilian opossum, Monodelphis domestica. Brain Res. 1195:28-42

  • Tyra Dunn-Thomas, Drena L. Dobbs, Donald S. Sakaguchi, Michael J. Young, Vasant G. Honavar, M. Heather West Greenlee. (2008) Proteomic differentiation between murine retinal and brain derived progenitor cells. Stem Cells and Development, Jan 22 [Epub ahead of print]

  • J. Smith, J. Greenlee, A. Hamir, and M. H. West Greenlee (2008) Retinal cell types are differentially affected in sheep with scrapie. Comparative Pathology: 138:12-22.

  • J. Eucher, E. Uemura, D. Sakaguchi, M. H. West Greenlee (2006) Amyloid-beta peptide affects viability but not differentiation of embryonic and adult rat hippocampal progenitor cells. J. Exp. Neurol. 203:486-92

Vita: Click here to download

Website: M. Heather West Greenlee

Xun Gu

BCB Faculty Member in the GDCB Department

Education: Ph.D., Texas, Houston, 1996

Research Interests: Computational biology, molecular evolution, comparative genomics

  • Genome Evolution-- Computational molecular biology; molecular evolution; comparative genomics


Selected Publications:

  • Lin, H., Moghe, G., Ouyang, S., Iezzoni, A., Shiu, S.-H., Gu, X., Buell, C.R. (2010). Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evolutionary Biology: 10, 41.

  • Wang, X., Huang, Y., Lavrov, D.V., and Gu, X. (2009). Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications. BMC Evolutionary Biology: 9, 275.

  • Huang Y., Zheng, Y., Su, Z., Gu, X. (2009). Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective. BMC Genomics: 10, Supplement 1, S14.

  • Zou, Y., Su, Z., Yang, J., Zeng, Y., and Gu, X. (2009). Uncovering Genetic Regulatory Network Divergence between Duplicate Genes Using Yeast eQTL Landscape. JEZ-B: Mol Dev Evolution: 312B, 722-733.

  • Mertz, B., Gu, X., & Reilly, P.J. (2009). Analysis of Functional Divergence within Two Structurally Related Glycoside Hydrolase Families. Biopolymer: 91, 479-495.

  • Gu, X. & Huang, Y. (2009). Expansion of Duplicated MicroRNAs and Protein-coding Genes during a Broad Time Window of Early Vertebrates. JEZ-B: Mol Dev Evol: 312B, 164-170.

  • Su, Z., Xu, L., Gu, Z., & Gu, X. (2009). Origins of digestive RNases in leaf monkeys are an open question. Mol Phylogene Evolution: 53, 610-611.

  • Xu, L., Su, Z., Gu, Z., & Gu, X. (2009). Evolution of RNases in Leaf Monkeys: Being Parallel Gene Duplications or Parallel Gene Conversions is a Problem of Molecular Phylogeny. Mol Phylogene Evol 50:397-400.

  • X. Gu. (2009). An Evolutionary Model for the Origin of Modularity in a Complex Gene Network. JEZ-B: Mol Dev Evol 312:75-82.

  • Cheng, Q., Su, Z., Zhong, Y., & Gu, X. (2009). Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: A simple evaluation. Genetics 441, 156-182.

  • Zhang, H., Zhong, Y., Hao B., & Gu, X. (2009). A simple method for phylogenomic inference using the information of gene content of genomes. Genetics: 441, 163-168.

Vita: Click here to download

Website: Xun Gu

Tracy Heath

BCB Faculty Member in the EEOB Department

Education: Ph.D., University of Texas, Austin, 2008

Research Interests: Develops novel computational and statistical approaches for estimating evolutionary parameters in a phylogenetic context. I evaluate the properties and performance of phylogenetic methods using biological data sets and through the development of new simulation tools. Additionally, my collaborators and I apply phylogenetic techniques to empirical data sets to understand patterns of biodiversity, morphological evolution, and historical biogeography. My primary approach to developing phylogenetic tools is to apply new statistical models as priors using Bayesian inference methods. I am a developer for a software project called RevBayes.

RevBayes is a program for Bayesian inference of evolutionary parameters including (but not limited to) phylogeny, divergence times, rates of character evolution, population dynamics, rates of selection across a genome, and patterns of species diversification. The RevBayes
framework uses an interpreted, interactive programming language and relies on probabilistic graphical models. This flexible design allows any user to implement, apply, and test new models and statistical methods. Thus, this software package represents a new paradigm for Bayesian phylogenetic inference by providing novel tools for describing and visualizing evolutionary models and affording all users the opportunity to easily develop and implement new models. I am seeking PhD students with strong interests in phylogenetics and statistical inference.

Selected Publications:

  • Software: RevBayes v1.0. Hohna, S., B. Boussau, T.A. Heath, M.J. Landis, N. Lartillot, J.P. Huelsenbeck, and F. Ronquist. Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. (
  • Software: DPPDiv - Heath, T.A. Bayesian estimation of species divergence times under a Dirichlet process prior. (
  • Heath, T.A., J.P. Huelsenbeck, and T. Stadler. "The fossilized birth-death process for coherent calibration of divergence-time estimates."
    Proceedings of the National Academy of Sciences, 111(29):E2957-E2966, 2014.
  • Heath, T.A. and B.R. Moore. "Bayesian inference of species divergence times." In: Bayesian Phylogenetics: Methods, Algorithms, and Applications, Chen, M.-H., L. Kuo, P.O. Lewis (editors), Chapman & Hall/CRC, 2014.
  • Cook, J.A., S.V. Edwards, E.A. Lacey, R.P. Guralnick, P.S. Soltis, D.E. Soltis, C.K. Welch, K.C. Bell, K.E. Galbreath, C. Himes, J.M. Allen,
    T.A. Heath, A.C. Carnaval, K.L. Cooper, M. Liu, J. Hanken and S. Ickert-Bond. "Natural history collections as emerging resources for innovative education." Bio-Science, 64:725-734, 2014.
  • Darriba, D., A. Aberer, T. Flouri, T.A. Heath , F. Izquierdo-Carrasco, and A. Stamatakis. "Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library." IPDPSW, 2013 IEEE 27th International, Boston, USA, pp. 539-548, 2013.
  • Heath, T.A. "A hierarchical Bayesian model for calibrating estimates of species divergence times." Systematic Biology, 61:793-809, 2012.
  • Heath, T.A., M.T. Holder, and J.P. Huelsenbeck. "A Dirichlet process prior for estimating lineage-specific substitution rates." Molecular Biology and Evolution, 29:939-255, 2012.
  • Hohna, S., T.A. Heath, B. Boussau, M.J. Landis, F. Ronquist, and J.P. Huelsenbeck. "Probabilistic graphical model representation in phylogenetics." Systematic Biology, 63:753-771, 2014.
  • Heath, T.A., S.M. Hedtke, and D.M. Hillis. "Taxon sampling and the accuracy of phylogenetic analyses", Journal of Systematics and Evolution, 46:239-257, 2008.

Vita: Click here to download.


*Eric Henderson

BCB Faculty Member in the GDCB Department

Education: Ph.D., UCLA, 1984

Research Interests: We are interested in the interface between biology and nanotechnology. This has recently been labeled either bionanotechnology or synthetic biology. The label is of no importance. What is important is that 3.6 billion years of biological evolution has resulted in fantastic developments that are the stuff of which the dreams of nanotechnology is made. The challenge is to understand and, in a practical fashion, transfer these insights to the emerging field of nanotechnology so that the wheel (and eyeball, nose, etc. ) need not be invented twice. This is no small challenge. We have created a few tools that will facilitate this effort and a portion of my time is spent determining how best to provide these tools to researchers. A conclusion I have drawn is that a commercial enterprise accomplishes this and also provides an avenue (in theory) by which future developments may be funded and manifest. This theory is far from proven, however.

Selected Publications:


  • Mathur, D. and Henderson, E. (2013) Complex DNA Nanostructures from Oligonucleotide Ensembles, ACS Synthetic Biology, 2, 180-185.
  • Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Divita Mathur, and Dalia Abo Sheasha, Engineering and verifying requirements for programmable self-assembling nanomachines, Proceedings of the Thirty-Fourth International Conference on Software Engineering (ICSE 2012, Zurich, Switzerland, June 2-9, 2012), pp. 1361-1364.
  • Robyn R. Lutz, Jack H. Lutz, James I. Lathrop, Titus H. Klinge, Divita Mathur, D. M. Stull, Taylor G. Bergquist, and Eric R. Henderson, Requirements analysis for a product family of DNA nanodevices, Proceedings of the Twentieth IEEE International Requirements Engineering Conference (RE 2012, Chicago, IL, September 24-28, 2012), pp. 211-220.
  • Vengasandra, S.R., Lynch, M., Xu, J. and Henderson, E. (2005) Microfluidic Ultramicroscale deposition and patterning of quantum dots. Nanotechnology 16: 2052-2055.
  • Nettikadan, S.R., Johnson, J.C.,Vengasandra S. G., Muys, J., and Henderson, E. (2004) ViriChip: A solid phase assay for detection and identification of viruses by AFM. Nanotechnology 15: 383-389.
  • Lynch, M., Mosher, C., Huff, J.L., Nettikadan, S. and Henderson, E. (2004) Functional protein nanoarrays for biomarker profiling. Proteomics 4: 1695-1702.
  • Huff, J.L., Lynch, M.P., Nettikadan, S., Johnson, J.C., Ding, G., and Henderson, E. (2004) Label-free protein and pathogen detection using the atomic force microscope. J. Biomol.Screening, 9(6): 491-498.
  • Xu, J., Lynch, M., Huff, J., Mosher, C., Ding, G., and Henderson, E. (2004) Microfabricated quill-type deposition tools for the creations of biological micro/nano arrays. Biomedical Microdevices 6(2): 117-123.
  • Nettikadan, S. R., Johnson, J. C., Mosher, C., and Henderson, E. (2003) Virus particle detection by solid phase immunocapture and atomic force microscopy. Biophys. Biochem. Res. Comm. 311(2): 540-545.

Vita: Click here to download.

Website: Personal Departmental

Kai-Ming Ho

BCB Faculty Member in the Physics and Astronomy Department

Education: Ph.D., Berkeley, 1978

Research Interests: Protein structure and dynamics, membranes.

Selected Publications:

  • H. B. Cao, Y. Ihm, C. Z. Wang, J. R. Morris, M. Su, D. Dobbs, and K. M. Ho. Three-dimensional
    threading approach to protein structure recognition, Polymer 45:687 (2004).
  • W. C. Lu, C. Z. Wang, and K. M. Ho, "Effect of Chain Connectivity on the Structure of Lennard-Jones Liquid and Its Implication on Statistical Potentials for Protein Folding",Phys. Rev. E 69, 061920 (2004).
  • D. M. Deaven and K. M. Ho. Molecular geometry optimization with a genetic algorithm, Phys. Rev. Lett. 75:288 (1995).
  • H. B. Cao, C. Z. Wang, D. Dobbs, Y. Ihm, and K. M. Ho " Codability criterion for picking proteinlike
    structures from random three-dimensional configurations", Phys. Rev. E 74, 031921 (2006).
  • W. C. Lu, C. Z. Wang, E. W. Yu, and K. M .Ho Dynamics of the trimeric AcrB transporter protein
    inferred from B-factor analysis of the crystal structure, Proteins 62, 152 (2006).
  • T. Z. Sen, A. Kloczkowski, R. L. Jernigan, C. H. Yan, V. Honavar, K. M. Ho, C. Z. Wang, Y. Ihm, H. B. Cao, X. Gu, and D. Dobbs Predicting binding sites of hydrolase-inhibitor complexes by combining several
    methods, BMC Bioinformatics 5, 205 (2004).
  • H. B. Cao, C. Z. Wang, and K. M. Ho Fast method for estimating the energy distribution of globular states
    of proteins", Phys. Rev. E 72, 021907 (2005).
  • Y. Ihm, W. O. Sparks, J.-H. Lee, H. B. Cao, C. Z. Wang, S. Carpenter, K. M. Ho, and D. Dobbs,
    Structural Model of the Rev Regulatory Protein from Equine Infectious Anemia Virus (EIAV) submitted.

Vita: Click here to download

Website: Kai-Ming Ho

Heike Hofmann

BCB Faculty Member in the Statistics Department

Education: Ph.D., Augsburg University, Germany, 2000

Research Interests: Data Visualization, Multivariate Categorical Data Analysis, Statistical Computing, Exploratory Data Analysis and Interactive Statistical Graphics. My main research area is Statistical Graphics and its part of Exploratory Data Analysis. I am particularly interested in Explorations of Large Data Sets.

Selected Publications:
  • Buja A., Swayne D.F., Littman M., Dean N., Hofmann H.: Interactive Data Visualization with Multidimensional Scaling, Journal of Computational and Graphical Statistics, 2008, Vol 17 (2): pp. 444-472.

  • Cook D., Hofmann H., Nikolau B., Wurtele E., Lee Eun-kyung, Yang H.: Exploring gene expressions using plots. Journal of Data Science 5, pp.151-182, 2007.

  • Wickham H., Lawrence M., Cook D., Buja A., Hofmann H., Swayne D.: The plumbing of interactive graphics}, Computational Statistics, May, 2008 (online).

  • Buja A., Swayne D.F., Littman M., Dean N., Hofmann H., Chen L.: Interactive Data Visualization with Multidimensional Scaling. Journal of Computational and Graphical Statistics, 17, 2, 444--472, 2008.

  • Yan A, Kloczkowski A, Hofmann H, Jernigan RL.: Prediction of side chain orientations in proteins by statistical machine learning methods. Journal of biomolecular structure and dynamics, 3, 275--288, 2007.

  • J. Hobbs, H. Wickham, H. Hofmann, and D. Cook: Glaciers melt as mountains warm: A graphical case study, Computational Statistics, Invited submission. Special issue for ASA Statistical Computing and Graphics Data Expo 2007.

  • Hofmann H.: Interview with a Centennial Chart. CHANCE, 20 (3), pp. 26--35, 2007.

  • Cook D., Hofmann H., Nikolau B., Wurtele E., Lee Eun-kyung, Yang H.: Exploring gene expressions using plots Journal of Data Science, 5(2), 2007.

Vita: Click here to download

Website: Heife Hofmann

Richard Honzatko

BCB Faculty Member in the BBMB Department

Education: Ph.D., Harvard, 1982

Research Interests: Structure-function studies of proteins, X-ray diffraction

  • Macromolecular Structure and Function--Structure-function studies of proteins by X-ray diffraction and biochemical techniques

Description: Structure determination of macromolecules of biological interest, crystallization of proteins and x-ray crystallography, energy-conformation analysis of protein ligand interactions

Selected Publications:

  • Skaff, D.A., Kim, C.S., Tsai, H.J., Honzatko, R.B. and Fromm, H.J. (2005) Glucose 6-phosphate release of wild-type and mutant human brain hexokinases from mitochondria. J. Biol. Chem. 280,38403-38409.
  • Iancu, C.V., Mukund, S., Fromm, H.J. and Honzatko, R.B. (2005) R-state AMP complex reveals initial steps of the quaternary transition of fructose-1,6-bisphosphatase. J. Biol. Chem. 280, 19737-19745.

Vita: Click here to download

Website: Richard Honzatko

Adina Howe

BCB Faculty Member in the AgBiosystems and Engineering Department

Education: Ph.D., Iowa City, 2009

Research Interests: Her lab's research integrates molecular and computational biology to study, model, and manage complex microbial systems in both natural and engineered environments.

Selected Publications:

  • Williams, R.J., Howe, A., and Hofmockel, K. 2014. Demonstrating microbial co-occurrence patter analyses within and between ecosystems. Frontiers in Microbiology 5(358). doi: 10.3389/fmicb.2014.00358
  • Zhang, Q.P., Pell, J., Canino-Koning, R., Howe, A.C., and Brown, C. T. 2014. These are not the k-mers you are looking for: Efficient online k-mer counting using a probabilistic data structure. PLoS ONE 9(7): e1011271. doi:10.1371/journal.pone.0101271.
  • Howe, A.C., Jansson, J., Malfattie, S., Tringe, S., Tiedje, J., and Brown, C.T. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. PNAS. Accepted February 11, 2014. doi:10.1073/pnas.1402565111.
  • Vital, M, Howe, A.C., and Tiedje, J. 2014. Revealing the bacterial butyrate-synthesis pathways from (meta)genomic data. mBio 5(2):e00889-14. doi: 10.1128/mBio. 00889-14. Featured in Faculty of 1000 Prime.
  • Schwarz, E., Korhonen, P., Campbell, B., Young, N., Jex, Aaron, Jabbar, A., Hall, R. Mondal, A., Howe, A.C., Pell, J. Hofmann, A., Boag, P., Zhu, X., Gregory, T., Loukas, A., Williams, B., Antoshechkin, I., Brown, C.T., Sternberg, P., and Gasser, R. 2013. The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biology 14(R89). doi:10.1186/gb-2013-14-8-r89.
  • Pell, J., Hintze, A., Canino-Koning, R., Howe, A.C., Tiedje, J.M., and Brown, C.T. 2012. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. PNAS 109(33):13272-13277. doi:10.1073/pnas.1121464109.

Vita: Click here to download

Website: Adina Howe

Xiaoqiu Huang

BCB Faculty Member in the Computer Science Department

Education: Ph.D., Penn State, 1990

Research Interests: Computational problems in genome sequencing and analysis

  • Bioinformatics-- Computational problems in genome sequencing and analysis

Description: Assembly of DNA fragments into longer sequences, identification of genes in genomic DNA sequences, comparison of genomic DNA sequences.Xiaoqiu Huang is an associate professor in computer science at Iowa State University. He received his Ph.D. in computer science from Pennsylvania State University in 1990. Xiaoqiu Huang is interested in computational problems in genome sequencing and analysis. He is the author of a widely used CAP3 assembly program. He and his colleagues have recently developed a whole-genome assembly program named PCAP. PCAP has been used by Washington University Genome Center in chimpanzee and chicken genome projects.

Selected Publications:

  • Agrawal, A. & Huang, X.  (2010). Pairwise Statistical Significance of Local Sequence Alignment, Using Sequence-Specific and Position-Specific Substitution Matrices. IEEE/ACM Transactions on Computational Biology and Bioinformatics: to appear.
  • Huang, X. & Vingron, M. (2009). Maximum Similarity: A New Formulation of Phylogenetic Reconstruction, Journal of Computational Biology: 16, 887-896.
  • Agrawal, A. & Huang, X.  (2009). PSIBLAST_PairwiseStatSig: Reordering PSI-BLAST Hits Using Pairwise Statistical Significance. Bioinformatics: 25, 1082-1083.
  • Agrawal, A. & Huang, X.  (2009). Pairwise Statistical Significance of Local Sequence Alignment Using Multiple Parameter Sets and Empirical Justification of Parameter Set Change Penalty. BMC Bioinformatics: 10, Suppl 3, S1.
  • Huang, X. and Brutlag, D.L. (2007) Dynamic Use of Multiple Parameter Sets in Sequence Alignment,
    Nucleic Acids Research, 35: 678-686.
  • Huang, X., Yang, S.-P., Chinwalla, A., Hillier, L., Minx, P., Mardis, E. and Wilson, R.  (2006) Application of a Superword Array in Genome Assembly, Nucleic Acids Research, 34: 201-205.
  • Ye, L. and Huang, X. (2005) MAP2: Multiple Alignment of Syntenic Genomic Sequences. Nucleic Acids Research, 33: 162-170.
  • Huang, X., Ye, L., Chou, H.-H., Yang, I-H. and Chao, K.-M. (2004) Efficient Combination of Multiple Word Models for Improved Sequence Comparison, Bioinformatics, 20: 2529-2533.
  • Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003) PCAP: A Whole Genome Assembly Program, Genome Research, 13: 2164-2170.
  • Huang, X. and Chao, K.-M. (2003) A Generalized Global Alignment Algorithm, Bioinformatics, 19: 228-233.
  • Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877.
  • Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997) A Tool for Analyzing and Annotating Genomic Sequences. Genomics, 46: 37-45.

Vita: Click here to download

Website: Xiaoqiu Huang

*Matthew Hufford

BCB Faculty Member in the EEOB Department

Education: Ph.D., UC, Davis, 2010

Research Interests:

We are interested in studying both the evolution and ecology of crops and their wild relatives with a particular focus on maize and the teosintes. Current research in the lab is utilizing genomic data to study independent adaptations of maize landraces to highland environments, gene flow across taxa in the genus Zea, and the unique role of centromeres in Zea evolution.

Selected Publications:

  • Pyhajarvi, T., M.B.Hufford, S.Mezmouk, and J.Ross-Ibarra. 2013. Complex patterns of local adaptation inteosinte. Genome Biology and Evolution (In Press) Preprint:
  • Hufford, M.B., P. Lubinsky, T. Pyhajarvi, M. T. Devengenzo, N.C.Ellstrand, J.Ross-Ibarra. 2013. Thegenomic signature of crop--wild introgression in maize. PLoS Genetics 9: e1003477
  • Kanizay, L.B., T. Pyhajarvi, E.G.Lowry, M.B.Hufford, D.G.Peterson, J.Ross-Ibarra, R.K. Dawe. 2013. Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zeamays. Heredity 110:570-577
  • Hufford, M.B., E.Martinez-Meyer, B.S. Gaut, L.E. Eguiarte, and M.I. Tenaillon. 2012. Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight. PLoSONE7: e47659
  • Hufford, M.B., P. Bilinski, T. Pyhajarvi, J. Ross-Ibarra. 2012. Teosinteas a model system for population and ecological genomics. Trends in Genetics 28:606-615
    vanHeerwaarden, M.B.Hufford, and J.Ross-Ibarra. 2012. Historicalgenomics of North American maize. 2012. Proceedings of the National Academy of Sciences of the United States of America109:12420-12425
  • Hufford, M.B., X. Xu, J.vanHeerwaarden, T. Pyhajarvi, J.-M.Chia, R.A.Cartwright, R.J. Elshire, J.C. Glaubitz, K.E. Guill, S. Kaeppler, J. Lai, P.L. Morrell, L.M. Shannon, C. Song, N.M. Springer, R.A. Swanson-Wagner, P. Tiffin, J.Wang, G. Zhang, J. Doebley, M.D. McMullen, E.S. Buckler, D.Ware, S.Yang, and J.Ross-Ibarra. 2012. Comparative population

Vita: Click here to download

Website: Matt Hufford

*Fred Janzen

BCB Faculty Member in the EEOB Department

Education: Ph.D., Chicago, 1992

Research Interests: Modeling phenotypic selection, demography, phylogenetics

  • Genome Evolution--Theoretical and empirical investigations of natural selection and phenotypic evolution; phylogenetic reconstruction and molecular evolution; modelling population demography and cycling environmental parameters

Description: Research interests in the Janzen Lab involve the study of ecology and evolution, including mechanistic work at the molecular and organismal levels, field studies that document the importance of phenotypic variation, and a comparative view of the long-term consequences of this variation. To do so, we often integrate molecular and quantitative genetic techniques with experimental laboratory and field studies, largely focusing on the impact of environmental and genetic factors in mediating the expression of physiological, behavioral, and life-history traits. Using these conceptual approaches in concert with comparative and computational approaches enables us to assess important biological issues, including

  1. the biological significance of diverse sex-determining mechanisms,
  2. the impacts of environmental and genetic factors on variation in early life-history traits, and
  3. the current and historical genetic and demographic structure of populations, with an emphasis on elucidating adaptive processes and solving conservation concerns.

Selected Publications:

  • Mitchell, T. S., D. A. Warner, and F. J. Janzen. 2013. Phenotypic and fitness consequences of maternal nest-site choice across multiple early life stages. Ecology 94:336-345.

  • Sethuraman, A., S. E. McGaugh, M. L. Becker , C. H. Chandler, J. L. Christiansen, S. Hayden, A. LeClere, J. Monson-Miller, E. M. Myers, R. T. Paitz, J. M. Refsnider, T. VanDeWalle, and F. J. Janzen. 2013. Population genetics of Blanding's turtle (Emys blandingii) in the midwestern United States. Conservation Genetics 14:accepted pending revision.

  • Shaffer, H. B. et al.. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28.

  • Telemeco, R. S., K. C. Abbott, and F. J. Janzen. 2013. Modeling the effects of climate change-induced shifts in reproductive phenology on temperature-dependent traits. American Naturalist 181:637-648.

  • Chandler, C. H., G. E. Chadderdon, P. C. Phillips, I. Dworkin, and F. J. Janzen. 2012. Experimental evolution of the Caenorhabditis elegans sex determination pathway. Evolution 66:82-93.

  • Refsnider, J. M., and F. J. Janzen. 2012. Behavioural plasticity may compensate for climate change in a long-lived reptile with temperature-dependent sex determination. Biological Conservation 152:90-95.

  • McGaugh, S. E., and F. J. Janzen. 2011. Effective heritability of targets of sex-ratio selection under environmental sex determination. Journal of Evolutionary Biology 24:784-794.

Vita: Click here to download

Website: Fred Janzen

Laura Jarboe

BCB Faculty Member in the Chemical and Biological Engineering Department

Education: Ph.D., UCLA, 2006

Description: My research area is metabolic engineering, with a focus on understanding inhibition of biocatalyst growth and metabolism, such as that mediated by the desired product, substrate or a growth media contaminant. The goal of understanding the mechanism of the inhibition is subsequent rational engineering of the biocatalyst for increased tolerance. The tools used in my lab include transcriptome analysis, phenotype analysis and directed evolution and reverse engineering of tolerant strains. Bioinformatics and computational biology are especially relevant to the analysis of transcriptome data and in the interpretation of genome sequence data for evolved mutants.

Selected Publications:

  • X. Liang, M. Soupir*, S. Rigby, L. Jarboe, W. Zhang. “Flow cytometry is a promising and rapid method for differentiating between freely suspended E. coli and E. coli attached to clay particles” submitted to Applied Microbiology, 2014

  • T.J. Claypool, D.R. Raman, L.R. Jarboe, D.R Nielsen. “Technoeconomic evaluation of Bio-Based Styrene production by Engineered Escherichia coli” Journal of Industrial Microbiology and Biotechnology, 2014, 41(8):1211-6; DOI 10.1007/s10295-014-1469-5
  • L.A. Royce, E. Boggess, Y. Fu, P. Liu, J.V. Shanks, J. Dickerson, L. Jarboe. “Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage” PLOS ONE 2014, 9(2):e89580; doi:10.1371/journal.pone.0089580
  • A.L. Teh, D. Layton, D.R. Hyduke, L. Jarboe, D.K. Rollins, Sr. “Data Mining Based on Principal Component Analysis: Application to the Nitric Oxide Response in Escherichia coli” Journal of Statistical Science and Application 2:1-18 (2014)
  • L. Jarboe* , Z. Chi "Inhibition of microbial biocatalysts by biomass-derived aldehydes and methods for engineering tolerance" pp 101-120 New Developments in Aldehydes Research 2013. ISBN #978-1-62417-090-4.
  • Y. Liang, X. Zhao, Z. Chi, M. Rover, P. Johnston, R. Brown, L. Jarboe, Z. Wen* "Utilization of acetic acid-rich pyrolytic bio-oil by microalga Chlamydomonas reinhardtii: Reducing bio-oil toxicity and enhancing algal toxicity tolerance" Bioresource Technology 2013 133:500 – 506.
  • L.A. Royce, E. Boggess, T. Jin, J. Dickerson, L. Jarboe*. "Identification of Mutations in Evolved Bacterial Genomes" Methods in Molecular Biology (vol 985): Systems Metabolic Engineering: Methods and Protocols, Hal Alper (ed). 2013
  • P. Liu, A. Chernyshov, T. Najdi, Y. Fu, J. Dickerson, S. Sandmeyer, L. Jarboe* "Membrane stress caused by octanoic acid in Saccharomyces cerevisiae" Applied Microbiology and Biotechnology 2013 97(7):3239-3251 10.1007/s00253-013-4773-5
  • K. B. Kautharapu, J. Rathmacher, L. Jarboe* "Growth condition optimization for docosahexaenoic acid (DHA) production by Moritella marina MP-1" Applied Microbiology and Biotechnology 2013 97 (7): 2859-2866 DOI: 10.1007/s00253-012-4529-7
  • P. Liu, L. Jarboe* "Metabolic Engineering of biocatalysts for carboxylic acids production" Computational and Structural Biology 2012. 3(4) e201210011,
  • L. Jarboe* , P. Liu, K. Kautharapu, L.O. Ingram "Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals" Computational and Structural Biotechnology Journal. October 2012. 3(4) e201210005,
  • K.B. Kautharapu, L. Jarboe*, "Genome sequence of psychrophilic deep sea bacterium Moritella marina MP-1" Journal of Bacteriology, November 2012. 194:6296-6297.
  • P.C. Turner, L.P. Yomano, L.R. Jarboe, S.W. York, C.L. Baggett, B.E. Moritz, E.B. Zentz, K.T. Shanmugam, L.O. Ingram*. "Optimal mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes" J Ind Micro Biotech. 2011. 39(4):629-639.
  • L. R. Jarboe *, Ping Liu, Liam Royce "Engineering inhibitor tolerance for the production of biorenewable fuels and chemicals". Current Opinion in Chemical Engineering. 2011 (invited) 1:38-42. DOI 10.1016/j.coche.2011.08.003
  • Liu, P., M.L. Soupir, M. Zwonitzer, B. Huss, L. Jarboe* "Antibiotic Resistance in Agricultural E. coli Isolates is Associated with Attachment to Quartz"AEM. 2011. 77(19):6945-6953. doi:10.1128/AEM.00717-11
  • L. R. Jarboe *, Z. Wen, D.W. Choi, R.C. Brown "Hybrid thermochemical processing: fermentation of pyrolysis-derived bio-oil". Applied Microbiology and Biotechnology. 2011 (invited) 91(6):1519-1523. 10.1007/s00253-011-3495-9
  • Yao Fu, Laura R. Jarboe, Julie Dickerson*. " Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities". BMC Bioinformatics. 2011 12:233.
  • Jarboe, L.R.* 2010. "YqhD: A broad-substrate range aldehyde reductase with various applications in production of biorenewable fuels and chemical"Applied Microbiology and Biotechnology. 89(2):249.
  • Turner, P.C., E.N. Miller, L. Jarboe, C.L. Baggett, K.T. Shanmugam, L.O. Ingram*. YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance. J Industr Microbiol Biotechnol.38:431. 2011. DOI 10.1007/s10295-010-0787-5
  • Miller, E.N., P.C. Turner, L.R. Jarboe, L.O. Ingram.* 2010. Genetic changes that increase 5-hydroxymethyl furfural resistance in ethanol-producing Escherichia coli LY180. Biotechnology Letters. 32(5):661-667.
  • L. R. Jarboe , X. Zhang, X. Wang, J.C. Moore, K.T. Shanmugam, L.O. Ingram*. 2010. Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology (invited) Journal of Biomedicine and Biotechnology. Article ID 761042

Vita: Click here to download

Website: Laura Jarboe

*Robert Jernigan

BCB Faculty Member in the BBMB Department

Education: Ph.D., Stanford, 1967

Research Interests: Computational structural biology and bioinformatics

  • Macromolecular Structure and Function-- theoretical and computational studies of the structures of proteins, nucleic acids, and small molecules, and their interactions. Applications are made to develop molecular models and to select new drugs. more

Description: Elastic network models of bio-structures are used to develop mechanisms of processing, refine and improve structures, predict conformational transitions. Applications to learn about the mechanics of the ribosome are pursued. Sequence matching is being improved by including structural information and to improve comparative genomics efforts.

Selected Publications:
  • Skliros A, Zimmermann MT, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A, Jernigan RL. The importance of slow motions for protein functional loops. Phys Biol 2012;9:014001.
  • Saraswathi S, Fernandez-Martinez JL, Kolinski A, Jernigan RL, Kloczkowski A. Fast learning optimized prediction methodology for protein secondary structure prediction. J Mol Modelling 2012; 18:4275-4289.
  • Burton B, Zimmermann MT, Jernigan RL, Wang Y. A Computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. PLoS Comp Biol 2012;8:e1002530 (13 pp).
  • Zimmermann MT, Leelananda SP, Kloczkowski A, Jernigan RL. Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses. J Phys Chem B 2012;116:6725-6731.
  • Zimmermann MT, Jernigan RL. Protein loop dynamics are complex and depend on the motions of the whole protein.  Entropy 2012;14,687-700.
  • Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. Elastic network normal modes provide a basis for protein structure refinement. J Chem Phys 2012;136:195101.
  •  Huang Y, Bonett S, Kloczkowski A, Jernigan R, Wu Z. P.R.E.S.S. An R-package for exploring residual-level protein structural statistics. J Bioinform Comput Biol. 2012;10:1242007.
  • Gu Y, Sun W, Wang G, Zimmermann MT, Jernigan RL, Fang N. Revealing rotational modes of functional nanoparticles on live cell membranes. Small 2013;9:785-792.
  • Jernigan RL. Possible alternative and extension to the use of dynamics for structure matching. Physics Life Rev 2013;S1571-0645:4-6.
  • Saraswathi S, Fernández-Martínez JL, Koliṅski A, Jernigan RL, Kloczkowski A. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure. J Mol Model 2013; 18:4337-4348.
  • Flatow D,  Leelananda SP, Skliros A, Kloczkowski A, Jernigan RL. Volumes and surface areas: Geometries and scaling relationships between coarse-grained and atomic structures.  Curr Pharm Des. 2014; 20:1208-1222.
  • Afonin KA, Wojciech KK,  Bindewald E, Puppala PS, Diehl AR, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA. Computational and experimental characterization of RNA cubic nanoscaffolds.  Methods 2013; pii: S1046-2023(13)00416-7. doi: 10.1016/j.ymeth.2013.10.013.
  • Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL. Factors correlating with significant differences between X-ray structures of myoglobin. Acta Crystall D Biol Crystallogr 2014;70 (Pt 2):481-491.
  • Park JK, Jernigan R, Wu Z. Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations. Bull Math Biol. 2013;75:124-60.
  • Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality . Protein Sci  2014;23:213-228.
  • Zimmermann MT, Yang L, Jernigan RL. Elastic network modes capture the motions apparent within ensembles of RNA structures.  RNA, 2014; 20:792-804.
  • Katebi A, Sankar K, Jia K, Jernigan RL.  The use of experimental structures to model protein dynamics and entropies. Submitted.
  • Boyken SE, Chopra N, Joseph RE, Wales TE, Fulton DB, Engen JR, Jernigan RL, Andreotti A. Substitution of Leu for a single Ile activates Bruton’s tyrosine kinase. Submitted.
  • Katebi AR, Jernigan RL. Aldolase – oligomerization, dynamics and functionality. To be submitted.
  • Leelananda SP, Jernigan RL. Improved sequence matching with fold-specific sequence scoring. Submitted.
Resume: Click here to download and here for publications

Website: Robert Jernigan

Douglas Jones

BCB Faculty Member in the Veterinary Pathology Department

Education: Ph.D., University of Pennsylvania, 1993

Research Interests: Host factors that influence the development of resistance and susceptibility to infectious diseases caused by intracellular pathogens

  • Macromolecular Structures and Functions--Dr. Jones researches the host factors that influence the development of resistance and susceptibility to infectious diseases caused by intracellular pathogens. The laboratory studies the murine immune response to the protozoal parasite Leishmania and the bovine immune response to Mycobacterium avium subs paratuberculosis


Selected Publications:

Vita: Click here to download

Website: Doug Jones

Julie Kuhlman

BCB Faculty Member in the GDCB Department

Education: Ph.D., Cornell University, 1999

Research Interests: Our lab focuses on understanding the development and function of the enteric nervous system (ENS) and its coor
dination with other cell types in regulating intestinal motility. Through my professional experience, I have gained a broad knowledge of developmental systems, models and mechanisms, and obtained extensive expertise in a variety of genetic, molecular and imaging techniques. I have now begun a series of studies aimed at understanding the transcriptional profile of enteric neurons as they migrate through the embryos and become specified. In additionto teaching, I mentor 2 graduate students, have graduate one masters student, and have mentored over 14 undergraduate students through research projects in my lab . I help promote and recruit under-represented groups into the STEM fields through the NSF funded LSAMP IINSPIRE program, an alliance of Midwest universities working to broaden the participation of underrepresented groups in (STEM) education.

Selected Publications:

  • McMenamin, S.K., Bain, EJ., McCann, AE., Patterson LB., Eom, DS., Waller ZP., Hamill JC., Kuhlman JA., Eisen, JS., Parichy DM. (2014) Thyroid hormone - dependent adult pigment cell lineage and pattern in zebrafish. Science Aug 28.
  • Kuhlman, J. and Eisen, J. S. (2007). A genetic screen for mutations affecting development and function of the enteric nervous system.
    Dev. Dyn. 236, 118 - 27.
  • Bates, J. M., Mittge, E., Kuhlman, J., Baden, K.N., Cheesman, S. E., and Guillemin, K. (2006). Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev Biol 297, 374 - 386.
  • Hyer, J., Kuhlman, J., Afif, E., and Mikawa, T. (2003). Optic cup morphogenesis requires pre-lens ectoderm but not lens differentiation,
    Dev Biol 15, 351 - 63.
  • Obara - Ishihara,T., Kuhlman, J., Niswander, L. and Herzlinger, D. (1997). Inductive interactions between intermediate mesoderm and surface ectoderm regulate nephric duct formation. Development 126, 1103 - 1108.
  • Kuhlman, J. and Niswander, L. (1997). Limb deformity proteins: role in mesodermal induction of the apical ectodermal ridge. Development
    124, 133 - 139

Vita: Click here to download

Website: Julie Kuhlman

*Susan Lamont

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Illinois Medical Center, 1980

Research Interests: Molecular markers, gene expression, quantitative trait loci, biodiversity. Structural and functional genomic associations with biological traits. Microbiomes.

  • Functional and Structural Genomics--Molecular genetic dissection of complex biological traits in poultry. Structural and functional genomics
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Estimation of genetic relationships by molecular analysis; characterization of gene regulatory regions; mathematical modelling and genetic dissection of complex biological traits; estimating epistatic effects of molecular markers

Description: Dr. Lamont's program investigates the associations of structural and functional genomic variation with complex biological traits in poultry.  Taking advantage of the complete draft genome sequence of the chicken genome, a 2.8-million SNP map, and unique genetic resource populations at Iowa State, specific projects seek to dissect the complex genetic architecture of traits such as resistance to disease and heat stress and growth and development.

Selected Publications:

  • Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S.J., Crooijmans, R., and Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Animal Genetics 45: 400-411.
  • Lee, M.O., Yang, E., Morisson, M., Vignal. A., Huang, Y.-Z., Cheng, H.H., Muir, W.M., Lamont, S.J., Lillehoj, H.S., Lee, S.H., and Womack, J.E. 2014. Mapping and genotypic analysis of NK-lysin gene in chicken. Genet. Sel. Evol.46: 43.
  • Ji, B., Middleton, J.L., Ernest, B., Saxton, A.M., Lamont, S.J., Campagna, S. R., and Voy, B.H. 2014. Genetic leanness in domestic chickens is associated with evidence of increased fatty acid oxidation in white adipose tissue. Physiological Genomics 46: 315–327.
  • Wang, Y., Lupiani, B., Reddy, S., Lamont, S.J., and Zhou, H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Sci. 93:485-493
  • Cheng, H.H., Kaiser, P., and Lamont, S.J. 2013. Integrated genomic approaches to enhance genetic resistance in chickens. Annu. Rev. Anim. Biosci. 2013. 1:239–260
  • Coble, D.J., Sandford, E. E., Ji, T., Abernathy, J., Fleming, D., Zhou, H., and Lamont, S.J. 2013. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Genesis 51:357–364
  • Wang, C., Habier, D., Peiris, L., Wolc, A., Kranis, A., Watson, K., Avendano, S., Garrick, D., Fernando, R., Lamont, S., Dekkers, J. 2013. Accuracy of genomic prediction using an evenly spaced, low-density SNP panel in broiler chickens. Poultry Sci. 92:1712–1723
    8. Kaiser, M.G., Block, S.S., Ciraci, C., Fang, W., Sifri, M., and Lamont, S.J. 2012. Effects of dietary vitamin E type and level on LPS-induced cytokine mRNA expression in broiler chicks. Poultry Sci.91:1893-1898.
  • Lian, L., Ciraci, C., Chang, G., Hu, J., and Lamont, S.J. 2012. NLRC5 knockdown in chicken macrophages alters response to LPS and poly (I:C) stimulation. BMC Vet. Res. 8:23 doi:10.1186/1746-6148-8-23
  • Lian, L., Qu, L., Chen, Y., Lamont S. J., and Yang, N. 2012. A systematic analysis of miRNA transcriptome in Marek’s disease virus-induced lymphoma reveals novel and differentially expressed miRNAs. PLoS ONE 7(11): e51003. doi:10.1371/journal.pone.0051003
  • Lian, L., Sun, H. Qu, L., Chen, Y., Lamont, S., Yang, N. 2012. Gene expression analysis of host responses to Marek’s disease virus infection in susceptible and resistant spleens of chickens. Poultry Sci. 91: 2130-2138
  • Nie, Q., Sandford, E.E., Nolan, L.K., Zhang, X., Lamont, S.J. 2012. Deep sequencing-based transcriptome analysis of chicken spleen in response to avian pathogenic Escherichia coli (APEC) infection, PLoS ONE 7(7): e41645. doi:10.1371/journal.pone.0041645
  • Sandford, E.E., Orr, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., Lamont, S.J. 2012. Strong concordance between transcriptomic patterns of spleen and peripheral blood leukocytes in response to avian pathogenic Escherichia coli infection. Avian Diseases 56:732-736.
  • Sandford, E.E., Orr, M., Shelby, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S.J. 2012. Transcriptome response of leukocytes from chickens infected with avian pathogenic Escherichia coli identifies pathways associated with resistance. Results in Immunol. 2: 44-53.
Vita: Click here to download

Website: Susan Lamont

*Dennis Lavrov

BCB Faculty Member in the EEOB Department

Education: Ph.D., University of Michigan, Ann Arbor, 2000

Research Interests: My main research interests are the evolution of major groups of animals and their mitochondrial genomes.  My current research is focused on three groups of non-bilaterian animals: Cnidaria, Ctenophora, and Porifera.  Ongoing projects include: Comparative animal mitochondrial genomics; Parallel mitochondrial genome evolution; Phylogenetic analysis of basal animal relationships; and Cell-cell communication in sponges.

  • Bioinformatics--Molecular evolution, phylogenetics, comparative and functional genomics; use of gene order data for the analysis of ancient relationships; evolution of animal mitochondrial DNA with a special emphasis on arthopods and sponges; bioinformatics
  • Functional and Structural Genomics--Same as above
  • Genome Evolution--Same as above


Selected Publications:

  • Haen, K. M., Pett, W., and Lavrov, D.V. (2010). Correlated loss of mitochondrial tRNAs and
    aminoacyl-tRNA synthetases in the cnidarian Nematostella vectensis. Molecular Biology and Evolution, doi:10.1093/molbev/msq112.

  • Rota-Stabelli, O., Kayal, E., Daub, J., Pisani, D., Telford, M., Blaxter, M., Boore, J., Gleeson, D., & Lavrov, D.V. (2010). Rapid proliferation of repetitive hairpin-forming elements in the mitochondrial genome of the endemic Lake Baikal sponge Lubomirskia baicalensis. Molecular Biology and Evolution 27: 757-760.

  • Wang, X., Huang, Y., Lavrov, D.V., & Gu, X. (2009). Comparative study of human mitochondrial proteome reveals extensive subcellular relocalization following ancient gene duplications. BMC Evolutionary Biology: 9, 275.

  • Erpenbeck, D., Voigt, O., Wörheide, G., & Lavrov, D.V. (2009). Mitochondrial genomes of sponges provide evidence for multiple invasions by repetitive hairpin-forming elements (RHE). BMC Genomics: 10, 591.

Vita: Click here to download

Website: Dennis Lavrov

*Carolyn Lawrence

BCB Faculty Member in the GDCB Department

Education: Ph.D., The University of Georgia, 2003

Research Interests: My group manages the operation of the Maize Genetics & Genomics Database (MaizeGDB) and also investigates functional aspects of maize chromosomes during cell division. The work at MaizeGDB is focused on creating data storage, access, and analysis solutions for information generated by the community of maize geneticists. The maize chromosome research focuses on how chromosome move and how the physical structure of chromosomes relates to maps and DNA sequences.

Selected Publications:

  • Campbell, MS, Law, MY, Holt, C, Stein JC, Moghe GD, Hufnagel DE, Lei, J, Achawanantakun, R, Jiao, D, Lawrence CJ, Ware, D, Shiu, SH, Childs, K, L, Sun, Y, Jiang, N, & Yandell, M (2014) MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiology 164(2): 513–524.
  • Monaco, MK, Sen, TZ, Dharmawardhana, PD, Ren, L, Schaeffer, M, Naithani, S, Amarasinghe, V, Thomason, J, Harper, L, Gardiner, J, Cannon, EKS, Lawrence, CJ, Ware, D, & Jaiswal, P (2013) Maize Metabolic Network Construction and Transcriptome Analysis. The Plant Genome, 2013(6), doi:10.3835/plantgenome2012.09.0025.
  • Robbins, RJ, Amaral-Zettler, L, Bik, H, Blum, S, Edwards, J, Field, D, Garrity, G, Gilbert, JA, Kottmann, R, Krishtalka, L, Lapp, H, Lawrence, C, Morrison, N, Tuama, EO, Parr, C, San Gil, I, Schindel, D, Schriml, L, Vieglas, D, & Wooley, J (2012) RCN4GSC Workshop Report: managing data at the interface of biodiversity and (meta) genomics, March 2011. Standards in Genomic Sciences, 7, 159.
  • Cannon, EKS, Birkett, SM, Braun, Bremen L, Kodavali, S, Jennewein, DM, Yilmaz, A, Antonescu, V, Antonescu, C, Harper, LC, Gardiner, JM, Schaeffer, ML, Campbell, DA, Andorf, CM, Andorf, D, Lisch, D, Koch, KE, McCarty, DR, Quackenbush, J, Grotewold, E, Lushbough, CM, Sen, TZ, & Lawrence, CJ (2011) POPcorn: an online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics, 2011 doi: 10.1155/2011/923035.
  • Green, JM, Harnsomburana, J, Schaeffer, ML, Lawrence, CJ & Shyu, C-R (2011). Multi-source and ontology-based retrieval engine for maize mutant phenotypes. Database: the Journal of Biological Databases and Curation, 2011, doi:10.1093/database/bar012.
  • Ghaffari, R, Cannon, EKS, Kanizay, LB, Lawrence, CJ & Dawe, RK (2012) Maize chromosomal knobs are located in gene-dense areas and suppress local recombination. Chromosoma, 122(1-2), 67-75.
  • Lushbough, C, Bergman, MK, Lawrence, CJ, Jennewein, D & Brendel, V (2010). BioExtract Server‚an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 7, 12-24.
  • Sen, TZ, Andorf, CM, Schaeffer, ML, Harper, LC, Sparks, ME, Duvick, J, Brendel, VP, Cannon, E, Campbell, DA & Lawrence, CJ (2009). MaizeGDB becomes ‘sequence-centric’. Database: The Journal of Biological Databases and Curation, 2009, bap020.
  • Lawrence, CJ, Harper, LC, Schaeffer, ML, Sen, TZ, Seigfried, TE & Campbell, DA (2008). MaizeGDB: The maize model organism database for basic, translational, and applied research. International Journal of Plant Genomics, 496957 doi: 10.1155/2008/496957.
  • Lawrence, CJ & Walbot, V (2007). Translational genomics for bioenergy production from fuelstock grasses: maize as the model species. The Plant Cell, 19, 2091-2094.
Vita: Click here to download

Website: Carolyn Lawrence

Peng Liu

BCB Faculty Member in the Statistics Department

Education: Ph.D., Cornell University, 2006

Research Interests: Functional and Structural Genomics-- Statistical design and analysis of microarray experiments, statistical methods for high-dimensional data including gene expression data and proteomic data.


  • Orr, M. & Liu, P. (2009). Sample size estimation while controlling false discovery rate for microarray experiments using the ssize.fdr package, R Journal: 1, 1, 47-53.

  • P. Liu and J. T. G. Hwang (2007), Quick estimation of sample size while controlling false discovery rate and application to microarray analysis, Bioinformatics, 23(6): 739-746

  • R. J. H. Sawers, P. Liu, K. Anufrikova, Q. Sun, G. Olsefski, J. T. G. Hwang, T. Brutnell (2007), Gene expression profiling of bundle sheath and mesophyll photosynthetic cell-types of maize, BMC genomics, 8:12

  • S. A. Jesch, P. Liu, X. Zhao, M.  T. Wells, and S. A. Henry (2006), Multiple endoplasmic reticulum-localized protein complexes respond to phospholipid metabolism and regulate gene expression by distinct mechanisms, Journal of Biological Chemistry, 281: 24070 - 24083

Vita: Click here to download

Website: Peng Liu

Catherine Logue

BCB Faculty Member in the VMPM Department

Education: University of Ulster, Jordanstown, Newtownabbey Co. Antrim. Ireland. D.Phil. in Food Microbiology October 1996

Selected Publications:

  • Logue, C.M., Doetkott, C., Mangiamele, P., Wannemuehler, Y.M., Johnson, T.J., Tivendale, K.A., Li, G., Sherwood, J.S., and Nolan, L.K. (2012) Genotypic and Phenotypic Traits that Distinguish Neonatal Meningitis Escherichia coli from Fecal E. coli Isolates of Healthy Human Hosts. Applied and Environmental Microbiology 78:16:5824-5830.
  • Li, G., Cai, W., Hussein, A., Wannemuehler, Y., Logue, C.M., and Nolan, L.K. (2012) Proteome response of an extraintestinal pathogenic Escherichia coli strain with zoonotic potential to human and chicken sera. Proteome Research Accepted 05/12. doi 10.1016/j.prot.2012.05.044
  • Li, G., Kariyawasam, S., Tivendale, K.A., Wannemuehler, Y., Ewers, C., Wieler, L., Logue, C.M., Nolan, L.K. (2012) tkt1, Located on a Novel Pathogenicity Island Contributes to Virulence of Avian Pathogenic Escherichia coli. BMC Microbiology 12:51
  • Johnson, T.J., Wannemuehler, Y., Kariyawasam, S., Johnson, J.R., Logue, C.M., Nolan, L.K. (2012) Prevalence of Avian Pathogenic E. coli strain APEC O1 genomic islands among extraintestinal and commensal E. coli isolates. Accepted J. Bacteriology 02/12 doi:10.1128/JB.06375-11
  • Wang, Y., Yang, J., Logue, C.M., Liu, K., Cao, X., Zhang, W., Shen, J-Z., Wu, C-M. (2012) Methicillin resistant Staphylococcus pseudintermedius isolated from canine pyoderma in North China. Journal of Applied Microbiology 112:4:623-630.
  • Khot, L., Panigrahi, S.P., Doetkott, C., Chang, Y., Glower, J., Amamcharla, J., Logue, C.M., Sherwood, J.S. (2012) Evaluation of technique to overcome small dataset problems during neural-network based contamination classification of packaged beef using integrated olfactory sensor system. LWT - Food Science and Technology 45:2:233-240.
  • Johnson, T.J., Logue, C.M., Sherwood, J.S., Johnson, J.R., Kuskowski, M.A., Barnes, J.A., DebRoy, C., Wannemuehler, Y.M., Obata-Yasouka, M., Spanjaard, L., Nolan, L.K. (2012) Associations between multidrug resistance, plasmid content and virulence potential among extraintestinal pathogenic and commensal Escherichia coli from humans and poultry. Foodborne Pathogens and Disease 9, 37-46.
  • Lynne, A.M., Kariyawasam, S., Wannemuehler, Y., Johnson, T.J., Johnson, S.J., Sinha, A.S., Lynne, D.K., Moon, H.W., Jordan, D.M., Logue, C.M., Foley, S.L., and Nolan L.K. (2012) Recombinant Iss as a Potential Vaccine for Avian Colibacillosis. Avian Diseases 56:1:192-199.

Website: Catherine Logue


Jack Lutz

BCB Faculty Member in the Computer Science Department

Education: Ph.D., California Institute of Technology, 1987

BCB Research Interests: Molecular programming and DNA nanotechnology: DNA tile self-assembly, DNA origami, and DNA strand displacement reactions. Universality, randomness, dynamics, complexity, and fractal geometry. Specifications, simulation, programming, and verification to make DNA nanotechnology more productive, predictable, and safe.

Selected Publications

Vita: Click here to download

Website: Jack Lutz

Robyn Lutz

BCB Faculty Member in the Computer Science Department

Education: Ph.D., University of Kansas, 1980.

Research Interests: Computational analysis and verificatin of requirements for molecular programming and DNA nanaotechnology; design specification; robustness and fault tolerance; safety-critical systems; computational modeling and simulation; DNA origami product families.

Selected Publications:

  • R. Lutz, J. Lutz, J. Lathrop, T. Klinge, D. Mathur, D.M. Stull, T. Bergquist and E. Henderson, "Requirements Analysis for a Product Family of DNA Nanodevices," 20th IEEE International Requirements Engineering Conference (RE 2012), Chicago, IL, Sept. 24-28, 2012. pdf
  • R. Lutz, J. Lutz, J. Lathrop, T. Klinge, E. Henderson, D. Mathur and D. Abo Sheasha, "Engineering and Verifying Requirements for Programmable Self-Assembling Nanomachines," International Conference on Software Engineering (ICSE 2012), Zurich, Switzerland, June 2-9, 2012. pdf
  • J. Dehlinger and R. Lutz, "Gaia-PL: A Product-Line Engineering Approach for Efficiently Designing Multi-Agent Systems," ACM Transactions on Software Engineering and Methodology (TOSEM), 20(4):17, 2011. pdf
  • J. Liu, S. Basu, and R. Lutz, "Generating Variation Point Obligations for Compositional Model Checking of Software Product Lines," Journal of Automated Software Engineering, Vol. 18 (1), pp. 39-76, 2011. pdf
  • R. Lutz and C. Mikulski, "Empirical Analysis of Safety-Critical Anomalies During Operations," IEEE Transactions on Software Engineering , vol. 30, no. 3, March, 2004, pp. 172-180. ps , pdf

Website: Robyn Lutz

Gustavo MacIntosh

BCB Faculty Member in the BBMB Department

Education: Ph.D., University of Buenos Aires, 1997

Research Interests: My laboratory is engaged in understanding the interaction between plants and pests. We use different approaches to study this problem, including metabolomics and transcriptomics analyses. We then use bioinformatics tools to analyze the large amount of data generated. While not fully there yet, we are working towards a “systems biology” interpretation and model generation of these interactions. Another area of research in my laboratory is the analysis of protein structure/function and the acquisition of novel functions by duplicated genes during evolution. Bioinformatics tools are also used in this project, from phylogenetic analysis to protein threading and structure prediction.

Selected Publications:

  • MacIntosh, G.C., Hillwig, M.S., Meyer, A., & Flagel, L. (2010). RNase T2 genes from rice and the evolution of secretory ribonucleases in plants. Mol. Gen. Genom: 283, 381-396.
  • Hillwig, M.S., Rizshsky, L., Wang, Y., Umanskaya, A., Essner, J.J., & MacIntosh, G.C. (2009). Zebrafish RNase T2 genes and the evolution of ribonucleases in animals. BMC Evolutionary Biology: 9, 170. doi:10.1186/1471-2148-9-170
  • Studham, M., MacIntosh, G.C., Avendano, M.F., Soh, D., & Tylka, G., (2009). The soybean resistance gene Rag1 does not protect against soybean cyst and root knot nematodes. Plant Health Progress doi:10.1094/PHP-2009-0401-01-BR.
  • Hillwig MS, Rizshsky L, Wang Y, Umanskaya A, Essner JJ, MacIntosh GC (2008) Zebrafish RNase T2 genes and the evolution of ribonucleases in animals. Submitted to Mol. Biol. Evol.
  • Hillwig MS, LeBrasseur ND, Green PJ and MacIntosh GC (2008) Impact of transcriptional, ABA-dependent, and ABA-independent pathways on wounding regulation of RNS1 expression. Mol. Gen. Genom. 280: 249-261
  • Raices M, MacIntosh GC, Ulloa RM, Gargantini PR, Vozza NF, Tellez-Inon MT (2003) Sucrose increases calcium-dependent protein kinase and phosphatase activities in potato plants. Cell Mol Biol 49: 959-964
  • Raices M, Ulloa RM, MacIntosh GC, Crespi M and Tellez-Inon MT (2003) StCDPK1 is expressed in potato stolon tips and is induced by high sucrose concentration. J. Exp. Bot. 54: 2589-2591.
  • LeBrasseur ND, MacIntosh GC, Pérez-Amador MA, Saitoh M and Green PJ (2002) Local and systemic wound-induction of RNase and nuclease activities in Arabidopsis: RNS1 as a marker for a JA-independent systemic signaling pathway . Plant J., 29: 393-403.

Vita: Click here to download

Website: Gustavo MacIntosh

Leslie Miller

BCB Faculty Member in the Computer Science Department

Education: Ph.D., SMU, 1980

Research Interests: Multidatabases for biology data sources, biological data warehouse

  • Bioinformatics-- Multidatabases for biology data sources; biological data warehouses; protein structure prediction

Selected Publications

  • Fu, Fengli, Jeffry Sander, Morgan Maeder, Stacy Thibodeau-Beganny, J. Joung, Drena Dobbs, Leslie Miller, Daniel Voytas. (2008). Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc finger arrays. To appear in the database Nucleic Acids Research issue.
  • Miller, Les, Sree Nilakanta, and Meghana Rao. (2008). Supporting Knowledge Management Within Process and Group Settings Using Visual Topic Maps. ISCA 23rd International Conference on Computers and Their Applications (CATA-2008). April 9-11, 2008. Cancun, Mexico.
  • L. Miller, S. Nilakanta, Y. Song, L. Zhu, M. Hua. 2008. Managing Knowledge in Organizational Memory Using Topic Maps. International Journal of Knowledge Management, IGI Publishing. Vol. 4. No. 1. pp. 17-28.
  • Wurtele, E.S., L. Li, D. Berleant, D. Cook, J.A. Dickerson, J. Ding, H. Hofmann, M. Lawrence, E.K. Lee, J. Li, W. Mentzen, L. Miller, B.J. Nikolau, N. Ransom, Y. Wang, (2007). MetNet: Systems Biology Software for Arabidopsis. In: Concepts in Plant Metabolomics. Springer. pp 145-158.
  • Miller, Les, Hua Ming, Hsine-Jen Tsai, Becca Wemhoff and Sarah Nusser. 2007. Supporting
    Geographic Data in the Mobile Computing Environment. ISCA 20th International Conference on Parallel
    and Distributed Computing Systems. Las Vegas, NV. pp. 56-61.

Vita: Click here to download

Website: Leslie Miller

*Allen Miller

BCB Faculty Member in the Plant Pathology and Microbiology Department

Education: Ph.D., Wisconsin, Madison, 1984

Research Interests: We study molecular biology of plant RNA viruses with three different but overlapping perspectives

  • Functional and Structural Genomics-- Prediction of RNA secondary and tertiary structure; plant virus genome sequencing and database, novel translation mechanisms
  • Macromolecular Structure and Function-- Same as above


RNA virus replication:  from plants to humans

We employ plant viruses as easy-to-use model systems to provide basic understanding of how viruses replicate and express genes.  Because of similarities in replication mechanisms across kingdoms, this knowledge may be relevant to major human viruses. Viruses are fascinating as the smallest, minimal replicating entities.  They allow detailed understanding of what it takes to replicate, the essential property that defines life.

How cells decode the genetic code

We investigate the plethora of tricks by which viral messenger RNA usurps and controls the host translational machinery (translation factors and ribosomes).  This gives us a better understanding of fundamental mechanisms of protein synthesis.  This knowledge may allow us to modify viral sequences and mechanisms to control expression of host and viral genes in beneficial ways.

Sustainable control of crop diseases and pests

We strive to improve the knowledge base needed to control the economically important yellow dwarf viruses and the aphids that transmit them.  They vary remarkably in sequence.  We are determining complete nucleotide sequences of dozens of virus isolates from around the world.  We are also attempting to exploit aphid viruses, and aphid-transmitted plant viruses, to control aphids in cereal crops and soybeans.

Selected Publications:

  • Kraft JJ, Treder K, Peterson MS, Miller WA (2013) Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G. Nucleic Acids Res 41 , 3398 - 3413.  doi:10.1093/nar/gkt026

  • Simon AE, Miller WA (2013) 3' cap-independent translation enhancers of plant viruses.  Annu Rev Microbiol 67, DOI: 10.1146/annurev-micro-092412-155609 .

  • Vijayapalani P, Maeshima M, Nagasaki-Takekuchi N , Miller WA (2012) Interaction of the trans-frame potyvirus protein P3N-PIPO with host protein PCaP1 facilitates potyvirus movement.  PLoS Pathogens 8: e1002639. doi:10.1371/journal.ppat.1002639

  • Wang Z, Parisien M, Scheets K, Miller WA (2011) The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element Structure 19, 868-880.   doi: 10.1016/j.str.2011.03.013

Vita: Click here to download

Website: W. Allen Miller

*Chris Minion

BCB Faculty Member in the VMPM Department

Education: Ph.D., Alabama, Birmingham, 1983

Research Interests: Microbial pathogenomics, gene regulation

  • Functional and Structural Genomics-- Analysis of genome sequence data; motif signatures; protein structure prediction; gene regulatory regions

Description: Dr. Minion's research interests focus on the molecular basis of pathogenesis and persistence of bacterial pathogens in domestic animals. Major emphasis is on pathogenomics, identification of virulence factors, gene profiling, and development of molecular vaccines in mycoplasmas. His laboratory also studies the molecular basis of persistence of Escherichia coli O157:H7 in ruminants and Salmonella enteritidis in poultry using genetic tools such as signature tagged mutagenesis. Microarray studies are being conducted in Mycoplasma hyopneumoniae, E. coli O157:H7 and L. monocytogenes to understand bacterial in vivo gene expression and its relationship to virulence. Comparative genomics and genome sequencing is being performed to identify virulence factors in mycoplasmas.

KEY WORDS: Microbial virulence, bacterial genetics, food safety, bacterial gene regulation, molecular vaccines, bacteria-host interactions, gene profiling, swine, respiratory diseases, sheep.

Selected Publications:

  • LaRock, C., J. Yu, A. R. Horswill, M. R. Parsek, and F. C. Minion. 2013. Transcriptome analysis of acetyl-homoserine lactone-based quorum sensing regulation in Yersinia pestis. PLos One
  • Yu, J., M. L. Madsen, M. D. Carruthers, G. J. Phillips, J. S. Kavanaugh, J. M. Boyd, A. R. Horswill, and F. C. Minion. 2013. Analysis of autoinducer-2 quorum sensing in Yersinia pestis. Infect. Immun. 81: 4053-4062.
  • Pendarvis, K. M. P. Padula, J. L. Tacchi, M. L. Madsen, S. P. Djordjevic, S. C. Burgess and F. C. Minion. 2013. Analysis of the proteome of Mycoplasma hyopneumoniae virulent strain 232. BMC Genomics (In press).
  • Raymond, B. B. A., J. L. Tacchi, V. M. Jarocki, F. C. Minion, M. P. Padula, S. P. Djordjevic. 2013. P159 from Mycoplasma hyopneumoniae binds porcine cilia and heparin and is cleaved by multiple proteases in a manner akin to ectodomain shedding. J. Proteome Research 12: 5891-5903.
  • Deutscher, A. T., J. L. Tacchi, F. C. Minion, M. P. Padual, B. Crossett, D. R. Bogema, C. Jenkins, M. J. Walker, S. P. Djordjevic. 2012. Mycoplasma hyopneumoniae surface proteins Mhp385 and Mhp384 bind host cilia and glycosaminoglycans and are endoproteolytically processed by proteases that recognize different cleavage motifs. J. Proteome Res. 11: 1924-1936.
  • Bogema, D. R., A. T. Deutscher, L. M. Seymour, B. B. A. Raymond, J. L. Tacchi, M. P. Padula, N. E. Dixon, F. C. Minion, C. Jenkins, M. J. Walker, and S. P. Djordjevic. 2012. Characterization of cleavage events in the multifunctional cilium adhesin Mhp684 (P146) reveals a novel mechanism by which Mycoplasma hyopneumoniae regulates surface topography. mBio 3: e00282-11.
  • Li, J., F. C. Minion,  A. C. Petersen, F. Jiang, S. Yang, P. Guo, J. Li, and W. Wu. 2012. Loop-mediated isothermal amplification for rapid and convenient detection of Mycoplasma hyopneumoniae. World J. Microbiol. Biotechnol. DOI 10.1007/s11274-012-1216-x.
  • Puttamreddy, S., and F. C. Minion. 2011. Linkage between cellular adherence and biofilm formation in Escherichia coli O157:H7 EDL933. FEMS Microbiol. Lett. 315: 46-53.
  • Seymour, L. M., L. Falconer, A. T. Deutscher, F. C. Minion, M. P. Padula, N. E. Dixon, S. P. Djordjevic and M. J. Walker. 2011. Mhp107 is a member of the multifunctional adhesin family of Mycoplasma hyopneumoniae. J. Biol. Chem. 286:10097-10104.
  • Kong, C. S., J. Yu, F. C. Minion, and K. Rajan. 2011. Identification of biologically significant genes from combinatorial microarray data. ACS Combi. Sci. 13:562-571.
  • Bogema, D. R, N. E. Scott, M. Padula, J. L. Tacchi, C. Jenkins, S. J. Cordwell, F. C. Minion, M. J. Walker, S. P. Djordjevic. 2011. The peptide sequence TTKF | QE defines the site of proteolytic cleavage in Mhp683 (P135), a novel glycosaminoglycan and cilium binding adhesin of Mycoplasma hyopneumoniae. J. Biol. Chem. 286:41217-41229.

Vita: Click here to download

Website: Chris Minion

Kirk Moloney

BCB Faculty Member in the EEOB Department

Education: Ph.D., Duke, 1986

Research Interests: Spatial ecology, ecological modeling, invasive species

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Modeling the dynamics of spatial processes in ecological systems; analysis of spatial pattern; disturbance ecology; spatial ecology of invasions; complexity in ecological systems

Description: (1) experimental and observational studies of plant and animal populations and communities in a spatial context; (2) development of spatially explicit simulation models as experimental tools for studying fundamental ecological relationships in a spatial context; and (3) development of analytical techniques for characterizing pattern over a range of spatial and temporal scales as a means of identifying critical, pattern forming ecological processes

Selected Publications:

  • Martin, L. M,. K. A. Moloney and B. J. Wilsey. In press. An assessment of grassland restoration success using species diversity components. Journal of Applied Ecology
  • Eccard JA, Dean WRJ, Wichmann MC , Moloney KA, Jeltsch F. In press Use of large Acacia trees by the cavity dwelling Black-tailed Tree Rat in the Southern Kalahari . Journal of Arid Environments.
  • Wiegand T. , E. Revilla, and K.A. Moloney. 2005. Effects of habitat loss and fragmentation on population dynamics. Conservation Biology 19(1):108-121.

Vita: Click here to download

Website: Kirk Moloney

*Dan Nettleton

BCB Faculty Member in the Statistics Department

Education: Ph.D., Iowa, 1996

Research Interests: Statistical design and analysis of microarray experiments, statistical methods for mapping QTL

  • Functional and Structural Genomics-- Statistical design and analysis of gene expression experiments; Statistical methods for mapping quantitative trait loci


Selected Publications:

(* Indicates Nettleton student and/or research assistant co-author)

  • *Orr, M., Liu, P., Nettleton, D. (2014). An improved method for computing q-values when the distribution of effect sizes is asymmetric. Bioinformatics. Accepted.
  • Jeffrey, B., Nettleton, D., Kuzhiyil, N., Rover, M., Brown, R. C., Lamkey, K., Lübberstedt, T. (2014). Significant variation for bio-oil compounds after pyrolysis/gas chromatography- mass spectrometry of cobs and stover among five near-isogenic brown midrib hybrids in maize. BioEnergy Research. 7 693-701.
  • *Wang, H. Ying, K., Nettleton, D. (2014). Copy number variation detection using next generation sequencing read counts. BMC Bioinformatics. 15 109. DOI: 10.1186/1471- 2105-15-109
  • *Lock, D., Nettleton, D. (2014). Using random forests to estimate win probability before each play of an NFL game. Journal of Quantitative Analysis in Sports. Accepted.
  • *Ji, Tieming, Liu, P., Nettleton, D. (2014). Estimation and testing of gene expression heterosis. Journal of Agricultural, Biological, and Environmental Statistics. Accepted.
  • Knetter, S. M., Bearson, S. M. D., Huang, T.-H., *Kurkiewicz, D., Schroyen, M., Nettleton, D., Berman, D., Cohen, V., Lunney, J. K., Ramer-Tait, A. E., Wannemuehler, M. J., Tuggle, C. K. (2014). Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes. Innate Immunity. DOI: 10.1177/1753425914525812
  • Cernadas, R. A., Doyle, E. L., Niño-Liu, D. O., Wilkins, K. E., *Bancroft, T., Wang, L., Schmidt, C. L., Caldo, R., Yang, B., White, F. F., Nettleton, D., Wise, R. P., Bogdanove, A. J. (2014). Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with blight and a novel susceptibility gene. PLOS Pathogens. Accepted.
  • *Xu, R., Nettleton, D., Nordman, D. J. (2014). Predictor augmentation in random forests. Statistics and Its Interface. 7 177–186.
  • Tang, H. M., Liu, S., Hill-Skinner, S., Wu, W., Reed, D., Yeh, C.-T., Nettleton, D., Schnable, P. S. (2014). The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. The Plant Journal. 77 380–392.
  • *Bancroft, T., *Du, C., Nettleton, D. (2013). Estimation of false discovery rate using sequential permutation p-values. Biometrics. 69 1–7.
  • Froelich, A., Nettleton, D. (2013). Does my baby really look like me? Using tests for resemblance between parent and child to teach topics in categorical data analysis. Journal of Statistics Education. 21 19 pages.
  • Plego, C., Nowara, D., Bonciani, G., Gheorghe, D. M., *Xu, R., Surana, P., Whigham, E., Nettleton, D., Bogdanove, A. J., Wise, R. P., Schweizer, P., Bindschedler, L.V., Spanu, P. D. (2013). Host-induced gene silencing in barley powdery mildew reveals a class of RNAselike effectors. Molecular Plant-Microbe Interactions. 26 633–642.
  • Yu, X., *Lund, S. P., Scott, R. A., Greenwald, J. W., Records, A. H., Nettleton, D., Lindow, S. E., Gross, D. C., Beattie, G. A. (2013). Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites. Proceedings of the National Academy of Sciences. 110 E425–E434. doi:10.1073/pnas.1221892110.

Vita: Click here to download

Website: Dan Nettleton

*Basil Nikolau

BCB Faculty Member in the BBMB Department

Education: Ph.D., Massey University, New Zealand, 1982

Research Interests: Functional genomics of metabolism, metabolic modeling and metabolic networks.

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Biochemistry and molecular biology of biotin and biotin-containing enzymes; Regulation of plant lipid metabolism.

Selected Publications:

  • Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES. 2013. A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep. 2013 Apr 12;30(4):565-83. doi: 10.1039/c3np20111b.
  • Bais P, Moon SM, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Roth MR, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau BJ, Rhee SY, Dickerson JA. 2010. a web portal for plant metabolomics experiments. Plant Physiology 152:1807-1816.
  • Jun JH, Song Z, Liu Z, Nikolau BJ, Yeung ES, Lee YJ.  2010. High-spatial and high-mass resolution imaging of surface metabolites of Arabidopsis thaliana by laser desorption-ionization mass spectrometry using colloidal silver. Analytical Chemistry 82(8):3255-65.
  • Huang N, Hauck C, Yum MY, Rizshsky L, Widrlechner MP, McCoy JA, Murphy PA, Dixon PM, Nikolau BJ, Birt DF.  2009. Rosmarinic acid in Prunella vulgaris ethanol extract inhibits lipopolysaccharide-induced prostaglandin E2 and nitric oxide in RAW 264.7 mouse macrophages. Journal of Agricultural Food Chemistry 57:10579-89.
  • Oliver DJ, Nikolau BJ, Wurtele ES. 2009. Acetyl-CoA-Life at the metabolic nexus. Plant Science 176: 597-601.
  • Cha S, Song Z, Nikolau BJ and Yeung ES. 2009. Direct profiling and imaging of epicuticular waxes on Arabidopsis thaliana by laser desorption/ionization mass spectrometry using silver colloid as a matrix. Analytical Chemistry 81: 2991-3000.
  • Brindley MA, Widrlechner MP, McCoy JA, Murphy P, Hauck C, Rizshsky L, Nikolau BJ and Maury W. 2009. Inhibition of lentivirus replication by aqueous extracts of Prunella vulgaris. Virology Journal 6: 8.
  • LaLone CA, Rizshsky L, Hammer KD, Wu L, Solco AK, Yum M, Nikolau BJ, Wurtele ES, Murphy PA, Kim M and Birt DF.  2009. Endogenous levels of Echinacea alkylamides and ketones are important contributors to the inhibition of prostaglandin E2 and nitric oxide production in cultured macrophages. Journal of Agricultural Food Chemistry 57: 8820-8830.
  • Maury W, Price JP, Brindley MA, Oh C, Neighbors JD, Wiemer DF, Wills N, Carpenter S, Hauck C, Murphy P, Widrlechner MP, Delate K, Kumar G, Kraus GA, Rizshsky L and Nikolau BJ. 2009. Identification of light-independent inhibition of human immunodeficiency virus-1 infection through bioguided fractionation of Hypericum perforatum. Virology Journal 6:101.

Vita: Click here to download

Publications: here

Website: Basil Nikolau

Marit Nilsen-Hamilton

BCB Faculty Member in the BBMB Department

Education: Ph.D., Cornell, 1973

Research Interests: Gene expression, aptamers, imaging, modeling biology

  • Functional and Structural Genomics-- Regulation of gene expression, the application of functional nucleic acids (aptamers and ribozymes) to medicine and microanalysis.
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- In collaboration with Boushaba,  Levine and Smiley, modeling biochemical processes, cell movement and differentiation.  In collaboration with Lamm, modeling molecular structure and molecular movement.

Description: Understanding the structure/ function relationships of aptamers in order to apply them as sensors and regulators of cell behavior.

Selected Publications:

  • Boushaba K, Levine HA and Nilsen-Hamilton M (2009) A mathematical feasibility argument for the use of aptamers in chemotherapy and imaging.Mathematical Biosciences, 220:131-42 [PMID: 19540245]
  • Wang T, Hoy JA, Lamm MH and Nilsen-Hamilton M (2009) Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity. JACS, J. Am Chem Soc. 131:14747-55 [PMID:19778045]
  • Seo Y-J, Chen S, Nilsen-Hamilton M, Levine HA (2010) A Mathematical Analysis of Multiple-Target SELEX. Bull Math Biol 72:1623-65 [PMID: 20077028]
  • Kang K, Sachan A, Nilsen-Hamilton M and Shrotriya P (2011) Aptamer Functionalized Microcantilever Sensors for Cocaine Detection. Langmuir  27:14696-702 [PMID:  21875108]Howk CL, Levine HA, Smiley MW, Mallapragada SK, Nilsen-Hamilton M, Oh J, Sakaguchi DS (2012) A mathematical model for selective differentiation of neural progenitor cells on micropatterned polymer substrates.  Math Biosci 238:65-79 [PMID: 22569338]
  • Zhai L, Wang T, Kang K, Zhao Y, Shrotriya P, Nilsen-Hamilton M (2012) An RNA aptamer-based microcantilever sensor to detect the inflammatory marker, mouse lipocalin-2. Analytical Chemistry 84:8763-70  [PMID: 22946879]
  • lgu M, Wang T, Lamm M, Nilsen-Hamilton M (2013) Investigating the malleability of RNA aptamers. Methods. 63:178–187 [PMID: 23535583]
  • Ilgu M, Yennamalli RM, Fulton BD, Lamm MH, Sen TZ and  Nilsen-Hamilton M (2014) “An Adaptable Pentaloop Defines a Robust Neomycin-B RNA Aptamer with Conditional Ligand-Bound Structures” RNA 20(6):815-24 [PMID: 24757168]
  • Shin I, Ray J, Gupta V, Ilgu M, Beasley J, Bendickson L, Mehanovic S, Kraus GA and Nilsen-Hamilton M (2014) "Live-cell Imaging of Pol II Promoter Activity to Monitor Gene Expression with RNA reporters" Nucleic Acids Research 42(11):e90 [PMID: 2475340]
  • Seo Y-J, Nilsen-Hamilton M and Levine HA (2014) A Computational Study of Alternate SELEX. Bulletin of Mathematical Biology 76:1455–1521 [PMID: 24878869]

Vita: Click here to download

Website: Marit Nilsen-Hamilton

*Thomas Peterson

BCB Faculty Member in the GDCB Department

Education: Ph.D. California, Santa Barbara, 1984

Research Interests: Transposons elements, genome rearrangements

  • Functional and Structural Genomics--Isolation and characterization of transposon-induced genome rearrangements via wet-lab and computational approaches.  Analysis of how transposable elements affect gene expression and genome structure.


Selected Publications:

  • Vitte, C., Peterson, T., and J. Bennetzen.  2011.  Transposable elements and the evolving structure of the maize genome.  In Advances in Maize (editor: J.-L. Prioul)
  • Xuan, Y.H., H.L. Pioa, B.I. Je, S.J. Park, S.H. Park, J. Huang, J. Zhang, T. Peterson, and C.D. Han, 2011.  Transposon Ac/Ds-induced chromosomal rearrangements at the rice OsRLG5 locus.  Nucleic Acids Research 39: 22 e149 doi:10.1093/nar/gkr718
  • Zhang, J., Yu, C., Krishnaswamy, L., and Peterson, T.  2011.  Transposable elements as catalysts for chromosome rearrangements Methods Mol Biol 701: 315-326.
  • Yu, C., Han, F., Zhang, J., Birchler, J., and T. Peterson.  2012. A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice.  Theor Appl Genet. 125: 1449 - 1462.
  • Xuan, Y.H., J. Zhang, T. Peterson, and C.D. Han. 2012. Ac/Ds-induced chromosomal rearrangements in rice genomes, Mobile Genetic Elements, 2:  67 – 71.
  • Peterson, T. and Zhang, J.  2012.  The mechanism of Ac/Ds transposition.  In Plant Transposons and Genome Dynamics in Evolution, Nina V. Fedoroff, editor.  Wiley-Blackwell, 2013.
  • Zhang J, Zuo T, Peterson T.  2013. Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements. PLoS Genet 9(8): e1003691. doi:10.1371/journal.pgen.1003691
  • Plant Transposable Elements, Methods and Protocols, in Methods in Molecular Biology, Volume 1057.  T. Peterson, editor.  Humana Press, 2013.
  • Krishnaswamy L, Peterson T.  2013.  Survey of natural and transgenic gene markers used to monitor transposon activity. Methods Mol Biol. 1057:43-58. doi: 10.1007/978-1-62703-568-2_4.
  • Wang D, Peterson T.  2013.  Isolation of sequences flanking Ac insertion sites by Ac casting.  Methods Mol Biol. 1057:117-122. doi: 10.1007/978-1-62703-568-2_8

Vita: Click here to download

Website: Agronomy: Thomas Peterson; GDCB Page

Gregory Phillips

BCB Faculty Member in the VMPM Department

Education: Ph.D., University of Georgia, Athens, 1987

Research Interests: Use of genomic approaches to determine gene function in pathogenic bacteria

  • Macromolecular Structure and Function-- Our research includes understanding how the structure of the signal recognition particle (SRP) contributes to its function to target proteins to the cytoplasmic membrane in bacteria, and use of genomic approaches to determine gene function in pathogenic bacteria

Selected Publications:

  • Birt, D. F., and G. J. Phillips. 2014. Diet, genes, and microbes: complexities of colon cancer prevention. Toxicol Pathol. 42:182-188.
  • Wannemuehler, M.J., A. M. Overstreet, D. V. Ward, and G. J. Phillips. 2014.  Draft genome sequences of the Altered Schaedler Flora-a defined bacterial community from gnotobiotic mice. Genome Announc. 2:e00287-14.
  • Krull, A. C., J. K. Shearer, P. J. Gorden, V. L. Cooper, G. J. Phillips, P. J. Plummer. 2014. Deep sequencing analysis reveals the temporal microbiota changes associated with the development of bovine digital dermatitis. Infect Immun. 82:3359–3373.
  • Ariosa AR, Duncan SS, Saraogi I, Lu X, Brown A, Phillips GJ, Shan SO.  Fingerloop activates cargo delivery and unloading during co-translational protein targeting. Mol Biol Cell. 2013 Jan;24(2):63-73. doi: 10.1091/mbc.E12-06-0434. PMID: 23135999.
  • Slattery, A., A. H. Victorsen, A. Brown, K. Hillman and G. J. Phillips. 2013. Isolation of highly persistent mutants in Salmonella enterica serovar Typhimurium reveals a new toxin antitoxin module. J. Bacteriol. 195:647-657. PMID: 23204462.
  • Kuehn, J. S., P. J. Gorden, D. Munro, R. Rong, Q. Dong, P. J. Plummer, C. Wang, and G. J. Phillips. 2013. Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis. PLoS One. 8:e61959.
  • Kraus, G. A., Chaudhary, D. Riley, S., Liu, F., Schlapkohl, A., Weems, M. and G. J Phillips. 2013. Synthesis of 3-farnesyl salicylic acid, a novel antimicrobial from Piper multiplinervium. Nat. Prod. Commun. 8:911-913.
  • Birt, D. F., T. Boylston, S. Hendrich, J.-L. Jane, J. Hollis, L. Li, J. McClelland, S. Moore, G. J. Phillips, M. Rowling, K. Schalinske, M. P. Scott, and E. M. Whitley. Digestion resistant starch: Promise for improving human health. Adv. Nutr. 2013. Adv. Nutr. 4:587-601.
  • Kuehn, J. S., K. B. Register, and G. J. Phillips. Draft Genome Sequences for 10 Isolates of the Swine Pathogen Haemophilus parasuis. 2013. Genome Announc. 1:e00739-13.
  • Yu, J., M. L. Madsen, M. D. Carruthers, G. J. Phillips, J. S. Kavanaugh, J. M. Boyd, A. R. Horswill, and F. C. Minion. 2013. Analysis of autoinducer-2 quorum sensing in Yersinia pestis. Infect. Immun. 81:4053-4062.
  • Duncan, S., R. Sirkanungo, L. Miller, and G. J. Phillips. 2010. DraGnET: Software for storing, managing and analyzing draft genome data. BMC Bioinformatics, 11:100.
  • Schmidt K, L., N. D. Peterson, R. J. Kustusch, M. C. Wissel, B. Graham, G. J. Phillips, D. S. Weiss 2004. A predicted ABC transporter, FtsEX, is needed for cell division in Escherichia coli. J. Bacteriol. 186:785-793.
  • Platt, R., Reynolds, D. L., Phillips, G. J. 2003. Development of a novel method of lytic phage delivery by use of a bacteriophage P22 site-specific recombination system. FEMS Microbiol. Lett. 2003 223:259-265.

Vita: Click here to download

Website: Gregory Phillips

Krishna Rajan

BCB Faculty Member in the Materials Science Department

Education: Sc.D., MIT, 1978.

Research Interests: Linking bioinformatics with materials informatics.


  • Learning from Systems Biology: An “omics” approach to materials design JOM 53-55 (March 2008)
  • Repression of the “Host-Adapted” phenotype of Francisella tularensis: implications for basic and applied research : K.R. O. Hazlett, S. D. Caldon, D. G. McArthur, K. A. Cirillo, G. S. Kirimanjeswara, M. L. Magguilli, M.Malik, A. Shah, S. Broderick, I. Golovliov, D.W. Metzger, K. Rajan, T.J. Sellati, and D. J. Loegering Infect. Immun.76: 4479-4488 (2008)
  • Combinatorial Materials Sciences: Experimental Strategies for Accelerated Knowledge Discovery; Annual Reviews of Materials Research vol 347 , (August 2008)
  • Scientific Data Analysis : C. Kamath, N.Wade, G. Karypis, G. Pandey, V. Kumar, K. Rajan, N.F. Samatova,P. Breimyer, G. Kora, C. Pan and S. Yoginath in Scientific Data Management eds. A. Shoshani and D. Rotem, Taylor and Francis (2008)
  • Combinatorial Methods and Informatics Provide Insight into Physical Properties and Structure Relationships during IPN Formation J. Nowers, S.R.Broderick, K.Rajan and B. Narasimhan:: Macromolecular Rapid Communications 28 972-976 (2007)

Vita: Click here to download


James Reecy

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Purdue, 1995

Research Interests: Regulation of gene expression, gene discovery, skeletal muscle growth, microarray analysis

  • Bioinformatics – Development of livestock genomics databases to facilitate discovery of gene function; Annotation of the cattle genome
  • Functional and Structural Genomics-- Identification of genes controlling skeletal muscle growth and development; Application of whole genome selection methodology to improve healthfulness of beef, resistance to disease, and growth.

Description: My research interests cut across Animal Science, Genetics, and Information Sciences. This research is driven by fundamental scientific questions or important practical problems such as the following:

  • How can we facilitate the discovery of gene function?
  • How can we build useful tools/databases to aid molecular geneticists?
  • How can we develop ontologies to facilitate effective communication between scientists?
  • How can we identify molecular markers that are associated with traits of interest?
  • How can we use whole genome selection to improve society (e.g. can we select for the production of food that is healthier to eat)?
  • Can we identify livestock species specific genes?

Selected Publications:

  • Casas E, Duan Q, Schneider MJ, Shackelford SD, Wheeler TL, Cundiff LV, Reecy JM. 2014. Polymorphisms in calpastatin and mu-calpain genes are associated with beef iron content. Anim Genet. 2013 Dec 5. doi: 10.1111/age.12108. [Epub ahead of print]
  • Boddicker NJ, Garrick DJ, Rowland RR, Lunney JK, Reecy JM, Dekkers JC. 2014. Validation and further characterization of a major quantitative trait locus associatedwith host response to experimental infection with porcine reproductive and respiratory syndrome virus. Anim Genet. 45(1):48-58. doi: 10.1111/age.12079. [Epub ahead of print]
  • Funk LD, Reecy JM, Wang C, Tait RG Jr, O'Connor AM. 2014. Associations between infectious bovine keratoconjunctivitis at weaning and ultrasongraphically measured body composition traits in yearling cattle. J Am Vet Med Assoc. 2014 Jan 1;244(1):100-6. doi: 10.2460/javma.244.1.100.
  • Boddicker NJ, Bjorkquist A, Rowland RR, Lunney JK, Reecy JM, Dekkers JC. 2014. Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection. Genet Sel Evol. 2014 Mar 4;46(1):18. [Epub ahead of print]
  • Cesar AS, Regitano LC, Tullio RR, Lanna DP, Nassu RT, Mudado MA, Oliveira PS, do Nascimento ML, Chaves AS, Alencar MM, Sonstegard TS, Garrick DJ, Reecy JM, Coutinho LL. 2014. Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. BMC Genet. 2014 Mar 25;15(1):39. [Epub ahead of print]
  • Decker JE, McKay SD, Rolf MM, Kim J, Molina Alcalá A, Sonstegard TS, Hanotte O, Götherström A, Seabury CM, Praharani L, Babar ME, Correia de Almeida Regitano L, Yildiz MA, Heaton MP, Liu WS, Lei CZ, Reecy JM, Saif-Ur-Rehman M, Schnabel RD, Taylor JF. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genet. 2014 Mar 27;10(3):e1004254. doi: 10.1371/journal.pgen.1004254. eCollection 2014 Mar.
  • Hu ZL, Park CA, Wu XL, Reecy JM. 2013. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 2013 Jan 1;41(D1):D871-9. doi: 10.1093/nar/gks1150. Epub 2012 Nov 24.
  • Badaoui B, Tuggle CK, Hu Z, Reecy JM, Ait-Ali T, Anselmo A, Botti S. 2013. Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach. BMC Genomics. 2013 Apr 3;14:220. doi: 10.1186/1471-2164-14-220.
  • Kizilkaya K, Tait RG, Garrick DJ, Fernando RL, Reecy JM. 2013. Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle. BMC Genet. 2013 Mar 26;14(1):23. [Epub ahead of print]
  • Nafikov RA, Schoonmaker JP, Korn KT, Noack K, Garrick DJ, Koehler KJ, Minick-Bormann J, ReecyJM, Spurlock DE, Beitz DC. 2013. Sterol regulatory element binding transcription factor 1 (SREBF1) polymorphism and milk fattyacid composition. J Dairy Sci. 2013 Apr;96(4):2605-16. doi: 10.3168/jds.2012-6075. Epub 2013 Feb 10.
  • Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK. 2013. Structural and functional annotation of the porcine immunome. BMC Genomics. 15;14:332
  • Bauermann FV, Harmon A, Flores EF, Falkenberg SM, Reecy JM, Ridpath JF. 2013. In vitro neutralization of HoBi-like viruses by antibodies in serum of cattle immunized with inactivated or modified live vaccines of bovine viral diarrhea viruses 1 and 2. Vet Microbiol. 166(1-2):242-5. doi: 10.1016/j.vetmic.2013.04.032. Epub 2013 May 20.
  • Koesterke L, Milfeld K, Vaughn MW, Stanzione D, Koltes JE, Weeks NT, Reecy JM. 2013. Optimizing the PCIT algorithm on stampede’s Xeon Xeon Phi processors for faster discovery of biological networks. XSEDE ’13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. ISBN: 978-1-4503-2170-9. doi>10.1145/2484762.2484794
  • Mateescu RG, Garrick DJ, Tait RG Jr, Garmyn AJ, Duan Q, Liu Q, Mayes MS, Van Eenennaam AL, Vanoverbeke DL, Hilton GG, Beitz DC, Reecy JM. 2013. Genome-wide association study of concentrations of iron and other minerals in longissimus muscle ofAngus cattle. J Anim Sci. 2013 Aug;91(8):3593-600. doi: 10.2527/jas.2012-6079. Epub 2013 Jul 23.
  • Downey ED, Tait RG Jr, Mayes MS, Park CA, Ridpath JF, Garrick DJ, Reecy JM. 2013. An evaluation of circulating bovine viral diarrhea virus type 2 maternal antibody level and response to vaccination in Angus calves. J Anim Sci. 91(9):4440-50. doi: 10.2527/jas.2012-5890. Epub 2013 Jul 23.
  • Nafikov RA, Schoonmaker JP, Korn KT, Noack K, Garrick DJ, Koehler KJ, Minick-Bormann J, Reecy JM, Spurlock DE, Beitz DC. 2013. Association of polymorphisms in solute carrier family 27, isoform A6 (SLC27A6) and fatty acid binding protein-3 and fatty acid binding protein-4 (FABP3 and FABP4) with fatty acid composition of bovine milk. J Dairy Sci. 96(9):6007-21. doi: 10.3168/jds.2013-6703. Epub 2013 Jul 5.
  • Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M,Eppig JT,Reecy JM. 2013. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J Biomed Semantics. 4(1):13. doi: 10.1186/2041-1480-4-13.
  • Tait RG Jr, Downey ED, Mayes MS, Park CA, Ridpath JF, Garrick DJ, Reecy JM. 2013. Evaluation of response to bovine viral diarrhea virus type 2 vaccination and timing ofweaning on yearling ultrasound body composition, performance, and carcass quality traits in Angus calves. J Anim Sci. 91(11):5466-76. doi: 10.2527/jas.2012-5891. Epub 2013 Sep 17.
  • Saatchi, M, Garrick DJ, Tait Jr. RG, Mayes MS, Drewnoski M, Schoonmaker J, Diaz C, Beitz DC and Reecy JM. 2013. Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle. BMC Genomics. 2013 Oct 25; 14:730. doi: 10.1186/1471-2164-14-730.
  • Cheng Y, Rachagani S, Canovas A, Mayes MS, Tait Jr. RG, Dekkers JCM, and Reecy JM. 2013. Body composition and geneexpression QTL mapping in mice reveals imprinting and interaction effects. BMC Genetics 14:103. doi: 10.1186/1471-2156-14-103.
  • Duan, Q., R.G. Tait, Jr, M.S. Mayes, D.J. Garrick, Q. Liu, A.L. Van Eenennaam, R.G. Mateescu, D.L. Van Overbeke, A.J. Garmyn, D.C. Beitz and J.M. Reecy. 2012. Genetic polymorphisms in bovine transferrin receptor 2 (TFR2) and solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1) gene and their associations with beef iron content. Animal Genetics 43(2):115-22.
  • Hu Z.L., Reecy J.M., Wu X.L. 2012. Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis. Methods Mol Biol. 2012;871:121-44.
  • Mateescu R.G., Garmyn A.J., O'Neil M.A., Tait R.G. Jr, Abuzaid A., Mayes M.S., Garrick D.J., Van Eenennaam A.L., Vanoverbeke D.L., Hilton G.G., Beitz D.C., Reecy J.M. 2012. Genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in longissimus muscle and their association with palatability traits in Angus cattle. J Anim Sci. 2012 Sep 5. [Epub ahead of print]
  • Hu ZL, Park CA, Wu XL, Reecy JM. 2013. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 2013 Jan 1;41(D1):D871-9. doi: 10.1093/nar/gks1150. Epub 2012 Nov 24.
  • Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424):393-8.

Vita: Click here to download

Website: James Reecy

Peter Reilly

Has Retired !

Education: Ph.D., Pennsylvania, 1964

Research Interests:

  • Macromolecular Structure and Function--Enzyme-substrate docking, molecular mechanics and molecular dynamics, computed sugar conformations.

Description: Peter Reilly works in biochemical engineering, and more specifically in determining structures and evolutionary patterns of primitive hydrolases, in determining optimal sugar structures by computational molecular mechanics, in computationally docking oligosaccharides into hydrolase active sites to understand their mechanisms, and in using liquid and gas chromatography and mass spectroscopy to identify and quantitate components of agricultural and food processing residues.

Selected Publications:

  • Warner, C.D., Hoy, J.A., Shilling, T.C., Linnen, M.J.,  Ginder,  N.D., Ford, C.F., Honzatko, R.B., & Reilly, P.J. (2010). Tertiary structure and characterization of a glycoside hydrolase family 44 endoglucanase from Clostridium acetobutylicum. Applied and Environmental Microbiology: 76, 338-346.
  • Petersen, L., Ardavol, A., Rovira, C., & Reilly, P. J. (2009). Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: A QM/MM metadynamics study. Journal of Physical Chemistry B: 113, 7331-7339.
  • Johnson, G. P., Petersen, L., French, A. D., & Reilly, P. J. (2009). Twisting of glycosidic bonds by hydrolases. Carbohydrate Research: 344, 2157-2166.
  • Mulakala, C., W. Nerinckx, and P. J. Reilly. The Fate of b-D-Mannopyranose after Its Formation By Endoplasmic Reticulum a-(1 -> 2)-Mannosidase I Catalysis. Carbohydr. Res., 342, 163 (2007).
  • Hill, A. D., and P. J. Reilly. Puckering Coordinates of Monocyclic Rings by Triangular Decomposition. J. Chem. Informat. Model., 47, 1031 (2007).
  • Mulakala, C., W. Nerinckx, and P. J. Reilly. Docking Studies on Glycoside Hydrolase Family 47 Endoplasmic Reticulum a -(1 -> 2)-Mannosidase I to Elucidate the Pathway to the Substrate Transition State. Carbohydr. Res., 341, 2233 (2006).

Vita: Click here to download

Website: Peter Reilly

Steve Rodermel

BCB Faculty Member in the GDCB Department

Education: Ph.D., Harvard, 1986

Research Interests: Organelle genetics, chloroplast biogenesis

  • Functional and Structural Genomics--Molecular genetics of chloroplasts and regulation of chloroplast biogenesis; proteomics of plant organelles


Selected Publications:

  • Baerr, J.N., J.D. Thomas, B.G. Taylor, S.R. Rodermel and G.R. Gray. 2005. Differential photosynthetic compensatory mechanisms exist in the immutans mutant of Arabidopsis thaliana. Physiologia Plantarum 124: 390-402. (Cover Article).
  • Yu, F., S. Park and S.R. Rodermel. 2005. Functional redundancy of AtFtsH metalloproteases in thylakoid membrane complexes. Plant Physiol. 138: 1957- 1966.
  • Alsheikh, M., and S. Rodermel. 2005. Genetics and genomics of chloroplast biogenesis. Maydica 50: 443-449. (Invited review: 50th anniversary of Maydica).
  • Fu, A., S. Park and S. Rodermel. 2005. Sequences required for the activity of PTOX (IMMUTANS), a plastid terminal oxidase: in vitro and in planta mutagenesis of iron-binding sites and a conserved sequence that corresponds to Exon 8. J. Biol. Chem. 280: 42489-42496. (Cover Article).
  • Aluru, M.R., F. Yu, A. Fu and S. Rodermel. 2006. Arabidopsis variegation mutants: new insights into chloroplast biogenesis. J. Experimental Botany 57: 1871-1881.
  • Rosso, D., A.G. Ivanov, A. Fu, J. Geisler-Lee, L. Hendrickson, M. Geisler, G. Stewart, M. Krol, V. Hurry, S.R. Rodermel, D.P. Maxwell and N.P.A. Hüner. 2006. IMMUTANS does not act as a stress-induced safety valve in the protection of the photosynthetic apparatus of Arabidopsis during steady state photosynthesis. Plant Physiol. 142: 574-585.
  • Aluru, M.R., D.J. Stessman, M.H. Spalding and S.R. Rodermel. 2007. Alterations in photosynthesis in Arabidopsis lacking IMMUTANS, a chloroplast terminal oxidase. Photosynthesis Research 91: 11-23.
  • Yu, F., A. Fu, M. Aluru, S. Park, Y. Xu, H. Liu, X. Liu, A. Foudree, M. Nambogga and S. Rodermel. 2007. Variegation mutants and mechanisms of chloroplast biogenesis. Plant Cell & Environment 30: 350-365. (Refereed review)
  • Varbanova, M., S. Yamaguchi, Y. Yang, K. McKelvey, A. Hanada, R. Borochov, F. Yu, Y. Jikumaru, J. Ross, D. Cortes, C.-J. Ma, J. P. Noel, L. Mander, V. Shulaev, Y. Kamiya, S. Rodermel, D. Weiss and E. Pichersky. 2007. Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell 19: 32-45.
  • Lee, E.K., D. Cook, H. Hofmann, M. Aluru and S. Rodermel. 2007. The ProbeR Package (software)
  • Taber, H. G., P. Perkins-Veazie, S. Li, W. White, S. Rodermel and Y. Xu. 2008. Enhancement of tomato fruit lycopene by potassium is cultivar dependent. HortScience 43: 159-165.
  • Yu, F., X. Liu, M. Alsheikh, S. Park and S. Rodermel. 2008. Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. Plant Cell 20: 1786-1804.
  • Aluru, M., Y. Xu, R. Guo, Z. Wang, S. Li, W. White, K. Wang and S. Rodermel. 2008. Generation of transgenic maize with enhanced provitamin A content. J. Experimental Botany (in press).
  • Fu, A., F. Yu and S. Rodermel. 2008. Translocation of a mitochondrial protein to the chloroplast: functional substitution of PTOX by AOX. Proc. Natl. Acad. Sci. (in press).
Vita: Click here to download

Website: Steve Rodermel

Max Rothschild

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Cornell, 1978

Research Interests: Comparative genomics, for prediction of gene structure, genetic dissection of complex traits. Discovery of genes controlling traits of economic interest in the pig, dog and shrimp

  • Functional and Structural Genomics--Comparative genomics and gene discovery; analysis of QTL data, large scale SNP discovery and association analysis  of genes controlling traits of economic interest in the pig, dog and shrimp

Selected Publications:

  • Du, Z.Q., C.X. Yang, M.F. Rothschild and J.W. Ross. 2013. Novel expanded microRNA families in the human Genome. BMC Genomics. 14:98 doi:10.1186/1471-2164-14-98
  • Nikkilä, M. T., K. J. Stalder, B. E. Mote, M. F. Rothschild, F. C. Gunsett, A. K. Johnson, L. A. Karriker, M. V. Boggess, and T. V. Serenius. 2013. Genetic parameters for growth, body composition, and structural soundness traits in commercial gilts. J. Anim. Sci. 91:2034–2046.
  • Nikkilä, M. T., K. J. Stalder, B. E. Mote, M. F. Rothschild, F. C. Gunsett, A. K. Johnson, L. A. Karriker, M. V. Boggess, and T. V. Serenius. 2013. Genetic associations for gilt growth, compositional, and structural soundness traits with sow longevity and lifetime reproductive performance. J. Anim. Sci. 91:1570–1579.
  • Onteru, S.K., D.M. Gorbach, J.M. Young, J.C.M. Dekkers, D.J. Garrick and M.F. Rothschild. 2013. Whole genome association studies of residual feed intake and related traits in the pig. PloSOne DOI: 10.1371/journal.pone.0061756
  • Renaville B., A. Prandi, B. Fan, A. Sepulcri, M.F. Rothschild, and E. Piasentier. 2013. Candidate gene marker associations with fatty acids profiles in heavy pigs. Meat Science 93:495-500.
  • Tart J.K., R.K. Johnson, J.W. Bundy, N.N. Ferdinand, A.M. McKnite, J.R. Wood, P.S. Miller, M.F. Rothschild, M.L. Spangler, D.J. Garrick, S.D. Kachman, D.C. Ciobanu. 2013. Genome-wide prediction of age at puberty and reproductive longevity in sows, Animal Genetics, Aug;44(4):387-97. doi: 10.1111/age.12028.
  • Zhao, X., S. Onteru, M. Saatchi, D. Garrick and M. Rothschild. 2013. A genome-wide association study for canine cryptorchidism in Siberian Huskies. J Anim Breed Genet. doi: 10.1111/jbg.12064. [Epub ahead of print]
  • Ros-Freixedes R., L.J. Stalder, S.K. Onteru, R.M. Smith , J.M. Young, A.K. Johnson, S.M. Lonergan, E. Huff-Lonergan, J.C.M. Dekkers, M.F. Rothschild. 2014. Relationships gilt behavior and meat quality using principal component analysis. Meat Science 96: 264-269

Vita: Click here to download

Website: Max Rothschild

Donald Sakaguchi

BCB Faculty Member in the GDCB Department

Education: Ph.D. State University of New York, Albany, 1984

Research Interests: Developmental neurobiology, stem cell biology, development and regeneration of vertebrate visual systems, glaucoma and other retinal diseases, cellular and molecular basis of neuron/glial cell interactions

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Developmental neurobiology, stem cell transplantation, development and regeneration of vertebrate visual systems, glaucoma and other retinal diseases, coupled biological and mathematical modeling of neural stem cell pattern formation


Selected Publications:

  • Sharma, A.D., Brodski, P.A., Petersen, E.M. Dagdeviren, M., Ye, E., Mallapragada, S.K. and Sakaguchi, D.S. High throughput characterization of adult stem cells engineered for delivery of therapeutic factors for neuroprotective strategies. J. Visualized Experiments. (in press).
  • Oh, J., Daniels, G.J., Chiou, L.S., Ye, E.-A., Jeong, Y.S. and Sakaguchi, D.S. Multipotent  adult hippocampal progenitor cells maintained as neurospheres favored differentiation toward glial lineages. Biotechnology Journal. 9(7): 921-933.
  • Mohan, K., Harper, M.M., Kecova, H., Ye, E.A., Lazic, T., Sakaguchi, D.S., Kardon, R.H., Grozdanic, S.D. (2012) Characterization of structure and function of the mouse retina using pattern electroretinography, pupil light reflex, and optical coherence tomography. Vet. Ophthalmology. 15(2): 94-104.
  • Howk, C., Levine, H.A., Smiley, M.W., Mallapragada, S.K., Nilsen-Hamilton, M., Oh. J. and Sakaguchi, D.S. (2012) A mathematical model for selective differentiation of neural progenitor cells on micropatterned polymer substrates. Mathematical Biosciences. 238(2): 65-79.
  • M.M. Harper, S. Grozdanic, B. Blits, M. Keuhn D. Zamzow, J. Buss, R.H. Kardon, D.S. Sakaguchi (2011) Transplantation of BDNF secreting mesenchymal stem cells provides neuroprotection in chronic hypertensive rat eyes. Invest. Ophthalmol. Vis. Sci. published 15 April 2011, 10.1167/iovs.11-7346.
  • Ariza, C.A., Fluery, A.T., Toromos, C.J., Petruk, V., Chawla, S., Oh, J., Sakaguchi, D.S., and Mallapragada, S.K. (2010) Altered Neurogenesis, Alignment, and Viability: The influence of an Electric Field on Hippocampal Neural Progenitor Cells. Stem Cell Reviews and Reports. Dec; 6(4):585-600.
  • Oh, J., Blong, C.C., McCloskey, M.A., Nilsen-Hamilton, M., and Sakaguchi, D.S. (2010) Astrocyte-derived interleukin-6 promotes specific neuronal differentiation of neural progenitor cells from adult hippocampus. J. Neurosci. Res. Oct;88(13):2798-809.
  • Ariza, C.A., McHugh, K.P., White, S.J., Sakaguchi, D.S., and Mallapragada, S.K. (2010) Extracellular Matrix Proteins and Astrocyte-Derived Soluble Factors Influence the Differentiation and Proliferation of Adult Neural Progenitor Cells. Journal of Biomedical Materials Research A. Sep 1;94(3):816-24.
  • Grozdanic, S.G., Lazic, T., Harper, M.M., Kardon, R.H., Kuehn, M.H., Lavik, E., Kwon, Y.H., Sakaguchi, D.S. (2010) Exogenous modulation of intrinsic optic nerve neuroprotective activity. Graefes Arch Clin Exp Ophthalmol 248(8): 1105-16.
  • Harper, M.M., Ye, E.A., Blong, C.C., Jacobson, M.L., & Sakaguchi, D.S. (2010). Integrins contribute to initial morphological development and process outgrowth in adult hippocampal progenitor cells. Journal of Molecular Neuroscience: 40, 3: 269-283.
  • Perdian, D. C., Cha, S., Oh, J., Sakaguchi, D.S., Yeung, E.S., & Lee, Y.-J. (2010). In Situ Probing of Cholesterol in Astrocytes at the Single Cell Level using Laser Desorption Ionization Mass Spectrometric Imaging with Colloidal Silver. Rapid Communications in Mass Spectrometry: 24, 8, 1147-1154.
  • Blong, C.C., Jeon, C.-J., Yeo, J.-Y., Ye, E.-A., Oh, J., Callahan, J.M., Law, W.D., Mallapragada, S., & Sakaguchi, D.S. (2010). Differentiation and Behavior of Human Neural Progenitor Cells on Micropatterned Substrates and After Transplantation into the Developing Retina. Journal of Neuroscience Research: 88, 7, 1445-1456.
  • Oh, J., Recknor, J.B., Recknor, J.C., Mallapragada, S.K., & Sakaguchi, D.S. (2009). Soluble factors from neocortical astrocytes enhance neuronal differentiation of neural progenitor cells from adult rat hippocampus on polymer substrates. Journal of Biomedical Materials Research: A. 91, 2, 575-85.
  • Harper, M.M., Adamson, L., Blits, B., Bunge, M.B., Grozdanic, S.D., & Sakaguchi, D.S. (2009). Brain-derived neurotrophic factor released from engineered mesenchymal stem cells attenuates glutamate- and hydrogen peroxide-mediated death of staurosporine differentiated RGC-5s. Exp. Eye. Res.: 89, 4, 538-548.
  • E. N. Boote Jones, D.S. Sakaguchi, & Mallapragada, S.K. (2009). Development and differentiation of neural stem and progenitor cells on synthetic and biological-based surfaces. In Biological Interactions on Materials Surfaces: Understanding and Controlling Protein, Cell, and Tissue Responses, D.A. Puleo and R. Bizios (eds.) Springer Science/Business Media, LLC.

Vita: Click here to download

Website: Donald Sakaguchi Department

Patrick Schnable

BCB Faculty Member in the Agronomy and GDCB Department

Education: Ph.D., Iowa State, 1986

Research Interests: Plant genomics and bioinformatics

  • Bioinformatics
  • Functional and Structural Genomics--structural and functional genomics; mechanisms responsible for heterosis, gene duplication, meiotic recombination, epigenetic phenomena, and carbon sequestration.


Selected Publications:

  • Li L, K Petsch, R Shimizu, S Liu, W Wenzhong Xu, K Ying, J Yu, MJ Scanlon, PS Schnable, MCP Timmermans, NM Springer, GJ Muehlbauer (2013) Mendelian and non-Mendelian regulation of gene expression in the maize shoot apex. PLOS Genetics, 9(1): e1003202. (Selected as an Editors’ Choice by MaizeGDB)
  • Schnable PS, NM Springer (2013) Progress toward understanding heterosis in crop plants. Annu. Rev. Plant Biol., 64: 71-88.
  • Muthreich N, C Majer, M Beatty, A Paschold, A Schützenmeister, Y Fu, WA Malik, PS Schnable, H-P Piepho, H Sakai, F Hochholdinger (2013) Comparative transcriptome profiling of maize (Zea mays L.) coleoptilar nodes during shoot-borne root initiation. Plant Physiology, 163(1): 419-430.
  • Liu S, AP Hsia, PS Schnable (2013) Digestion-ligation-amplification (DLA): a simple genome walking method to amplify unknown sequences flanking Mutator (Mu) transposons and thereby facilitate gene cloning. Methods Mol Biol, 1057: 167-176.
  • Soltis DE, MA Gitzendanner, G Stull, M Chester, A Chanderbali, S Chamala, IE Jordon-Thaden, PS Soltis, PS Schnable, WB Barbazuk (2013) The potential of genomics in plant systematics. taxon, 62(2): 886-898.
  • Li L, D Li, S Liu, X Ma, CR Dietrich, HC Hu, G Zhang, Z Liu, J Zheng, G Wang, PS Schnable (2013) The maize glossy13 gene, cloned via BSR-Seq and Seq-Walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes. PLOS ONE, 8(12): e82333.
  • Tang HM*, S Liu*, S Hill-Skinner*, W Wu, D Reed, CT Yeh, DS Nettleton, PS Schnable (2013) The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. Plant J, 77(3): 380-392.
  • Thompson AM, J Crants, PS Schnable, J Yu, MCP Timmermans, NM Springer, MJ Scanlon, GJ Muehlbauer (2014) Genetic control of maize shoot apical meristem architecture. G3. (Epub ahead of print)
  • Wang X, J Chen, Z Xie, S Liu, T Nolan, H Ye, M Zhang, H Guo, PS Schnable, Z Li, Y Yin (2014) Histone lysine methyltransferase SDG8 is involved in brassinosteroid regulated gene expression in Arabidopsis thaliana. Mol Plant. (Epub ahead of print)
  • Li L, SR Eichten, R Shimizu, KA Petsch, CT Yeh, W Wu, AM Chettoor, SA Givan, RA Cole, JE Fowler, MMS Evans, MJ Scanlon, J Yu, PS Schnable, MCP Timmermans, NM Springer, GJ Muehlbauer (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biology, 15(2): R40.
  • Cai W, C Wang, Y Li, C Yao, L Shen, S Liu, X Bao, PS Schnable, J Girton, J Johansen, KM Johansen (2014) Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila. Nucleic Acids Res, 42(9): 5456-5467. (Epub 2014 Mar 5)
  • J Nestler*, Sanzhen Liu*, T-J Wen, A Paschold, C Marcon, HM Tang, D Li, L Li, RB Meeley, H Sakai, W Bruce, PS Schnable, F Hochholdinger (2014) Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongationencodes a monocot-specific NADPH oxidase. Plant J, in press.
  • Zhang Y, A Paschold, C Marcon, S Liu, H Tai, J Nestler, CT Yeh, N Opitz, C Lanz, PS Schnable, F Hochholdinger (2014) The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots. J Exp Bot, in press.

Vita: Click here to download

Website: Patrick Schnable

*Stephan Schneider

BCB Faculty Member in the GDCB Department

Education: Diploma in Biology, Johannes Gutenberg University, Mainz, Germany, 1990
Ph.D. in Genetics, Max Planck Institute for Developmental Biology, Eberhard Karl-University, Tubingen, Germany, 1996

Description: Evolution of developmental and cell biological mechanisms: genesis of animal form and function. (1) Study of early development of a marine worm model system, the polychaete annelid Platynereis dumerilii, especially its early asymmetric cell divisions and their role within the early gene regulatory networks. (2) Reconstruction of ancestral features especially the developmental properties of the last common ancestor of fruit fly, nematode, sea urchin, and vertebrate - the bilaterian ancestor or more specifically the protostome/deuterostome ancestor.

Selected Publications:

  • Gillis, W.J., Bowerman, B.A., and Schneider, S.Q. 2008. The evolution of protostome GATA Factors: molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships. BMC Evolutionary Biology 8(112):1-15.
  • Gillis, W.J., Bowerman, B.A., and Schneider, S.Q. 2007. Ectoderm- and endomesoderm- specific GATA transcription factors in the marine polychaete Platynereis dumerilii. Evol & Dev 1:39-50.
  • Schneider, S.Q. and Bowerman, B.A. 2007. Beta-catenin asymmetries after all animal/vegetal- oriented cell divisions in Platynereis dumerilii mediate binary cell-fate specification. Dev Cell 13:73-86.
  • Schneider, S.Q. and Bowerman, B. 2003. Reviews: Cell Polarity and the Cytoskeleton in the Caenorhabditis elegans Zygote. Annu Rev Genet 37(221-49).
  • Schneider, S.Q., Finnerty, J.R. and Martindale, M.Q. 2003. Protein Evolution: Structure-Function Relationships of the Oncogene beta-catenin in the Evolution of Multicellular Animals. JEZ (MDE) 295B:25-44.
  • Schneider, S., Steinbeisser, H., Warga, R.M. and Hausen, P. 1996. Beta-catenin Translocation into Nuclei Demarcates the Dorsalizing Centers in Frog and Fish Embryos. Mech Dev 57:191-198.
  • Schneider, S., Herrenknecht, K., Butz, S., Kemler, R. and Hausen, P. 1993. Catenins in Xenopus Embryogenesis and their Relation to the Cadherin-Mediated Cell-Cell Adhesion System. Development 118:629-640.
  • Schneider, S., Fischer, A. and Dorresteijn, A.W.C. 1992. A Morphometric Comparison of Dissimilar Early Development in Sibling Species of Platynereis (Annelida, Polychaeta) . Roux`s Arch Dev Biol 201:243-256.

Website: Stephan Schneider

Taner Sen

BCB Faculty Member in the GDCB Department

Education: Ph.D., University of Akron, 2003.

Research Interests: Maize bioinformatics, protein structure prediction, protein binding, biological networks.

Description: Analysis, interpretation, and representation of maize sequence as part of MaizeGDB; protein sequence and structure-based methods to understand function as part of the elaborate networks of cellular interactions; protein modeling and dynamics to elucidate structure-function relationships; development and improvement of secondary and tertiary structure prediction methods; protein-protein binding site predictions; structural and functional interpretations of protein-protein interaction networks.

Selected Publications:

  • Yennamalli, R.M., Rader, A.J., Kenny, A.J., Wolt, J.D., Sen, T.Z., “Endoglucanases: Insights into Thermostability and Biofuel Applications”, Biotechnology for Fuels, 6:136, 2013. (review)
  • Andorf, C.M., Honavar, V., Sen, T.Z., “”Predicting the binding patterns of hub proteins:  A case study using yeast protein interaction networks”, PLoS ONE, 8(2):e56833, 2013.
  • Monaco, M.K., Sen, T.Z., Dharmawardhana, P.D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E.K.S., Lawrence, C.J., Ware, D., Jaiswal, P., “Maize Metabolic Network Construction and Transcriptome Analysis”, The Plant Genome, 6(1), 2013.
  • Panos, M., Sen, T.Z., Ahunbay, M.G., “Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces”, Langmuir, 34, 12619-28, 2012.
  • Rader, A.J., Yennamalli, R.M., Harter, A.K., Sen, T.Z., “A rigid network of long-range contacts increases thermostability in a mutant endoglucanase”, Journal of Biomolecular Structure and Dynamics, 30(6), 628-637,2012.
  • Cannon, E.K., Birkett, S.M., Braun, B.L., Kodavali, S., Jennewein, D.M., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, L.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D.A., Andorf, C.M., Andorf, D., Lisch, D., Koch, K.E., McCarty, D.R., Quackenbush, J., Grotewold, E., Lushbough, C.M., Sen, T.Z., Lawrence, C.J., “POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data”, International Journal of Plant Genomics, 2011:923035, 2011.
  • Yennamalli, R.M., Wolt, J.D., Sen, T.Z., “Dynamics of endoglucanase catalytic domains: implications towards thermostability”, Journal of Biomolecular Structure and Dynamics, 29(3), 509-526, 2011.
  • Schaeffer, M.L., Harper, L.C., Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K.S., Sen, T.Z., Lawrence, C.J., “MaizeGDB: curation and outreach go hand-in-hand”, Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/bar022, 2011.
  • Harper, L.C., Schaeffer, M.L., Thistle, J.,Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K.S., Braun, B.L., Birkett, S., Lawrence, C.J., Sen, T.Z., “The MaizeGDB Genome Browser Tutorial: One Example of Database Outreach to Biologists via Video”, Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/bar016, 2011.
  • Yennamalli R.M., Rader A.J., Wolt J.D., Sen T.Z., “Thermostability in Endoglucanases is Fold-Specific”, BMC Structural Biology, 11(1):10, 2011.

Website: Taner Z. Sen

Jacqueline Shanks

BCB Faculty Member in the CBE Department

Education: Ph.D.,California Institute of Technology, 1989

Research Interests: Biochemical engineering, metabolic engineering of plant secondary metabolites, NMR for metabolic evaluation of in vivo fluxes, phytoremediation

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Experimental and mathematical approaches to metabolic flux analysis in plants; plant metabolic engineering


Selected Publications:

  • Sriram, G., D. B. Fulton, V. Iyer, J. M. Peterson, R. Zhou, M. E. Westgate, M. H. Spalding and J. V. Shanks. 2004. Quantification of Compartmented Metabolic Fluxes in Developing Soybean (Glycine max) Embryos by Employing Biosynthetically Directed Fractional 13C Labeling, 2-D [ 13C,  1H] NMR and Comprehensive Isotopomer Balancing. Plant Physiol.136: 3043-3057
  • Sriram, G. and J. V. Shanks. 2004. Improvements in Metabolic Flux Analysis using Carbon Bond Labeling Experiments: Bondomer Balancing and Boolean Function Mapping. Metabol. Eng, 6, 116-132.
  • Morgan, J., and J.V. Shanks. 2002. Metabolic flux analysis of plant secondary metabolism using a biogenetic organizational approach. Metabolic Engr. 4, 257-262.
  • Shanks, J.V. and G. Stephanopoulos. 2000. Biochemical Engineering: bridging the gap between gene and product. Current Opinion in Biotechnology11, 169-70.

Vita: Click here to download

Website: Jacqueline Shanks

Ravindra Singh

BCB Faculty Member in the VMPM Department

Education: Ph.D., Russian Academy of Sciences, 1993

Research Interests:

  • Singh group works on the interface of fundamental and translational biology. General interest of his group has been to understand the mechanism of alternative splicing, a vital process that increases the coding potential of genome in all higher eukaryotes. Alternative splicing is also associated with a growing number of diseases including neurological and neuromuscular disorders, cardiovascular disorders and cancer. Particular focus of his group has been to understand the molecular basis of Spinal Muscular Atrophy (SMA), a debilitating genetic disease of infants and children. His award-winning discovery relates to finding a unique regulatory element located within the non-coding region (or intron) of Survival Motor Neuron (SMN) gene. He has termed this novel regulatory element as "Intronic Splicing Silencer N1", which is abbreviated as "ISS-N1". Currently, his group is working on the mechanistic details of how ISS-N1 could be used as a therapeutic target. His other interests include RNA-protein interactions and isolation of RNA aptamers as detection and diagnostic tools.

Selected Publications:

  • Singh NN, Hollinger K, Bhattacharya D and Singh RN (2010) An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing. RNA 16, 1167-1181.
  • Singh NN, Shishimorova M, Cao LC, Gangwani L and Singh RN. A short antisense oligonucleotide masking a unique intronic motif prevents skipping of a critical exon in spinal muscular atrophy. RNA Biology 6, 341-350, 2009.
  • Papp LV, Wang J, Kennedy D, Boucher D, Zhang Y, Gladyshev VN, Singh RN and Khanna KK. Functional characterization of alternatively spliced human SECISBP2 transcript variants. Nucleic Acids Research 36, 7192-206, 2008.
  • Singh NN, Singh RN and Androphy EJ. Modulating role of a RNA structure in skipping of a critical exon in the spinal muscular atrophy genes. Nucleic Acids Research 35, 371-389, 2007.
  • Singh RN. Evolving concepts on human SMN pre-mRNA splicing. RNA Biology 4, 7-10, 2007.
  • Singh NK, Singh NN, Androphy EJ and Singh RN. Splicing of a Critical Exon of Survival Motor Neuron genes is regulated by a human-specific silencer element located in the last intron. Molecular and Cellular Biology 26, 1333-1346, 2006.
Vita: Click here to download.

Website: Ravindra Singh

Michael Smiley

BCB Faculty Member in the Mathematics Department

Education: Ph.D., Michigan, 1980

Research Interests:

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking
Description: Mathematical modeling of cell growth and motility in response to environmental signals such as growth factors, for example as in the process of angiogenesis or neuronal pattern formation. Models consist of systems of ordinary and partial differential equations and require numerical solution methods.  Computational algorithms and codes for this purpose are also developed, which allow for simulations with, and validation of, the models.

Selected Publications:

  • Smiley, M.W., A monotone conservative Eulerian-Lagrangian scheme for reaction-diffusion-convection equations modeling chemotaxis, Numerical Methods for Partial Differential Equations, Vol. 23, (2007), pp. 553-586. Published online: March 22, 2007.
  • Smiley, M.W., H.A. Levine, M. Nilsen-Hamilton, and A. Tucker, A mathematical model for the onset of avascular tumor growth in response to the loss of P53 function, Cancer Informatics -- 2006 Edition (this is electronic journal published by Libertas Academica and can be accessed from the web page
Vita: Click here to download

Website: Michael Smiley

Jonathan Smith

BCB Faculty Member in the Mathematics Department

Education: Ph.D., Cambridge, 1975

Research Interests: Combinatorics and information theory, modeling of complex systems, mathematical biology

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Combinatorics and information theory; modelling of complex systems; mathematical biology

Description: As a model for the use of top-down, information-theoretic techniques for handling data describing the evolution of complex systems, the intensive demographic state of a human population has been reduced from the full Leslie matrix description to a single five-dimensional parameter vector. The next stage in the development of this technique involves an analysis of the long-term kinematics of the parameter vector for a given population. It is proposed to use the data for Sweden, which are of high quality and trace back several hundred years. Understanding the kinematics is a preliminary to the development of a dynamics, which should then provide more reliable long-term demographic projections than those obtained from the ergodic theory of Leslie matrices.

Selected Publications:

  • Patterns of information storage and senescence, in "Proceedings of FIS2005, The Third Conference on the Foundations of Information Science, Paris, July 4-7, 2005" (ed. M. Petitjean), Electronic Edition, ISBN 3-906980-17-0.
  • A macroscopic approach to demography, J. Math. Biol. 48 (2004), 105-118.

Vita: Click here to download

Website: Jonathan Smith

*Guang Song

BCB Faculty Member in the Computer Science Department

Education: Ph.D., Computer Science, Texas A&M University, 2003

Research Interests: Protein Structure and Dynamics; Protein Folding Pathways, Energy Landscape, and Kinetics; Ligand Migration Pathways; Ligand Binding; Structure-Function Studies of Biophysical Processes; Computer Modeling and Simulation; Motion Planning


Our research goals are to understand the mechanism of biological systems and functions, especially the dynamic processes of how they take place. We are interested in studying: how proteins fold; ligand migration pathways; how proteins change conformations upon ligand binding, to name a few. We design computational models and simulation programs to study, simulate, and understand biological processes.

Selected Publications:

  • Kloczkowski, A., Jernigan, R.L., Wu, Z., Song, G., Yang, L., Kolinski, A., & Pokarowski, P. (2009). Distance Matrix-Based Approach to Protein Structure Prediction. Journal of Structural and Functional Genomics: 10, 67-81.

  • Tu-Liang Lin and Guang Song. Generalized Spring Tensor Models for Protein Fluctuation Dynamics and Conformation Changes. IEEE BIBM Workshop on Computational Structural Bioinformatics, Washington DC. pp. 136-143, 2009.

  • Lei Yang, Guang Song, and Robert L. Jernigan. Comparison of Experimental and Computed Protein Anisotropic Temperature Factors. Proteins. Vol. 76. pp. 164-175, 2009.

  • Tu-Liang Lin and Guang Song. Predicting Allosteric Communication Pathways Using Motion Correlation Network. 7th Asia Pacific Bioinformatics Conference (APBC), Beijing, China. pp. 588-598, 2009.

  • Lei Yang, Guang Song, and Robert L. Jernigan. Protein Elastic Network Models and the Ranges of Cooperativity. Proceedings of the National Academy of Sciences (USA). Vol. 106. pp. 12347-52, 2009.

  • Lei Yang, Guang Song, Alicia Carriquiry and Robert L. Jernigan. Close Correspondence between the Essential Protein Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, Cell Press. Vol. 16. No. 2. pp. 321-330, 2008.

  • Guang Song and Robert L. Jernigan. vGNM: a Better Model for Understanding the Dynamics of Proteins in Crystals. Journal of Molecular Biology. Vol. 369. No. 3. pp. 880-93, 2007.

  • Lei Yang, Guang Song, and Robert L. Jernigan. How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models?. Biophysical Journal. Vol. 93. No. 3. pp. 920-9, 2007.

  • Guang Song and Robert L. Jernigan. An Enhanced Elastic Network Model to Represent the Motions of Domain-Swapped Proteins. Proteins. Vol. 63. No. 1. pp. 197-209, 2006.

Vita: Click here to download

Website: Guang Song

Xueyu Song

BCB Faculty Member in the Chemistry Department

Education: Ph.D., Caltech, 1995

Research Interests: Theory of protein crystallization, protein-protein/RNA interactions

  • Bioinformatics-- Three-dimensional atomic structures of proteins form the foundation of our molecular understanding of biology. X-ray crystallography is the major and sometimes only tool for the determination of these detailed protein structures. The bottleneck of this method is to grow a large and good quality crystal used in diffraction. For membrane proteins which carry out some of the most fundamental processes in biology such as photosynthesis, vision and nerve communications, it is exceedingly difficult to find the optimal crystallization conditions because of their peculiar molecular properties. This difficulty is in no small part due to the lack of a transparent and reliable theoretical model to describe the crystallization process. Our research goal is to develop such a theoretical model and to explore the physical principles of finding optimal crystallization conditions. By studying the relationship between the crystallization conditions and the physical parameters of the protein solution, we should be able to provide useful guidance to the search for protein crystallization conditions.
  • Functional and Structural Genomics-- Same as above


Selected Publications:

  • T. Xiao and X. Song, Reorganization energy of electron transfer processes in ionic fluids:a molecular Debye-Huckel approach , J. Chem. Phys.,138,114105 (2013).
  • T. Xiao and X. Song, A molecular Debye-Huckel theory and its applications to electrolyte solutions, J. Chem. Phys.135, 104104(2011).
  • S. Bose, R. Adhikary, C. Barnes, D. Fulton, M. Hargrove, X. Song and J. W. Petrich, Comparison of the Dielectric Response Obtained from Fluorescence Upconversion Measurements and Molecular Dynamics Simulations for Coumarin 153-Apomyoglobin Complexes and Structural Analysis of the Complexes by NMR and Fluorescence Methods, J. Phys. Chem. A115, 3630(2011).
  • B. Kim and X. Song,Calculations of the Second Virial Coefficients of Protein Solutions with an Extended Fast Multipole Method, Phys. Rev. E83, 011915(2011).
  • V.B. Warshavsky and X.Song, Perturbation theory for solid–liquid interfacial free energies, J. Phys. Condens. Matter, 22, 364112(2010).
  • Bose, S. Adhikary, R., Mukherjee, P., Song, X., & Petrich, J.W. (2009). Considerations for the Construction of the Solvation Correlation Function and Implications for the Interpretation of Dielectric Relaxation in Proteins. Journal of Physical Chemistry: B, 113, 11049.
  • Song, X. (2009). Solvation dynamics in ionic uids: An extended Debye-Huckel dielectric continuum model. Journal Chemical Physics: 131, 044503.

Vita: Click here to download

Website: Xueyu Song

*Amy Toth

BCB Faculty Member in the EEOB Department

Education: PhD, University of Illinois, 2006

Research Interests: The mechanisms and evolution of animal social behavior.

Description: Dr. Toth's work focuses on eusocial colonies of bees and wasps, whose highly integrated societies exhibit a bewildering complexity of individual and colony-level behaviors. She uses an integrative research approach involving field studies of naturally occurring colonies, experimental manipulations in semi-natural or lab settings, and numerous lab techniques to measure physiological, chemical, and genetic characters of individual insects. She has applied next generation sequencing methods to develop sequence databases for social wasp species, in order to enable comparative transcriptomic studies across insect species. The overarching goals of her research are to 1) gain insight into how complex social behavior can evolve from simpler forms of solitary behavior, 2) understand the roles of conservation and convergence in the molecular basis of complex phenotypes, and 3) use new genomic tools to empirically test long-standing ideas about the evolution of sociality.

Examples of ongoing projects include: comparative transcriptomic analysis of honey bee and Polistes paper wasp behavior and caste differences, chemical and transcriptomic characterization of dominance hierarchies in Polistes paper wasps, and exploring the role of DNA methylation in caste differences across multiple social insect species at different levels of sociality.

Selected Publications:

  • Daugherty, T.H.F., Toth, A.L., and Robinson, G.E. Nutrition and division of labor: Effects on foraging and brain gene expression in the paper wasp Polistes metricus. Molecular Ecology, submitted.
  • Singh, R., Levitt, A.L., Rajotte, E.G., Holmes, E.C., Ostiguy, N., vanEngelsdorp, D., Lipkin, W.I., dePamphilis, C.W., Toth, A.L., and Cox-Foster, D.L. 2010. RNA viruses in hymenopteran pollinators: evidence of inter-taxa virus transmission via pollen and potential impact on non- Apis hymenopteran species.  PLoS ONE, accepted.
  • Toth, A.L. 2010. Integrating evolution, development, and behavior. Encyclopedia of Animal Behavior, Breed, M.D. and Moore, J., eds. In: Evolution of Behavior, J.M. Herbers, section editor. Academic Press, Oxford. pdf   
  • Hunt , J.H. , Wolschin, F., Mutti, N., Henshaw, M.T., Newman, T.C., Toth, A.L. and Amdam , G.V. 2010. Differential gene expression and protein abundance evince ontogenetic bias toward castes in a primitively social wasp. PLoS ONE 5:e10674 . pdf
  • Toth, A.L ., Varala, K., Henshaw, M.T., Rodriguez-Zas, S.L., Hudson, M.E. and Robinson, G.E. 2010. Brain transcriptomic analysis in paper wasps identifies genes associated with division of labor across social insect lineages. Proceedings of the Royal Society B, 277:2139-2148 . pdf


Department website:

*Alex Travesset

BCB Faculty Member in the Physics and Astronomy Department

Education: Ph.D., Barcelona, 1997

Research Interests:

  • Computational Molecular Biology and Mathematical Biology--Theoretical models and simulations (including all atomic MD) of phospholipids and interactions of phospholipids with proteins. Signaling phospholipids (PIP2). Electrostatic properties of biological systems (theoretical).

Description: The research in my group focuses around two main topics:

1) Properties of phospholipids: What determines the phase diagram of phospholipids and, in particular, the influence of ions in solution. We are particularly interested in phospholipids such as Phophatidic acid and Phosphatidyl-Inositol Bisphosphate, which play a critical role in transducing signals.

2) Self assembly of soft matter systems (polymers, colloids, liquid crystals) and its relation to biological systems.

Selected Publications:

  • “Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model”, A. Kapoor and A. Travesset, Proteins 82, 505 (2014)
  • “Dynamics and Statics of DNA-programmable Nanoparticle Self-Assembly and Crystallization”, C.D. Knorowski, S. Burleigh and A. Travesset, Phys. Rev. Lett. 106, 215501 (2011).
  • “Materials Design by DNA-programmed Self-Assembly”, C.D. Knorowski and A. Travesset, Curr. Opin. In Solid State and Mat. Science. 15, 262 (2011).
  • “Ion Specific Induced Charges at Aqueous Soft Interfaces”, W. Wang, R. Park, A. Travesset and D. Vaknin, Phys. Rev. Lett. 106, 056102 (2011).
  • “Phosphatidic Acid Domains in Membranes: Effect of Divalent Counterions” J. Faraudo and A. Travesset, Biophys. J. 922806 (2007).
  • “Self-Assembly and Crystallization of Hairy (f-star) and DNA grafted Nanocubes’’C. Knorowski and A. Travesset, JACS 136, 653 (2014)
  •  “General purpose molecular dynamics simulations fully implemented on graphics processing units”, J.A. Anderson, C.D. Lorenz and A. Travesset, J. Comput. Phys, 227, 5342 (2008).
  • “Charge inversion at minute electrolyte concentrations”, J. Pitler, W. Bu, D. Vaknin, A. Travesset, D.J. McGillivray and M. Loesche, Phys. Rev. Lett. 97, 46102 (2006).
  • “Grain Boundary scars and spherical crystallography” A.R. Bausch, M. Bowick, A. Cacciuto, A. Disnmore, M. Hsu, D. Nelson, M. Nikolaides, A. Travesset and D. Weitz, Science  299, (2003) 1716-1718.
  • “The Statistical Mechanics of Membranes” Bowick and A. Travesset, Phys. Rep. 344 (2001) 255.

Vita: Click here to download

Website: Alex Travesset

Jeffrey Trimarchi

BCB Faculty Member in the GDCB Department

Education: Ph.D., MIT, 2002

Research Interests: Retinal cell biology, neuronal and retinal cell fate determination, retinal systems biology, single cell gene expression analysis, transcriptional networks, bioinformatics.

Dr. Trimarchi’s research group focuses on understanding the development and degeneration of neurons. An understanding of the gene programs responsible for the production of specific cell types is essential for researchers to generate a large number of any distinct cell-type from stem cell populations. Therefore, one aspect of our research aims to understand the global gene expression networks responsible for generating neuronal diversity in the developing mouse, zebrafish and chicken retina, specifically among the retinal ganglion cells. Single cell transcriptomics in conjunction with gain and loss of function experiments are utilized to examine the gene networks that produce distinct retinal ganglion cell subsets. The information gleaned from these experiments will be used to enhance the efficiency with which ganglion cells are generated for uses in cellular replacement therapies for optic neuropathies such as glaucoma. A second avenue of research uses the same single cell technology we developed to examine motor neurons that are resistant to the disease-causing mechanisms of Amyotrophic Lateral Sclerosis (ALS). These experiments will identify new potential drug targets for intervention in ALS patients.

Selected Publications:

  • Chew, K.S., Schmidt, T.M., Rupp, A.C., Kofuji, P., and Trimarchi, J.M. (2014). Loss of gq/11 genes does not abolish melanopsin phototransduction. PLoS ONE 9, e98356.
  • Goetz, J.J., Farris, C., Chowdhury, R., and Trimarchi, J.M. (2014). Making of a retinal cell: insights into retinal cell-fate determination. International review of cell and molecular biology 308, 273-321.
  • Emerson, M.M., Surzenko, N., Goetz, J.J., Trimarchi, J., and Cepko, C.L. (2013). Otx2 and onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors. Dev Cell 26, 59-72.
  • Mizeracka, K., Trimarchi, J.M., Stadler, M.B., and Cepko, C.L. (2013). Analysis of gene expression in wild-type and Notch1 mutant retinal cells by single cell profiling. Dev Dyn 242, 1147-1159.
  • Farris, C, and Trimarchi, JM. (2013). Plasma-seq: A novel strategy for metastatic prostate cancer analysis, Genome Medicine, 5:35.
  • Goetz JJ and Trimarchi JM. (2012). Transcriptome sequencing of single cells with SMART-Seq, Nat. Biotechnol. 30:763-5.
  • Goetz JJ and Trimarchi JM. (2012). Single-cell profiling of developing and mature retinal neurons, J Vis Exp, pii: 3824. doi: 10.3791/3824.
  • Cherry, TJ, Trimarchi, JM, Stadler, M, And Cepko, CL. (2009). Development and diversification of retinal amacrine interneurons at single cell resolution, Proc. Natl. Acad. Sci. U S A. 106:9495-9500.
  • Nygaard, V, Liu, F, Holden, M., Kuo, WP, Trimarchi, J, et al. (2008) Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 9:258.
  • Trimarchi JM, Stadler, M, and Cepko CL. (2008) Individual retinal progenitor cells display extensive heterogeneity of gene expression. PlosOne, 3:e1588.
  • Liu, F, Jenssen, TK, Trimarchi, J, Punzo, C et al. (2007). Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics. 8:153.

Vita: Click here to download

Website: Jeff Trimarchi

Geetu Tuteja

BCB Faculty Member in the GDCB Department

Education: Ph.D., University of Pennsylvania, 2009 in Genomics and Computational Biology

Research Interests: Transcriptional regulation; placental development; next-generation sequencing and data analysis.

Our lab is broadly interested in transcriptional regulation, which is directed in part by the binding of sequence-specific transcription factors (TFs) to enhancer regions. Identifying cell-type specific enhancers is crucial for understanding the genetic architecture underlying development and disease. Currently we are studying the molecular mechanisms underlying trophoblast invasion, a process that occurs in early placental development and establishes adequate blood flow between mother and fetus. Defects in trophoblast invasion can lead to a number of disorders, such as preeclampsia, intrauterine growth restriction, and placenta creta.

We are applying next-generation sequencing technologies to identify enhancers and transcription factor binding events specific to the process of trophoblast invasion using the mouse model. We use computational approaches to analyze and integrate our data sets, and to construct gene-enhancer networks. Finally, we test functionality of the gene enhancer network components using mouse and human cell lines. Ultimately, we hope that our findings will translate to early detection and prevention of common and serious placental disorders.


Selected Publications:

  • Soccio RE*, Tuteja G*, Everett L, Lazar MA, Kaestner KH. Metabolic transcription factors mediate conserved functions largely via species-specific binding regions. Mol Endocrinol; 25(4):694-706, April 2011. PMCID: PMC3386547. * Contributed equally to this work
  • Li Z, Schug J, Tuteja G, White P, Kaestner KH. The nucleosome map of the mammalian liver. Nat Struct Mol Biol; 18(6):742-6, Jun 2011. PMCID: PMC3148658.
  • Tuteja G. DNA-protein Interaction analysis (ChIP-Seq). In Bioinformatics for Next Generation Sequencing. Springer; 127-149, 2012.
  • Li Z, Tuteja G, Schug J, Kaestner KH. Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer. Cell; 148(1):72-83, Jan 2012. PMCID: PMC3266536.
  • Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell; 151(7):1608-1616, Dec 2012.
  • Tuteja G, Cheng E, Papadakis H, Bejerano G. PESNPdb: A comprehensive database of SNPs studied in association with pre-eclampsia. Placenta; 33(12):1055-1057, Dec 2012.
  • Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option. PLOS Genetics; 9(8):e1003728, Aug 2013. PMCID: PMC3757057
  • Tuteja G, Wenger AM, Moreira KB, Chung T, Bejerano G. Genomic approaches for the identification of genes and enhancers regulating placenta development. Placenta; 34(9):A69-A70, Sept 2013.
  • Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G. Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PLOS Computational Biology; 10(1):e1003449, Jan 2014. PMCID: PMC3907286

Website: Geetu Tuteja

Christopher Tuggle

BCB Faculty Member in the Animal Science Department

Education: Ph.D., Minnesota, 1986

Research Interests: Functional genomics and systems biology of regulatory pathways controlling inflammation and appetite.

  • Functional and Structural Genomics-- Transcriptional profiling to understand pathways controlling reproduction, development, growth and infectious disease. Characterization and prediction of gene regulatory regions. Large-scale gene discovery and mapping (EST sequencing and analysis)

Description: The research in my lab is currently focused on the following porcine functional genomic projects, all of which are externally funded.

  1. How the transcriptome of the developing embryo and the uterine endometrium changes during implantation, a critically important stage of successful reproduction.
  2. How the transcriptome of the immune system reacts to and controls infection by Salmonella spp., zoonotic pathogens impacting food safety.
  3. How the trancriptome of relevant tissues that control feed intake respond to food limitation and selection for decreased food intake.

Selected Publications:

  • Towfic, F., VanderPlas, S., Oliver, C.A., Couture, O., Tuggle, C.K., Greenlee, M.H.W., and Honavar, V. (2010). Detection of Gene Orthology Based On Biomolecular Networks. BMC Bioinformatics: 11, S7.

  • Ross, J. A., Ashworth, M. D., Stein, D. R. Couture, O., Tuggle, C.K., & Geisert, R. (2009). Identification of Differential Gene Expression during Porcine Conceptus Rapid Trophoblastic Elongation and Attachment to the Uterine Luminal Epithelium. Physiological Genomics: 36, 140-148.

  • Uthe, J. J., Wang, Y., Qu, L., Nettleton, D., Tuggle, C.K., & Bearson, S.M.D. (2009). Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Veterinary Microbiology: 135, 384-388.

  • Couture, O., Callenberg, K., Koul, N., Pandit, S., Younes, R., Hu, Z., Dekkers, J., Reecy, J., Honavar, V., & Tuggle, C.K. (2009). ANEXdb: an integrated animal Annotation and microarray EXpression database. Mammalian Genome: 20, 768-77.

  • Tuggle C.K., Y.F. Wang and O. Couture. 2007. INVITED REVIEW: Advances in Swine Transcriptomics. International Journal of Biological Sciences 3:132-152.

  • Uthe, J.J., Royaee, A., Lunney, J.K., Stabel, T.J., Zhao, S.-H., Tuggle, C.K., Bearson, S.M.D. 2007. Porcine differential gene expression in response to Salmonella enterica serovars Choleraesuis and Typhimurium. Molecular Immunology 44:2900-2914.

  • Wang, Y.F., Qu, L., Uthe, J.J., Bearson, S.M.D., Kuhar, D., Lunney, J.K., Couture, O.P., Nettleton, D., Dekkers, J.C.M., and C. K. Tuggle. 2007. Global Transcriptional Response of Porcine Mesenteric Lymph Nodes to Salmonella enterica serovar Typhimurium. Genomics 90:72-84.

  • Tuggle, C.K., Dekkers. J., J. Reecy. 2006. Integration of Structural and Functional Genomics. Animal Genetics 37 (Supp. 1): 1-6.

  • Zhao. S.H., D. Kuhar, J. K. Lunney, H. Dawson, C. Guidry, J.J. Uthe, S. M. D. Bearson, J. Recknor, D. Nettleton, C.K. Tuggle. 2006. Gene expression profiling in Salmonella Choleraesuis infected porcine lung using a long oligonucleotide microarray (Mammalian Genome 17:777-89).

Vita: Click here to download

Website: Christopher Tuggle

Eric Underbakke

BCB Faculty Member in the BBMB Department

Education: Ph.D., Univ. of WI, Madison, Biochemistry, 2008

Research Interests: A focus on mapping the architecture and assembly of protein signaling complexes involved in synaptic plasticity. We employ mass spectrometry to map protein-protein interactions and conformational changes.

Description: Dynamic, scaffolded, multi-protein complexes are hallmarks of sophisticated cellular signaling systems. The higher-order architecture of these signaling complexes confers sensitivity, adaptability, control, and crosstalk. Signaling complex architecture is especially notable in the nervous system, where dynamic post-synaptic protein assemblies underlie the molecular origins of learning and memory. Moreover, post-translational modifications within the signaling complexes induce conformational changes to modulate reorganization and retargeting. Understanding the dynamic architecture of these protein assemblies is crucial because disruptions in this system are implicated in neurological disorders such as Parkinson’s disease, autism spectrum disorders, depression, and schizophrenia.

Our lab employs mass spectrometry and chemical tools to probe the interactions and post-translational modifications that contribute to synaptic signaling strength and plasticity. Among these techniques, we use hydrogen-deuterium exchange mass spectrometry (HDX-MS) to map protein-protein interactions and conformational changes in dynamic signaling complexes. In addition, we employ diverse chemical tools for probing protein-protein interactions, such as crosslinkers, artificial amino acids, and spectroscopic tags. By integrating maps of protein interaction surfaces with the structures of the protein components, we can devise models of the higher-order architecture of the signaling assemblies. Furthermore, we can test how post-translational modifications and conformational changes remodel the architecture. Our targets of inquiry include kinases, trafficking chaperones, nitric oxide signaling components, and the scaffolding proteins that assemble these diverse signaling effectors together at the synaptic membrane.

Selected Publications:

  • Underbakke ES, Iavarone AT, Chalmers MJ, Pascal BD, Novick S, Griffin PR, Marletta, MA. Nitric oxide-induced conformational changes in soluble guanylate cyclase. Structure (2014) [in press]
  • Campbell MG, Underbakke ES, Potter CS, Carragher B, Marletta MA. Single particle EM reveals the higher order domain architecture of soluble guanylate cyclase. Proc. Natl. Acad. Sci USA. (2014) [in press]
  • Smith BC, Underbakke ES, Kulp DW, Schief W, Marletta MA. Nitric oxide synthase domain interfaces regulate electron transfer and calmodulin activation. Proc. Natl. Acad. Sci USA. (2013) 110:E3577-86.
  • Underbakke ES, Iavarone AT, Marletta MA. Higher-order interactions bridge the nitric oxide receptor and catalytic domains of soluble guanylate cyclase. Proc. Natl. Acad. Sci USA. (2013) 110: 6777-82.
  • Underbakke ES, Surmeli NB, Smith BC, Wynia-Smith SJ, Marletta MA. 3.10 - Nitric oxide signaling. Comprehensive Inorganic Chemistry (2nd edition), Vol. 3 Oxford: Elsevier (2013) 241-262.

Vita: Click here to download

Website: Eric Underbakke

*Nicole Valenzuela

BCB Faculty Member in the EEOB Department

Education: Ph.D., SUNY at Stony Brook, 1999

Research Interest: Evolutionary and functional ecogenomics of sex determination

  • Functional and Structural Genomics-- Evolutionary and ecological functional genomics associated with the development of the sexual phenotype. Modeling evolution of sex determination. Thermal sexual polyphenisms in vertebrates. Gene discovery. Comparative gene expression. Chromosome evolution.
  • Genome Evolution­-Evolution of gene networks underlying sexual development. Molecular evolution. Chromosome evolution.


Evolutionary and ecological functional genomics associated with the development of the sexual phenotype. Temperature-dependent sex determination (TSD) represents a form of phenotypic plasticity (a thermal sexual polyphenism) where identical genomes can permanently differentiate into either sex depending on the environmental conditions. I am interested in identifying how many distinct systems of sexual polyphenisms exist in nature, how do they work, and why did they come into being. My research addresses the question of whether multiple molecular pathways have evolved to produce ecologically equivalent TSD systems among taxa. I use a comparative evolutionary-genomic framework to examine the molecular basis of TSD in multiple species to identify the regulatory gene(s) that render TSD systems thermo-sensitive. Current projects in my lab encompass candidate gene-discovery and gene expression profiling of TSD and GSD taxa, in an attempt to understand the molecular network associated with sex differentiation in TSD and its regulation. I am particularly interested in understanding how TSD works in nature, and the relative role of adaptive versus neutral processes during its evolution. I am approaching these issues through studies of the functional genomics in an ecologically relevant context, assessing individual variation of gene expression within and among populations. Another research avenue in my lab is focused on comparing turtles possessing XX/XY, ZZ/ZW or TSD mechanisms to study the evolution of sex chromosomes and the genes they contain. This research will test that (1) all sex chromosomes in turtles derive from a common ancestral pair of non-sex chromosomes (or "autosomes"), and that (2) the molecular evolution of genes contained in turtle sex chromosomes differs from that of the same genes found in turtles with TSD since they lack sex chromosomes. Additionally, since I am interested in theoretical and empirical aspects of the evolution and ecology of sex determining mechanisms and related topics (e.g. the evolution of sex ratio, sex chromosomes, and sex-linked traits), modeling can be an effective tool to investigate sex ratio evolution in organisms with alternative sex determining mechanisms by contrasting the influence of thermal sensitivity in population dynamics for TSD taxa as compared to GSD taxa.

Selected Publications:
  • Valenzuela, N. (2010). Co-evolution of genomic structure and selective forces underlying sexual development and reproduction. Cytogenetics and Genome Research: DOI: 10.1159/000295809.

  • Valenzuela, N. (2010). Multivariate expression analysis of the gene network underlying sexual development in turtle embryos with temperature-dependent and genotypic sex determination. Sexual Development: 4, 1-2, 39-49.

  • Valenzuela, N. (2009). The painted turtle, Chrysemys picta: A model system for vertebrate evolution, ecology, and human health. Cold Spring Harbor Protocols: DOI:10.1101/pdb.emo124

  • Escalona, T., Adams, D.C., & Valenzuela, N. (2009). Nesting ecology in the freshwater turtle Podocnemis unifilis: spatiotemporal patterns and inferred explanations. Functional Ecology: 23, 826-835.

  • Escalona, T., Engstrom, T.N., Hernandez, O.E., Bock, B.C., Vogt, R.C. & Valenzuela N. (2009). Population genetics of the endangered South American freshwater turtle, Podocnemis unifilis, inferred from microsatellite DNA data. Conservation Genetics: 10, 1683–1696.

  • Martinez, P., Ezaz T., Valenzuela, N., Georges, A., and Graves J.A.M. 2008. An XX/XY heteromorphic sex chromosome system in the Australian chelid turtle Emydura macquarii, a new piece in the puzzle of sex chromosome evolution in turtles. Chromosome Research (DOI: 10.1007/s10577-008-1228-4).

  • Valenzuela, N. 2008. Sexual development and the evolution of sex determination. Sexual Development 2(2): 64-72.

  • Valenzuela, N. 2008. Evolution of the gene network underlying gonadogenesis in turtles with temperature-dependent and genotypic sex determination. Integrative and Comparative Biology. doi:10.1093/icb/icn031

  • Janes D.E., Organ C., and Valenzuela N. 2008. New resources inform study of genome size, content and organization in non-avian reptiles. Integrative and Comparative Biology. doi:10.1093/icb/icn010

  • Valenzuela, N. 2008. Relic thermosensitive gene expression in a turtle with genotypic sex determination. Evolution 62-1: 234-240.

Vita: Click here

Website: Nicole Valenzuela

Amy Vincent

BCB Faculty Member in the USDA NADC

Education: Ph.D., DVM, Iowa State University, 2004

Research Interests: The primary focus of her laboratory is influenza A virus (IAV) in swine. IAV represents a unique agent that is pathogen to pigs, humans, and numerous other species, and the NADC studies focus on IAV in the natural swine host. Three areas of IAV research involve investigating virulence properties, characterizing currently circulating and emerging IAV in swine, and developing novel vaccine approaches. Recent efforts focused on the 2009 pandemic H1N1, H3N2 variants in humans, swine H3N2 viruses, and the interplay between human seasonal and swine adapted IAV between the two host species. As an RNA virus with an immense capacity to undergo genetic change, monitoring genetic evolution and correlating the genetic changes with properties of virus and virus-host interaction is a critical area of research for IAV. This is the subject area that the Iowa State University BCB program has obvious potential for interaction between faculty and students and NADC scientists.

Selected Publications:

  • Nelson MI, Vincent AL. Reverse zoonosis of influenza to swine: new perspectives on the human - animal interface. Trends Microbiol. 2015 Jan 4. [Epub ahead of print
  • Henningson JN, Rajao DS, Kitikoon P, Lorusso A, Culhane MR, Lewis NS, Anderson TK, Vincent AL. Comparative virulence of wild - type H1N1pdm09 influenza A isolates in swine. Vet Microbiol. 2014 Dec 31. pii: S0378 - 1135(14)00594 - X. doi: 10.1016/j.vetmic.2014.12.021. Epub ahead of print]
  • Gauger PC , Loving CL, Khurana S, Lorusso A , Perez DR, Kehrli ME Jr, Roth JA, Golding H, Vi ncent AL . Live attenuated influenza A virus vaccine protects against A(H1N1)pdm09 heterologous challenge without vaccine associated enhanced respiratory disease. Virology. 2014 Oct 28;471 - 473C:93 - 104.
  • Nelson MI, Wentworth DE, Culhane MR, Vincent AL , Viboud C, LaPointe MP, Lin X, H olmes EC, Detmer SE. Introductions and evolution of human - origin seasonal influenza a viruses in multinational swine populations. J Virol. 2014 Sep 1;88(17):10110 - 9.
  • Loving CL, Brockmeier SL, Vincent AL , Gauger PC, Zanella EL, Lager KM, Kehrli ME Jr. Cross - fostering to prevent maternal cell transfer did not prevent vaccine - associated enhanced respiratory disease that occurred following heterologous influenza challenge of pigs vaccinated in the presence of maternal immunity. Viral Immunol. 2014 Sep;27(7):334 - 42.
  • Rajao DS, Loving CL, Gauger PC, Kitikoon P, Vincent AL. Influenza A virus hemagglutinin protein subunit vaccine elicits vaccine -
    associated enhanced respiratory disease in pigs. Vaccine. 2014 Sep 8;32(40):5170 - 6.
  • Lorusso A, Ciacci - Zanella JR, Zanella EL, Pena L, Perez DR, Lager KM, Rajao DS, Loving CL, Kitikoon P, Vincent AL. Polymorphisms in the hemagglutin in gene influenced the viral shedding of pandemic 2009 influenza virus in swine. J Gen Virol. 2014 Dec;95(Pt 12):2618 - 26.
  • Lewis, N.S., Anderson, T.K., Kitikoon, P., Skepner, E., Burke, D.F., and Vincent, A.L. 2014. Substitutions near the hemagglutinin receptor binding site determine the antigenic evolution of influenza A H3N2 viruses in U.S. swine. J. Virol. 88(9):4752 - 63.

Vita: Click here to download.

*Erik Vollbrecht

BCB Faculty Member in the GDCB Department

Education: Ph.D., UC, Berkeley, 1996

Research Description:

My research program is broadly focused on evolutionary developmental biology in plants and genome dynamics in maize. In the evolutionary work we employ a variety of computational approaches to questions in molecular evolution from routine phylogenetic reconstructions to quantifying histories of recombination, and using standard and maximum likelihood approaches to test for evidence for selection in nucleic acid sequence. As this work becomes increasingly genome-driven, the informatics techniques are becoming more computational (and in many cases, more rigorous). My research group is also developing a genome-wide collection of transposable element insertions in maize, to serve as distributed platforms for regional mutagenesis. Through this work we are probing mechanisms of endogenous transposable element insertion via statistical and computational analyses of large collections of transposon insertion sites. Our recently published analyses show a clear bias for the Ds transposon to insert into promoter and exon regions, and for DNA insertion sites with particular structural signatures.

Selected Publications:

  • Vollbrecht, E., Duvick, J., Schares, J.P., Ahern, K.R., Deewatthanawong, P., Xu, L., Conrad, L.J., Kikuchi, K., Kubinec, T.A., Hall, B.D., Weeks, R., Unger-Wallace, E., Muszynski, M., Brendel, V.P., and Brutnell, T.P. (2010). Genome-Wide Distribution of Transposed Dissociation Elements in Maize. Plant Cell.
  • Sigmon, B., and Vollbrecht, E. (2010). Evidence of selection at the ramosa1 locus during maize domestication. Mol Ecol 19, 1296-1311.
  • Ahern, K.A., P. Deewatthanawong, J. Schares, M. Muszynski, R. Weeks, E. Vollbrecht, J. Duvick, V. P. Brendel and T.P. Brutnell (2009) Regional mutagenesis using Dissociation in maize. Methods (submitted)
  • Bortiri, E., G. Chuck, E. Vollbrecht, T. Rocheford, R. Martienssen and S. Hake (2006) “ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize.” Plant Cell 18: 574-585
  • Vollbrecht, E., P.S. Springer, L. Goh, E.S. Buckler and R. Martienssen (2005) "Architecture of floral branch systems in maize and related grasses." Nature 436: 1119-1126.
  • May, B. P., H. Liu, E. Vollbrecht, L. Senior, P.D. Rabinowicz, D. Roh, X. Pan, L. Stein, M. Freeling, D. Alexander and R. Martienssen (2003) Maize-targeted mutagenesis: A knockout resource for maize. Proc. Natl. Acad. Sci. USA 100: 11541-11546.
  • Hake, S., E. Vollbrecht and M. Freeling (1989) Cloning Knotted, the dominant morphological mutant in maize using Ds2 as a transposon tag. EMBO J. 8: 15-22.
  • Vollbrecht, E. and R. S. Schmidt (2008) Development of the Inflorescences. In Handbook of Maize: Its Biology, (New York, Springer-Verlag) pp 13 - 40.
  • Bommert, P., C. Lunde, J. Nardmann, E. Vollbrecht, M. Running, D. Jackson, S. Hake and W. Werr (2005) thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucinerich repeat receptor-like kinase. Development 132, 1235-45.
  • Vollbrecht, E., L. Reiser and S. Hake (2000) Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene, knotted1. Development 127: 3161-3172.
  • Kerstetter, R., E. Vollbrecht, B. Lowe, B. Veit, J. Yamaguchi and S. Hake (1994) Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes. Plant Cell 6: 1877-1887.
  • Vollbrecht, E., B. Veit, N. Sinha and S. Hake (1991) The developmental gene knotted1 is a member of a maize homeobox gene family. Nature 350: 241-243.

Vita: Click here to download

Website: Erik Vollbrecht Departmental

Justin Walley

BCB Faculty Member in the Plant Pathology and Microbiology Department

Education: Ph. D., University of California, Davis, 2009

Research: Plant-Microbe Interactions, Systems Biology, Proteomics

Selected Publications:

  • Walley JW and Briggs SP (2015) Dual use of peptide mass spectra: protein atlas and genome annotation. Current Plant Biology - Accepted
  • Marcon C, Malik WA, Walley JW, Shen Z, Paschold A, Smith LG, Peipho H, Briggs SP, Hochholdinger F (2015) A high resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axis. Plant PhysiologyIn Press
  • Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V (2014) An Automated Proteogenomic Method Utilizes Mass Spectrometry to Reveal Novel Genes in Zea mays. Molecular & Cellular Proteomics 13(1); 157-167
  • Walley JW, Shen Z, Sartor RC, Wu KJ, Osborn J, Smith LG, Briggs SP (2013) Reconstruction of Protein Networks from an Atlas of Maize Seed Proteotypes. PNAS 110(49) E4808-4817
  • Walley JW, Kliebenstein DJ, Bostock RM, and Dehesh K (2013) Fatty acids and early detection of pathogens. Current Opinion in Plant Biology 16(4):526-520
  • Savchenko T, Walley JW, Chehab EW, Xiao Y, Kaspi R, Pye MF, Mohammed ME, Lazarus C, Bostock RM and Dehesh K (2010) Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks. Plant Cell 22(10):3193-3205
  • Walley JW and Dehesh K (2010) Molecular mechanisms regulating general stress signaling networks in Arabidopsis. Journal of Integrative Plant Biology 52(4):354-359 (Cover Article)
  • Walley JW, Kelley DR, Savchenko T and Dehesh K (2010) Investigating the function of CAF1 deadenylases during plant stress responses. Plant Signaling and Behavior 5(7):802-805
  • Rowe HC, Walley JW, Corwin J, Chan EKF, Dehesh K and Kliebenstein DJ (2010) Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis. PLoS Pathogens 6(4): e1000861
  • Walley JW* and Huerta AJ (2010) Exposure to environmentally relevant levels of cadmium primarily impacts transpiration in field-grown soybean. Journal of Plant Nutrition 33(10):1519-1530
  • Walley JW, Kelley DR, Nestorova G, Hirschberg DL, Dehesh K (2010) Arabidopsis deadenylasesAtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses. Plant Physiology 152(2):866-875.

Website: here

Kan Wang

BCB Faculty Member in the Agronomy Department

Education: Ph. D., University of Ghent, Ghent, Belgium, 1987

Research: Provide services in genetic transformation of corn, soybean and rice for academic researchers. Develop advanced technology for genetic transformation. Develop corn-based edible vaccines for livestock. Elucidate the molecular mechanisms by which plants respond to environmental stress and hormonal signals. Develop stress-tolerant crops. Develop cellulase producing corn for biorenewable material.

Selected Publications:

Website: Kan Wang

Jonathan F. Wendel

BCB Faculty Member in the EEOB Department

Education: Ph.D., North Carolina, 1983

Research Interests:

  • Genome Evolution-- Phylogenetics and molecular evolution, particularly in plants, with a special focus on the evolution of duplicated genes and genomes

Selected Publications:

  • Grover C. E., X. Zhu, K.K. Grupp, J. Jareczek, J. P. Gallagher., E. Szadkowski and J. F. Wendel. 2014. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum. Genetic Resources and Crop Evolution DOI 10.1007/s10722-014-0138-x.
  • Gong, L., M. Olson, and J. F. Wendel. 2014. Cytonuclear evolution of rubisco in four allopolyploid lineages. Molecular Biology and Evolution doi: 10.1093/molbev/msu
  • Crawford, D. J., J. J. Doyle, D. E. Soltis, P. S. Soltis, and J. F. Wendel (Eds). 2014. Contemporary and future studies in plant speciation, morphological/floral evolution, and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology. Philosophical Transactions of the Royal Society B, 369

  • Zhang, H., B. Zhu, B. Qi, X. Gou, Y. Dong, C. Xu, B. Zhang, W. Huang, C. Liu,  X. Wang, C. Yang, H. Zhou, K. Kashkush, M. Feldman, J. F. Wendel and B. Liu. 2014. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level. The Plant Cell doi/10.1105/tpc.114.128439.
  • Yoo, M.-J., E. Szadkowski, and J. F. Wendel (2013). Homeolog expression bias and expression level dominane in allopolyploid cotton. Heredity 110: 171-180.
  • Salmon, A., J. A. Joshua, J. A. Jeddeloh, and J. F. Wendel (2012). Targeted capture of homeologous coding and non-coding sequence in polyploid cotton. G3: Genes, Genomes, Genetics 2: 921-930.
  • Gong, L., A. Salmon, M. J. Yoo, K. Grupp, Z. Wang, A.H. Paterson and J.F. Wendel (2012). Thecytonuclear dimension of allopolyploid evolutio: an example from cotton using rubisco. Molecular Biology and Evolution 29: 3023-3036.
  • Flagel, L. E., J. A. Udall, and J. F. Wendel. 2012. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics, 13: 302; DOI: 10.1186/1471-2164-13-302.
  • Grover, C. E., A. Salmon, and J. F. Wendel. 2012. Targeted sequence capture as a powerful tool for evolutionary analysis. American Journal of Botany 99: 312–319.
  • Grover, C. E., K. K. Grupp, R. J. Wanzek, and J. F. Wendel. 2012 Assessing the monophyly of polyploid Gossypium species. Plant Systematics and Evolution, 298: 1177-1183.
  • Wendel, J. F., L. E. Flagel, and K. L. Adams. 2012. Jeans, genes, and genomes: cotton as a model for studying polyploidy. In Polyploidy and Genome Evolution (P. S. Soltis and D. E. Soltis, Eds). Springer, New York, pp. 181-207.
  • Wendel, J. F., J. Greilhuber, J. Dolozel, and I. J. Leitch. 2012. Plant Genome Diversity, Volume 1 (17 chapters). Springer, Vienna (in press)
  • Adams, K. L., and J. F. Wendel.  2012. Dynamics of duplicated gene expression in polyploid cotton.  In Polyploid and Hybrid Genomics (Z. J. Chen and J. Birchler, Eds.), Wiley Blackwell (in press).
  • Haen, K. M., M. Kemis, L. Bleeker, J. Wendel and A. Leshem. 2012. Elementary school science for a more sustainable future. Journal of Science Teacher Education (in press).
  • Leitch, I. J., J. Greilhuber, J. Dolozel, and J. F. Wendel. 2012. Plant Genome Diversity, Volume 2 (17 chapters). Springer, Vienna.
  • Richards, C. L. and J. F. Wendel. 2011. The hairy problem of epigenetics in evolution. New Phytologist 191: 7–9
  • Hu, G., N. L. Houston, D. Pathak, L. Schmidt, J. J. Thelen and J. F. Wendel. 2011. Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189: 1103–1115.
  • Wendel, J. F., and M. M. Goodman. 2011. Stanley George Stephens. Biographical Memoirs of the National Academy of Sciences , 93: 1-22
  • Bao, Y., G. Hu, L. Flagel, A. Salmon, M. Bezanilla, A. Paterson, Z. Wang, and J. F. Wendel. 2011. Convergent upregulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). Proceedings of the National Academy of Sciences USA 108: 21152–21157.
  • Pleasants, J. M, & Wendel, J. F. (2010). Reproductive and pollination biology of the endemic Hawaiian cotton, Gossypium tomentosum (Malvaceae). Pacific Science: 64, 45–55.
  • Betancur, L., Singh, B., Rapp, R. A., Wendel, J. F., Marks, M. D., Roberts, A. W., & Haigler, C. H. (2010). Phylogenetically distinct cellulose synthase genes support secondary wall thickening in Arabidopsis shoot trichomes and cotton fiber. Journal of Integrative Plant Biology: 52, 205-220.
  • Bao, Y., Wendel, J. F., & Ge, S. (2010). Multiple patterns of rDNA evolution following polyploidy in Oryza. Molecular Phylogenetics and Evolution: 55, 136-142.
  • Salmon, A., Flagel, L. E., Ying, B., Udall, J. A., & Wendel, J. F. (2010). Homoeologous gene conversion following allopolyploidy in cotton. New Phytologist: 186, 123–134.
  • Flagel, L. E., & Wendel, J. F. (2010). Evolutionary rate variation and scope of duplicate gene expression evolution in five allotetraploid cotton species. New Phytologist: 186, 184–193.

Vita: Click here to download

Recent Presentation

Website: Jonathan F. Wendel

*Steve Whitham

BCB Faculty Member in the Plant Pathology and Microbiology Department

Education: Ph.D., Univ. of CA, Berkeley, 1995

Research Interests:

  • My research program involves the functional genomic analysis of plant microbe interactions, and we have three major projects that would be suitable for a bioinformatics student. First, we have employed DNA microarrays to analyze the responses of plants to microbes and are now using these data to test the functions of genes that we hypothesize may be involved in disease defense networks. Second, we are developing high throughput methods to analyze gene functions in soybean using a technique called virus induced gene silencing. Third, we are preparing to do sequencing of the Asian soybean rust haustoria transcriptome using the 454 technology from Roche. I believe that the data sets that are available and the three complementary projects that are in progress in our lab present some excellent opportunities for research projects for a student in the BCB program. I am able to provide financial support for a graduate research assistantship through existing grant funds.

Selected Publications:

  • Zhang, C., Bradshaw, J. D., Whitham, S. A., & Hill, J. H. (2010). The development of an efficient multi-purpose BPMV viral vector set for foreign gene expression and RNA silencing. Plant Physiol.: 153, 1, 52-65, doi: 10.1104/pp.109.151639
  • Zhang, C., Hajimorad, M. R., Eggenberger, A. L., Tsang, S., Whitham, S. A., & Hill, J. H. (2009). Cytoplasmic inclusion cistron of Soybean mosaic virus serves as a virulence determinant on Rsv3-genotype soybean and a symptom determinant. Virology: 391, 240-248. doi:10.1016/j.virol.2009.06.020
  • Yang, C., Zhang, C., & Whitham, S. A. (2009). Differential requirement of RIBOSOMAL PROTEIN S6 by plant RNA viruses with different translation initiation strategies. Virology: 390:163-173. doi: 10.1016/j.virol.2009.05.018 .
  • Meyer, J. D. F., Silva, D. C. G., Yang, C., Pedley, K. F., Zhang, C., van de Mortel, M., Hill, J. H., Shoemaker, R. C., Abdelnoor, R. V., Whitham, S. A., & Graham, M. A. (2009). Identification and analyses of candidate genes for Rpp4-mediated resistance to Asian soybean rust in soybean (Glycine max (L.) Merr.). Plant Physiol.: 150, 295-307. doi: 10.1104/pp.108.134551
  • Zhang, C., Whitham, S. A., & Hill, J. H. (2009). Development and use of an efficient DNA-based viral gene silencing vector for soybean. Mol. Plant Microbe Interact.: 22, 123-131, doi: 10.1094/MPMI -22-2-0123. (Ranked in the Top 9 papers of 2009 in Mol. Plant Microbe Interact.,

Vita: Click here to download

Website: Steve Whitham

Stephen Willson

BCB Faculty Member in the Mathematics Department

Education: Ph.D., Michigan, 1973

Research Interests: Reconstruction of phylogenetic trees, supertrees, and networks.

  • Genome Evolution--Reconstruction of phylogenetic trees, networks, and supertrees from data, especially involving distance estimates.

Description: I study methods for analyzing phylogeny. I develop algorithms for constructing phylogenetic trees and networks from data, and I prove theorems about the methods. Of special interest are methods that give signals for hybridization or lateral gene transfer and methods such as supertrees to combine phylogenetic information from different researchers.

Selected Publications:

  • Tree-average distances on ertain phylogenetic networks have their weights uniquely determined. Algorithms for Molecular Biology (2012) 7:13, doi: 10.1186/1748-7188-7-13.
  • CSD homomorphisms between phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012) 9: 1128-1138.
  • Restricted trees: simplifying networks with bottlenecks. Bulletin of Mathematical Biology 73 (2011) 2322-2338.
  • Regular Networks Can Be Uniquely Constructed from thei Trees, IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011) 785-796.
  • Willson, S.J. (2010). Properties of normal phylogenetic networks. Bulletin of Mathematical Biology: 72, 340-358.
  • Willson, S. Unique determination of some homoplasies at hybridization events.   Bulletin of Mathematical Biology  69 (2007) 1709-1725.
  • Willson, S.  Reconstruction of some hybrid phylogenetic networks with homoplasies from distances.  Bulletin of Mathematical Biology 69 (2007) 2561-2590.
  • Willson, S. Unique reconstruction of tree-like phylogenetic networks from distances between leaves. Bulletin of Mathematical Biology 68 (2006) 919-944.
  • Willson, S. Unique solvability of certain hybrid networks from their distances. Annals of Combinatorics 10 (2006) 165-178.
  • Willson, S. Consistent formulas for estimating the total lengths of trees. Discrete Applied Mathematics 148 (2005) 214-239.
  • Willson, S. Minimum evolution using ordinary least-squares is less robust than neighbor-joining. Bulletin of Mathematical Biology 67 (2005) 261-279.
  • Willson, S. Constructing rooted supertrees using distances, Bulletin of Mathematical Biology 66 no 6 (2004): 1755-1783.

Vita: Click here to download

Website: Stephen Willson

*Roger Wise

BCB Faculty Member in the Plant Pathology and Microbiology Department

Education: Ph.D., Michigan State, 1983

Research Interests: Molecular signaling and parallel expression analysis in host-pathogen interactions

  • Bioinformatics--Large-scale genetical genomics and parallel expression profiling

  • Functional and Structural Genomics--Functional analysis of agronomically important genes selected from RNA-Seq and GeneChip profiling experiments

  • Effector Biology--Functional analysis of pathogen effectors as keys to understanding plant defense responses


Dissection of coexpression networks in barley-powdery mildew interactions: a multi-dimensional approach to understanding parasitism by obligate biotrophs

Regulation of gene expression in barley-powdery mildew interactions influences the establishment of fungal biotrophy and the development of host resistance. To identify global expression responses to the powdery mildew fungus, Blumeria graminis f. sp. hordei, 468 Barley1 GeneChips were used to profile the expression of 21,439 genes in inoculated vs. non-inoculated seedlings at hours 0, 8, 16, 20, 24, and 32 for each of nine variants of genes in the Mla resistance signaling pathway, as well as mutants programmed cell death ( NSF Plant Genome Award #0500461 ). We are analyzing these data to build coexpression networks containing genes involved in sugar transport, photosynthesis, WRKY signaling, secretion of PR proteins, signal peptide processing, and abiotic stress signaling. Single cell dsRNAi (TIGS), Virus Induced Gene Silencing (VIGS), transcript based cloning, and proteomics experiments are being used to dissect the various sub-networks and time-course interactions of disease defense pathways.

Selected Publications:

  • Cernadas, RA, E Doyle, DO Niño-Liu, KE Wilkins, T Bancroft, L Wang, C Schmidt, R Caldo†, B Yang, FF White, D. Nettleton, RP Wise, and AJ Bogdanove. Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with blight and a novel susceptibility gene. PLoS Pathogens 10 (2): e1003972. doi: 10.1371/journal.ppat.1003972.
  • Wise, RP*, P Surana, G Fuerst, D Mistry, J Dickerson, and D Nettleton. 2014. Flor revisited (again): eQTL and mutational analysis of NB-LRR mediated immunity to powdery mildew in barley. Journal of Integrated Agriculture 13 (2): 237-243. (Special Focus Issue -The Hot Spots in Cereal Rusts and Powdery Mildew Research: 13th International Cereal Rusts and Powdery Mildews conference, Beijing, China).
  • Xu, W†, Y Meng†, and RP Wise*. 2014. Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus. New Phytologist 201 (4): 1396-1412: DOI: 10.1111/nph.12598.
  • Hayes, N†, L Maffin†, L McGhee†, G Hall†, T Hubbard†, E Whigham†, and RP Wise*.2013. iTAG Barley: A 9-12 curriculum to explore inheritance of traits and genes using Oregon Wolfe barley. Digital iBook for iPAD. American Society of Plant Biologists (via iTUNES iBOOKs; 51 pp).
  • Mascher, M, GJ Muehlbauer, DS Rokhsar, J Chapman, J Schmutz, K Barry, M Muñoz-Amatriaín, TJ Close, RP Wise, AH Schulman, A Himmelbach, KFX Mayer, U Scholz, JA Poland, N Stein*, R Waugh. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal 76 (4): 718-727: DOI 10.1111/tpj.12319.
  • Ballini, E, N Lauter, and R Wise. 2013. Prospects for advancing defense to cereal rusts through genetical genomics. Frontiers in Plant Science 4: 117: DOI: 10.3389/fpls.2013.00117. [Full Text]
  • Pliego, C, D Nowara, G Bonciani, DM Gheorghe, R Xu, P Surana, E Whigham, D Nettleton, AJ Bogdanove, RP Wise, P Schweizer, LV Bindschedler, P Spanu. 2013. Host-Induced Gene Silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. Molecular Plant-Microbe Interactions 26 (6): 633-642: DOI: 10.1094/MPMI-01-13-0005-R. [Full Text]
  • Dash, S, J Van Hemert, L Hong, RP Wise, and JA Dickerson. 2012. PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Research (2012) 40 (D1): D1194-D1201. doi: 10.1093/nar/gkr938.
  • Meyer, J, D Pei, and RP Wise. 2011. Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. The Plant Genome 4(3): 283-299.
  • Moscou, MJ, N Lauter, RA Caldo, D Nettleton, and RP Wise. 2011. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Mol Plant Microbe Interactions 24:6, 694-705 DOI: 10.1094/MPMI-09-10-0211.
  • Moscou, MJ, N Lauter, B Steffenson, and RP Wise, 2011. Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional repression of defense regulons. PLoS Genetics 7(7): e1002208. doi:10.1371/journal.pgen.1002208.
  • Mach, Jennifer, 2009. Loss of an exosome complex component potentiates R-gene independent cell death in barley. The Plant Cell 21(10):2986.
  • Kronmiller BA and RP Wise. 2009. Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. Plant Physiol 151:483-95.
  • Meng, Y., Moscou, M.J., & Wise, R.P. (2009). Blufensin1 negatively impacts basal defense in response to barley powdery mildew. Plant Physiology: 149, 271-285. [Full Text]
  • Xi, L., Moscou, M.J., Meng, Y., Xu, W., Caldo, R.A., Shaver, M., Nettleton, D., & Wise, R.P. (2009). Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene–independent cell death in barley–powdery mildew interactions. The Plant Cell: 21, 3280-3295. [Full Text]
  • Abebe, T., Melmaiee, K., Berg, V., & Wise, R.P. (2009). Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed. Functional & Integrative Genomics. [Advance Online Publication]
  • Zhou S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas C., Pasternak, S., Forrest, D.K., Wise, R., Ware, D., Wing, R.A., Waterman, M.S., Livny, M., & Schwartz, D. C. (2009). A single molecule scaffold for the maize genome. PLOS Genetics: 5, 11, 1-14. [Full Text]
  • Wang, K., Frame, B., Xu, X., Moeller, L., Lamkey, K., & Wise, R. (2009). Strategies for the production of maize-derived pharmaceuticals using cytoplasmic male sterile lines: in vitro tissue culture/transformation and field breeding approaches. Maydica: 54, 199-210. [Full Text]
  • Abebe, T., Wise, R.P., & Skadsen, R.W. (2009). Comparative transcriptional profiling established the awn as the major photosynthetic organ of the barley spike while the lemma and the palea primarily protect the seed. The Plant Genome: 2, 3, 247-259. [Full Text]
  • Kronmiller, B.A., & Wise, R.P. (2009). Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. Plant Physiology: 151, 483-495. [Full Text]

Vita: Click here to download

Website: Roger Wise

*Zhijun Wu

BCB Faculty Member in the Mathematics Department

Education: Ph.D., Rice, 1991

Research Interests: Biomolecular and biosystems modeling and simulation, numerical linear algebra, nonlinear optimization, linear programming, integer and combinatorial optimization, numerical solution of ordinary and partial differential equations, parallel high-performance computing

  • Bioinformatics--

    Molecular distance geometry, protein structure refinement, simulation of transition of protein conformation, constrained molecular dynamics, potential energy minimization, protein geometry databases, multiscale protein modeling, metabolic network simulation and optimization

  • Macromolecular Structure and Function--Same as above
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking--Same as above


Research in Zhijun Wu’s group includes (1) development of efficient distance geometry algorithms for protein structure determination using inter-atomic or inter-residual distances; (2) refinement of protein structures using database-derived distance constraints or mean-force potentials; (3) simulation of protein conformational transitions via the solution of a boundary-value problem for the classical mechanical equation of motion; (4) algorithms for protein dynamics simulation and energy minimization with distance constraints; (5) global optimization algorithms for protein potential energy minimization; (6) databases of distributions of protein geometric elements (such as inter-atomic distances, torsion angles, contact patterns) in known proteins; (7) multiscale modeling methods for protein dynamics simulation and energy minimization; (8) steady-state solution of metabolic equations, flux balancing, control, and optimization.

Selected Publications:

  • A Penalty-Function Method for Constrained Molecular Dynamics Simulation, to appear in Numerical Analysis and Modeling, 2008 (with Ajith Gunaratne).
  • A Multiple Shooting Algorithm for Solving the Boundary Value Problems in Molecular Dynamics Simulation, to appear in Numerical Analysis and Modeling, 2008 (with Peter Vedell).
  • Enhancement of Torsion Angle Constraints in NMR Structure Refinement via Database Derived Distance Constraints, Journal of Bioinformatics and Computational Biology, Vol 6, No. 2, 2008, pp. 283-300 (with Feng Cui and Robert Jernigan).
  • Generating Rigid Protein Structures with Sparse Sets of Inter-Atomic and Inter-Residual Distances, Optimization Letters, Vol 2, No. 3, 2008, pp. 319- 331 (with Di Wu and Yaxiang Yuan).
  • PRTAD: A Protein Residue Torsion Angle Distribution Database, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2007, pp. 24-31 (with Xiaoyong Sun, Di Wu, and Robert Jernigan).
  • Improvement of Under-Determined Loop Regions of Human Prion Protein by Database Derived Distance Constraints, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, 2007, pp. 14-23 (with Feng Cui,
    Kriti Mukhopadhyay, Wonbin Young, and Robert Jernigan).
  • Refinement of NMR-Determined Protein Structures with Database Derived Mean Force Potentials, Proteins: Structure, Function, Bioinformatics, Vol. 68, 2007, pp. 232-242 (with Di Wu and Robert Jernigan).
  • PIDD: A Protein Inter-atomic Distance Distribution Database, Journal of Nucleic Acid Research, Vol. 35, 2007, pp. D202-D207 (with Di Wu, Feng Cui, and Robert Jernigan).

Vita: Click here to download

Website: Zhijun Wu

*Eve Wurtele

BCB Faculty Member in the GDCB Department

Education: Ph.D., UCLA, 1980

Research Interests: Regulation mechanisms of metabolism. Emergence of genes de novo.

  • Functional and Structural Genomics-- Metabolic networking in plants. How do plants regulate the allocation of resources to proteins, carbohydrates, lipids and specialized natural products.
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Design and implementation of user-centered software to facilitate hypothesis generation on the structure and components of biological networks.

Description: Plants can be considered "environmentally clean", solar-powered factories that produce a wide range of chemicals from simple precursors (carbon dioxide, nitrogen, sulfur, etc.). These complex plant-derived chemicals include carbohydrates, proteins, oils, and vitamins, and have nutritional, industrial, and medicinal uses. The metabolic processes that biosynthesize these complex molecules are responsive to growth and developmental signals determined by the genetic blueprint of the organism as it adapts to the ever-changing environmental stimuli. These metabolic processes are the chemical basis for life. My research, juxtaposed at the interface between biology and computational sciences, centers on this interplay between the metabolic and regulatory signals: the metabolic network of plants. My foci are 1) the development of software to explore the metabolic and regulatory network in conjunction with experimental data from millions of datapoints (, and 2) the elucidation of the metabolic networks associated with the two-carbon activated molecule, acetyl-CoA.

Selected Publications:

Five most closely related to proposal

  • Arendsee Z, Li L, Wurtele ES. 2014. Coming of age: orphan genes of plants. Trends in Plant Science. 10.1016/j.tplants.2014.07.003
  • Li L, Wurtele ES. 2014. The QQS orphan gene of Arabidopsis modulates carbon and nitrogen allocation in soybean. Plant Biotechnology Journal. doi: 10.1111/pbi.12238
  • Hur M, Cambell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Nikolau BJ, Wurtele ES. 2013. A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Natural Product Reports. 30:565-83, DOI:10.1039/C3NP20111B
  • Sucaet Y, Wang Y, Jie Li  J, Wurtele ES. 2012 MetNet Online: a novel integrated resource for plant systems biology. BMC: Bioinformatics. 13:267 doi:10.1186/1471-2105-13-267
  • Ngaki MN, Louie GV, RN, Manning G, Pojer F, Bowman ME, Li L, Elise Larsen E, Wurtele ES, Noel JP. 2012. Evolution of the chalcone isomerase fold from fatty acid-binding to stereospecific enzyme. Nature. 485:530-533. doi:10.1038/nature11009
Five other significant products
  • Almeida-de-Macedo MM, Ransom N, Feng Y, Hurst J, Wurtele ES. Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data. BMC Bioinformatics. 2013 Jul 4;14(1):214. doi: 10.1186/1471-2105-14-214. PubMed PMID: 23822712; PubMed Central PMCID: PMC3765419.
  • Quanbeck SMM, Brachova L, Campbell AA, Guan X, Perera A, Seung KA, Rhee Y, Bais P, Dickerson J, Dixon P, Wohlgemuth G, Fiehn O, Barkan L,  Lange BM, Lee I, Cortes D, Shuman J, Shulaev V, Huhman D, Lei Z, Sumner LW, Roth MR,  Welti R, Ilarslan H, Wurtele ES,  Nikolau BJ. 2012. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of "unknown function."  Frontiers of Plant Science, 3:15. PMCID: PMC3355754.
  • Li L, Foster C, Gan Q, Nettleton D, Myers AM, Wurtele ES.2009. Identification of the novel protein QQS as component of the starch metabolic network in Arabidopsis leaves. Plant J. Full Article
  • Mentzen W, Wurtele ES. 2008. Regulon Organization of Arabidopsis. BMC Plant Biology. 8:99 Sept 30 highly accessed article.
  • Lee JY, Wurtele E. 2014. MetNet: Graph-empowered visualization and analysis of integrated metabolic and regulátory networks.


Vita: Click here to download

Website: Eve Wurtele

Marna Yandeau-Nelson

BCB Faculty Member in the BBMB Department

Education: Ph.D., Iowa State University, Genetics, 2005

Research Interests: Integration of expertise in classical and molecular genetics with biochemical, molecular, bioinformatic and computational approaches to study the biosynthetic and regulatory genetic networks of metabolic traits, to increase both the fundamental knowledge of cellular metabolism and to use that knowledge for practical applications (i.e. plant breeding for resistance to stresses and the development of biorenewable chemicals and fuels).

Selected Publications:

  • Muszynski MG & Yandeau-Nelson MD. (2014) Molecular Genetics of Bioenergy Traits. In: Goldman SL & Kole C (eds) Compendium of Bioenergy Plants: Corn. CRC Press, 169-197.
  • Jing F,Cantu DC, Tvaruzkova J, Chipman J, Nikolau BJ,
    Yandeau-Nelson MD, Reilly PJ(2011)Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity.BMC Biochem 12:44
  • Yandeau-Nelson MD, Laurens L, Shi Z, Xia H, Smith AM, Guiltinan MJ (2011) Starch Branching Enzyme IIa is required for proper diurnal cycling of starch in leaves of Zea mays. Plant Physiol,156: 479-490.
  • Xia H, Yandeau-Nelson M, Thompson DB, Guiltinan MJ (2011) Deficiency of maize starch-branching enzyme I results in altered starch fine structure, decreased digestibility and reduced coleoptile growth during germination. BMC Plant Biol, 11:95.
  • Perera MA, Qin W, Yandeau-Nelson M, Fan L, Dixon P, Nikolau BJ (2010) Biological origins of normal-
    chain hydrocarbons: a pathway model based on cuticular wax analyses of maize silks. Plant J, 64: 618-632.

Vita: Click here to download.


*Edward Yu

BCB Faculty Member in the Physics and Astronomy Department

Education: Ph.D.,University of Michigan, 1997

Research Interests: Structural and mechanistic aspects of membrane transport; X-ray crystallography of membrane proteins; Biophysics

  • Macromolecular Structure and Function-- Structural and mechanistic aspects of membrane transport; X-Ray crystallography of membrane proteins; Biophysics


Selected Publications:

  • Su, C.C., Yang, F., Long, F., Reyon, D., Routh, M.D., Kuo, D.W., Mokhtari, A.K., Van Ornam, J.D., Rabe, K.L., Hoy, J.A., Lee, Y.J., Rajashankar, K.R., & Yu, E.W. (2009). Crystal Structure of the Membrane Fusion Protein CusB from Escherichia coli. J. Mol. Biology.

  • Su, C.-C., Long, F., McDermott, G., Shafer, W. M., and Yu, E.W. 2008. Crystallization and
    preliminary X-ray diffraction analysis of the multidrug efflux transporter NorM from Neisseria
    gonorrhoeae. Acta Cryst. F64:289-292.

  • Gu, R., Su, C.-C., Shi, F., Li, M., McDermott, G., Zhang, Q., and Yu, E.W. 2007. Crystal
    structure of the transcriptional regulator CmeR from Campylobacter jejuni. J. Mol. Biol. 372:583-

  • Li, M., Gu, R., Su, C.-C., Routh, M., Harris, K.C., Jewell, E.S., McDermott, G., and Yu, E.W.
    2007. Crystal structure of the transcriptional regulator AcrR from Escherichia coli. J. Mol. Biol.

  • Su, C.-C., and Yu, E.W. 2007. Ligand-transporter interaction in the AcrB multidrug efflux pump
    determined by fluorescence polarization assay. FEBS Lett. 581:4872-4976.

  • Su, C.-C., Rutherford, D.J., and Yu, E.W. 2007. Characterization of the multidrug efflux
    regulator AcrR from Escherichia coli. Biochem. Biophys. Res. Comm. 361:85-90.

  • Su, C.-C., Li, M., Gu, R., Takatsuka, Y., McDermott, G., Nikaido, H., and Yu, E.W. 2006.
    Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay
    Pathway. J. Bacteriol. 188:7290-7296.

Vita: Click here to download

Website: Edward Yu

* Asterisked Faculty currently serve as major or co-major professors for BCB Students.