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.



To View By Last Name: A B C D E F G H J L M N P R S T V W Y


To View by Research Area: Go here.


* 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. Our theoretical research focuses on the development of new evolutionary tools and analytical methods for assessing biological patterns and processes. Understanding the evolution of multi-dimensional traits (such as shape) is complex, and considerable effort is required to properly merge the mathematical properties of such traits with current evolutionary theory. Current theoretical work emphasizes the development of analytical approaches for evaluating macroevolutionary trends of phenotypic diversification. Specifically, we are developing approaches for characterizing the tempo and mode of evolution for high-dimensional complex traits in a phylogenetic context.

Select Recent Publications:

  • 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 . (In Press)
  • Adams, D.C., and E. Otárola-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.
  • Rabosky, D.L., and D.C. Adams. 2012. Rates of morphological evolution are correlated with species richness in salamanders. Evolution . 66:1807-1818.
  • Blankers, T., D.C. Adams, and J.J. Wiens. 2012. Ecological radiation with limited morphological diversification in salamanders. Journal of Evolutionary Biology . 25:634-646.
  • Adams, D.C. , and J.O. Church . 2011. The evolution of large-scale body size clines in Plethodon: evidence of heat-balance or species-specific artifact? Ecography . 34:1067-1075.
  • Adams, D.C. 2011. Quantitative genetics and evolution of head shape in Plethodon salamanders. Evolutionary Biology . 38:278-286.
  • Adams, D.C. A. Cardini, L. R. Monteiro, P. O’Higgins, and F.J. Rohlf. 2011. Morphometrics and Phylogenetics: principal components of shape from cranial modules are neither appropriate nor effective cladistic characters. Journal of Human Evolution . 60:240-243.

Vita: Click here to download

Website: Dean Adams

*Srinivas Aluru

BCB Faculty Member in the ECPE Department

Education: Ph.D., Iowa State, 1994

Research Interests: Computational and comparative genomics, systems biology, parallel computational biology, and string algorithms.

  • Bioinformatics: Sequential/parallel algorithms and software systems for bioinformatics, with emphasis on EST clustering, sequence alignments, sequence databases and protein structure

Selected Publications:

  • Wehe, Chang, W.-C., Eulenstein, O., & Aluru, S. (2010). A scalable parallelization of the gene duplication problem. Journal of Parallel and Distributed Computing: 70, 237-244.

  • Schnable, P.S., Ware, D., Aluru, S., Martienssen, R.A., Clifton, S.W., McCombie, W.R., Wing, R.A., & Wilson, R.K (2009). The B73 maize genome: complexity, diversity and dynamics. Science (cover article): 326, 5956, 1112-1115.

  • Wei, F., Stein, J.C., : : : , Bennetzen, J., Martienssen, R., McCombie, W.R., Aluru, S., Clifton, S.W., Schnable, P.S., Ware, D., Wilson, R.K., & Wing, R.A. (2009). Detailed analysis of a contiguous 22-Mb region of the maize genome. PLOS Genetics: 5, 11, 1-16.

  • Sarje & Aluru, S. (2009). Parallel genomic alignments on the Cell broadband engine. IEEE Transactions on Parallel and Distributed Systems: 20, 11, 1600-1610.

  • Jackson , B.G., Schnable, P.S., & Aluru, S. (2009). Parallel short sequence assembly of transcriptomes. BMC Bioinformatics: 10, 1, S14.

  • B. Jackson, P.S. Schnable and S. Aluru, "Consensus genetic maps as median orders from
    inconsistent sources," ACM/IEEE Transactions on Computational Biology and Bioinformatics, in

  • A. Kalyanaraman, S.J. Emrich, P.S. Schnable and S. Aluru, "Assembling genomes on large-scale
    parallel computers," Journal of Parallel and Distributed Computing, Vol. 67, pp. 1240-1255, 2007.

  • S.J. Emrich, L. Li, T.-J. Wen, M.D. Yandeau-Nelson, Y. Fu, L. Guo, H.-H. Chou, S. Aluru, D.A.
    Ashlock and P.S. Schanble, "Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution," Genetics, Vol. 175, pp. 429-439, 2007. (featured in Science, Vol. 315, No.
    5810, pp. 302 in Editor's Choice: Highlights of the recent literature).

Vita: Click here to download

Website: Srinivas Aluru

*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


Selected Publications:

  • Min, L., Wu, W., Joseph, R., Fulton, D.B., Berg, L., & Andreotti, A.H. (2010). Disrupting the intermolecular self-association of Itk enhances T cell signaling. Journal of Immunology: 184, 4228-4235.

  • Berge, T., Sundvold-Gjerstad, V., Granum, S., Andersen, T.C., Holthe, G.B., Claesson-Welsh, L., Andreotti, A.H., Inngjerdingen, M., & Spurkland, A. (2010). T cell specific adapter protein (TSAd) interacts with Tec kinase ITK to promote CXCL12 induced migration of human and murine T cells. PLoS One: 2010 5, 3, e9761.

  • Min, L., Joseph, R.E., Fulton, D.B., & Andreotti, A.H. (2009). Itk tyrosine kinase substrate docking is mediated by a nonclassical SH2 domain surface of PLCgamma1. Proceedings of the National Academy of Science, USA: 106, 21143-21148.

  • Joseph, R.E., Severin, A., Min, L., Fulton, D.B., & Andreotti, A.H. (2009). SH2-dependent autophosphorylation within the Tec family kinase Itk. J Mol Biol. 391, 164-177.

  • Severin, A., Joseph, R.E., *Boyken, S., Fulton, D.B., & Andreotti, A.H. (2009). Proline isomerization preorganizes the Itk SH2 domain for binding the Itk SH3 domain, Journal of Molecular Biology: 387, 726-743.

  • Joseph, R.E. & Andreotti, A.H. (2009). Conformational snapshots of Tec kinases during signaling. Immunological Reviews: 228, 74-92.

  • R.E. Joseph, A.H. Andreotti , Bacterial expression and purification of interleukin-2 tyrosine kinase: single step separation of the chaperonin impurity. Protein Expr Purif., 60, 194-7 (2008).

  • A. Severin, D.B. Fulton, A.H. Andreotti, Murine Itk SH3 domain. J Biomol NMR.40, 285-90 (2008).

Vita: Click here to download

Website: Amy Andreotti

Lyric Bartholomay

BCB Faculty Member in the Entomology Department

Education: Ph.D., University of Wisconsin-Madison, 2004

Research Interests:

  • Invertebrate immunity as a key contributor to host-pathogen interactions between mosquitoes and mosquito-borne pathogens, ticks and tick-borne pathogens, and cultured shrimp and pathogenic viruses. BCB tools and expertise are used in my lab in the context of transcriptomics, but also have been used to quantify and relay data from mosquito surveillance efforts from my lab.

Selected Publications:

  • Bartholomay, L. C., Loy, D. S., Loy, J. D., & Harris, D. L. H. (2012). Nucleic-acid based antivirals: augmenting RNA interference to ‘vaccinate’ Litopenaeus vannamei. Journal of Invertebrate Pathology: 110, 261-266.
  • Stentiford, G. D., Neil, D. M., Peeler, E., Shields, J. D., Small, H. J., Flegel, T. W., Vlak, J., Jones, B., Morado, F., Moss, S., Lotz, J., Bartholomay, L., Reantaso, M., Behringer, D. C., Hauton, C., & Lightner, D. V. (2012). Disease will limit future food supply from the global crustacean fishery and aquaculture sectors Journal of Invertebrate Pathology: 110, 141-157.
  • Loy, D. L., Mogler, M. A., Loy, D. S., Janke, B., Kamrud, K., Scura, E. D., Harris, D. L. H., & Bartholomay, L. C. (2012). Double Stranded RNA Provides Sequence Dependent Protection Against Infectious Myonecrosis Virus in Litopenaeus vannamei. Journal of Genetic Virology: 93, 880-888.
  • Oliver, J.D., Dusty Loy, J., Parikh, G., Bartholomay, L., 2011. Comparative analysis of hemocyte phagocytosis between six species of arthropods as measured by flow cytometry, Journal of Invertebrate Pathology doi: 10.1016/j.jip.2011.07.004
  • Song, C, Gallup, JM, Day, TA, Bartholomay, LC, Kimber, MJ, 2010. Development of an in vivo RNAi protocol to investigate gene function in the filarial nematode, Brugia malayi. PLoS Pathogens 6(12): e1001239.
  • Michalski ML, Erickson SM, Bartholomay LC, Christensen BM. 2010. Midgut barrier imparts selective resistance to filarial worm infection in Culex pipiens pipiens. PLoS Neglected Tropical Diseases 4:e875.
  • Bartholomay, LC, Waterhouse, RM, Mayhew, GF, Campbell, CL, Michel, K, Zou, Z, Ramirez, JL, Das, S, Alvarez, K, Arensburger, P, Byrant, B, Chapman, SB, Dong, Y, Erickson, SM, Pakarama Karunaratne, SHP, Kokoza, V, Kodira, CD, Pignatelli, P, Shin, SW, Vanlandingham, DL, Atkinson, PW, Birren, B, Christophides, GK, Clem, RJ, Hemingway, J, Higgs, S, Megy, K, Ranson, H, Zdobnov, EM, Raikhel, AS, Christensen, BM, Dimopoulos, G, Muskavitch, MAT. 2010.Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens. Science 330: 88-90.
  • Arensburger, P, Megy, K, Waterhouse, RM, Abrudan, J, Amedeo, P, Antelo, B, Bartholomay, L, Bidwell, S, Caler, E, Camara, F, Campbell, CL, Campbell, KS, Casola, C, Castro, MT, Chandramouliswaran, I, Chapman, SB, Christley, S, Costas, J, Eisenstadt, E, Feshotte, C, Fraser-Liggett, C, Guigo, R, Haas, B, Hammond, M, Hansson, BS, Hemingway, J, Hill, S, Howarth, C, Ignell, R, Kennedy, RC, Kodira, CD, Lobo, NF, Mao, C, Mayhew, G Michel, K, Mori, A, Liu, N, Naveira, H, Nene, V, Nguyen, N, Pearson, MD, Pritham, EJ, Puiu, D, Qi, Y, Ribeiro, JMC, Hugh M. Roberston, HM, Severson, DW, Shumway, M, Stanke, M, Strausberg, R, Sun, C, Sutton, G, Tu, Z, Tubio, JMC, Unger, MF, Vanlandingham, DL, Vilella, AJ, White, O, White, JR, Wortman, J, Zdobnov, EM, Birren, B, Christensen, BM, Collins, F, Cornel, A, Dimopoulos, G, Hannick, LI, Higgs, S, Lanzaro, G, Lawson, D, Lee, NH, Muskavitch, MAT, Raikhel, A, Atkinson, P. 2010. Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science 330: 86-88.
  • Staley, M. Dorman, KS, Bartholomay, LC, Fernández-Salas, I, Farfan-Ale, JA, Lorono-Pino, MA, Garcia Rejon, JE, Ibarra-Juarez, L, Blitvich, BJ. 2010. Universal primers for the amplification and sequence analysis of actin-1 from diverse mosquito species. Journal of the American Mosquito Control Association 26(2): 214-8.
  • Paluch, G, Bartholomay, L, Coats, J. 2010. Mosquito repellents: a review of chemical structure diversity and olfaction. Pest Management Science (Published Online: Jul 9 2010)
  • Larson, SR, DeGroote, JP, Bartholomay, LC, Sugumaran, R. 2010. Ecologicalniche modeling of potential West Nile virus vector mosquito species in Iowa. Journal of Insect Science vol. 10 article 110.
  • Girard, YA, Mayhew, GF, Fuchs, JF, Li, H, Schneider, BS, McGee, CE, Rocheleau, TA, Helmy, H, Christensen, BM, Higgs, S, Bartholomay, LC. 2010. Transcriptome changes in Culex quinquefasciatus (Diptera: Culicidae) salivary glands during West Nile virus infection. Journal of Medical Entomology47 (3): 421-35.
  • Farfan-Ale, JA, Lorono-Pino, MA, Garcia-Reion, JE, Soto, V, Lin, M, Staley, M, Dorman, KS, Bartholomay, LC, Hovav, E, Blitvich, BJ. 2010. Detection of flaviviruses and orthobunyaviruses in mosquitoes in the Yucatan Peninsula of Mexico in 2008. Vector-Borne and Zoonotic Diseases April 6 [Epub ahead of print].

Vita: Click here to download

Website: Lyric Bartholomay

*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

*Adam Bogdanove

Adam is no longer at ISU in the Plant Pathology Department

Education: Ph.D., Cornell, 1997

Research Interests: Genomic and proteomic approaches to bacterial plant diseases and plant disease resistance

  • Functional and Structural Genomics-- Genomic and proteomic approaches to bacterial plant pathology and plant disease resistance mechanisms, including bacterial genomic sequence analysis and protein profiling, and plant microarray and mutational analyses
  • Information Integration and Data Mining


Selected Publications:

  • Moscou, M.J. and Bogdanove, A.J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326 (5959):1501.

    See also About the Cover, Science 326 (5959)
  • Voytas, D.J. and Joung, J.K. (2009) DNA binding made easy. Science 326 (5959):1491-1492.
  • Pennisi, E. (2010). Sowing the seeds for the ideal crop. Science 327, 802-803.
  • Salzberg, S.L., Sommer, D.D., Schatz, M.C., Phillippy, A.M., Rabinowicz, P.D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A.L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P.B., Ishihara, H., Meyer, D.F., Szurek, B., Verdier, V., Koebnik, R., Dow, J.M., Ryan, R.P., Hirata, H., Tsuyumu, S., Lee, S.W., Ronald, P.C., Sonti, R.V., Van Sluys, M.-A., Leach, J.E., White, F.F., and Bogdanove, A.J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 9:204.

Vita: Click here to download

Publications: here

ebsite: Adam Bogdanove

*Volker Brendel

Volker has left ISU and is no longer a BCB Faculty Member in the GDCG Department

Education: Ph.D., Weizmann ( Israel), 1986

Research Interests: Gene identification, pre-mRNA splicing

Description: Plant genomics and molecular genetics

  • Bioinformatics-- Algorithms for gene identification in genomic sequences; sequence alignment methods; plant transposon molecular biology; molecular phylogeny

Selected Publications:

  • Lushbough, C., Bergman, M.K., Lawrence, C.J., Jennewein, D., & Brendel, V. (2010). BioExtract Server - an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data. IEEE/ACM Transactions Comp. Biol. Bioinformatics: 7, 7-24. [ PubMed ID: 20150665] [ online abstract] [ preprint request]
  • Sen, T.Z., *Andorf, C.M., Schaeffer, M.L., Harper, L.C., Sparks, M.E., Duvick, J., Brendel, V.P., Cannon, E., Campbell, D.A., & Lawrence, C.J. (2009). MaizeGDB becomes ‘sequence-centric’. Database 2009, bap020. [ PubMed ID: not yet available] [ online article] [ PDF]
  • Wilkerson, M.D., Ru, Y., & Brendel, V.P. (2009). Common introns within orthologous genes: software and application to plants. Briefings Bioinformatics: 10, 631-644. [ PubMed ID: 19933210] [ online abstract] [ online article] [ PDF]
  • Ahern, K.R., Deewatthanawong, P., Schares, J., Muszynski, M., Weeks, R., Vollbrecht, E., Duvick, J., Brendel, V.P., & Brutnell, T.P. (2009). Regional mutagenesis using Dissociation in maize. Methods: 49, 248-254. [ PubMed ID: 19394430] [ online abstract] [ reprint request]
Vita: Click here to download

Website: Volker Brendel

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

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:

  • Bolon, Y.-T., Joseph, B., Cannon, S. B., Graham, M. A., Diers, B.W., Farmer, A.D., May, G.D., Muehlbauer, G.J., Specht, J.E., Tu, Z.J., Weeks, N., Xu, W.W., Shoemaker, R.C., & Vance, C.P. (2010). Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biology: 10, 41.

  • Schmutz, J. and Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D., Song, Q., Thelen, J.J., Cheng, J., Xu, D., Hellsten, U., May, G.D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, S., Goodstein, D., Barry, K., Futrell-Griggs, M., Du, J., Tian, Z., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X.-C., Shinozaki, K., Nguyen, H.T., Wing, R.A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R.C., & Jackson, S.A. (2010). Genome sequence of the paleopolyploid soybean. Nature: 463, 178-183.

  • Hyten, D.L. and Cannon, S. B., Song, Q., Weeks, N. T., Fickus, E. W., Shoemaker, R. C., Specht, J.E., Farmer, A.D., May, G. D., & Cregan, P. B. (2010). High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and orient Scaffolds in the Soybean Whole Genome Sequence. BMC Genomics: 11, 38.

  • David, P. and Chen, N., Pedrosa-Harand, A., Sevignac, M., Thareau, V., Cannon, S. B., Debouck, D., Langin, T., & Geffroy, V. (2009). A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean. Plant Physiology: 151, 1048-1065.

  • Grant, D.M. and Nelson, R.T., Cannon, S.B., & Shoemaker, R. C. SoyBase, The USDA-ARS Soybean Genetics and Genomics Database. Nucleic Acids Research: 38, D847-D853.

  • Zhang, X.-C. and Cannon, S.B., Stacey, G. (2009). Evolutionary Genomics of LysM Genes in Land Plants. BMC Evolutionary Biology: 9, 183.

  • Singer, S.R. and Maki, S.L., Farmer, A.D., Ilut, D., May, G.D., Cannon, S.B., & Doyle, J.D. (2009). Venturing beyond beans and peas: what can we learn from Chamaecrista? Plant Physiology: 151, 1041-1047.

  • Cannon, S.B., May, G.D., & Jackson, S.A. (2009). Three sequenced legumes and many species: rich opportunities for translational genomics. Plant Physiology: 151, 970-977.

  • Bertioli, D. and Moretzsohn, M., Madsen, L.H., Sandal, N., Leal-Bertioli, S., Guimares, P., Hougaard, B.K., Fredslund, J., Shauser, L., Nielsen, A.M., Sato, S., Tabata, S., Cannon, S.B., & Stougaard, J. (2009). An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics: 10, 45.

  • O’Rourke, J.A. and Nelson, R.T., Grant, D., Schmutz, J., Grimwood, J., Cannon, S.B., Vance, C. P., Graham, M.A., & Shoemaker, R.C. (2009). Integrating microarray analysis and the soybean genome to understand the soybean's Iron Deficiency response. BMC Genomics: 10, 376.


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:

  • 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:
  • 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, 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

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:

  • 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
  • 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.

Vita: Click here to download

Website: Philip Dixon

*Drena Dobbs

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: Long-term research goals of the Dobbs group are to understand how proteins and nucleic acids achieve their functional three-dimensional structures and to elucidate mechanisms that determine recognition and regulate interactions among proteins, nucleic acids and other molecules in cells.  We use both computational and wet-lab experimental approaches to explore the structure and function of important macromolecular complexes, in close collaboration with several groups at Iowa State, University of Minnesota, and Harvard University.

Current areas of focus include: development of novel antiviral therapies against HIV-1 and other lentiviruses; rational design of zinc finger proteins (ZFPs) as tools for genomic modification and gene therapy; prediction of epitopes and nucleic acid binding residues in proteins; and prediction and experimental validation of structural and functional effects of mutations and SNPs in proteins. For details, please visit the Dobbs Lab website:

Selected Publications:

  • 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

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:

  • Krishnan, S., Strasburg, C. S.F, Lutz, R. R., Goseva-Popstojanova, K., & Dorman, K. S. (2012). Predicting failure-proneness in an evolving software product line. In formation and Software Technology, To Appear.
  • Blitvich, B. J., Loro~no-Pino, M. A., Garcia-Rejon, J. E., Farfan-Ale, J. A., & Dor man, 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., & Loro~no-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., Loro~no-Pino, M. A., Garcia-Rejon, J. E., Farfan-Ale, J. A., & Dorman, K. S. (2012). Identi cation of a novel subtype of South River virus (family Bunyaviridae). Archives of Virology, 157, 1205{1209.
  • Wu, W., Blythe, D. C.F., 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.
  • Yang, X., Aluru, S., and Dorman, K.S. (2011). Repeat-aware modeling and detection of short read errors. BMC Bioinformatics, 12, S52.
  • Yang, X., Dorman, K.S., and Aluru, S. (2010). Reptile: representative tiling for short read error correction, Bioinformatics, 26, 2526-2533.
  • 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, 3, 398-412.
  • Soto, V., Dorman, K.S., Miller, W.A., Farfan-Ale, J.A., Loroo-Pino, M.A., Garcia- Rejon, J.E., & Blitvich, B.J. (2009). Complete nucleotide sequences of the small and medium RNA genome segments of Kairi virus (family Bunyaviridae). Archives of Virology: 154, 9, 1555-1558.
  • Blitvich, B.J., Lin, M., Dorman, K.S., Soto, V., Hovav, E., Tucker, B.J., Staley, M., Platt, K.B., & Bartholomay, L.C. (2009). Genomic sequence and phylogenetic analysis of Culex flavivirus, an insect-specific flavivirus, isolated from Culex pipiens in Iowa. Journal of Medical Entomology: 46, 4, 934-941.
  • J. A. Farfan-Ale, M. A. Loro~no-Pino, J. E. Garcia-Rejon, E. Hovav, A. M. Powers, M. Lin, K. S. Dorman, K. B. Platt, L. C. Bartholomay, V. Soto, B. J. Beaty, R. S. Lanciotti, B. J. Blitvich. (2008) Detection of RNA from a novel West Nile-like virus and high prevalence of an insect-specific avivirus in mosquitoes in the Yucatan Peninsula of Mexico. American Journal of Tropical Medicine & Hygiene. Accepted.
  • E. W. Bloomquist, K. S. Dorman, M. A. Suchard (2008) StepBrothers: inferring spatially shared ancestries among recombinant viral sequences. Biostatistics. In press.
  • G. M. Dancik, K. S. Dorman (2008) mlegp: statistical analysis for computer models of biological systems using R. Bioinformatics. Accepted.
  • B. Su, W. Zhou, K. S. Dorman, D. E. Jones. (2008) Mathematical modeling of immune response in tissues. Computational and Mathematical Methods in Medicine. Accepted.
  • W. O. Sparks, K. S. Dorman, S. Liu, S. Carpenter. (2008) Selection on Rev during persistent equine infectious anemia virus infection. Journal of General Virology. 89:1043-1048.

Vita: Click here to download

Website: Karin Dorman

Oliver Eulenstein

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

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

M. H. West Greenlee

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

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

*Eric Henderson

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. (2012) Complex DNA Nanostructures from Oligonucleotide Ensembles, American Chemical Society: Synthetic Biology.
  • 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.


Kai-Ming Ho

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

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

*Vasant Honavar

Education: Ph.D., Wisconsin, Madison, 1990

Research Interests:

  • Artificial Intelligence: Intelligent agent architectures, Multi-agent organizations, Inter-agent interaction, and Multi-agent coordination, Logical, probabilistic, and decision-theoretic knowledge representation and inference, Neural architectures for knowledge representation and inference, Computational models of perception and action
  • Bioinformatics and Computational Molecular and Systems Biology: Data-driven discovery of macromolecular sequence-structure-function-interaction-expression relationships, identification of sequence and structural correlates of protein-protein, protein-RNA, and protein-DNA interactions, protein sub-cellular localization, automated protein structure and function annotation, modeling and inference of genetic regulatory networks from gene expression (micro-array, proteomics) data, modeling and inference of signal transduction and metabolic pathways, comparative analysis of biological networks (network alignment), integrative analysis of molecular interaction networks and macro-molecular interfaces.
  • Data Mining: Design, analysis, implementation, and evaluation of algorithms and software for data-driven knowledge acquisition, data and knowledge visualization, and collaborative scientific discovery from semantically heterogeneous, distributed data and knowledge sources, Applications to data-driven knowledge acquisition tasks in bioinformatics, medical informatics, geo-informatics, environmental informatics, chemo-informatics, security informatics, social informatics, critical national infrastructure (communication networks, energy networks) e-government, e-commerce, and e-science.
  • Machine Learning: Statistical, information theoretic, linguistic and structural approaches to machine learning, Learning and refinement of bayesian networks, causal networks, decision networks, neural networks, support vector machines, kernel classifiers, multi-relational models, language models (n-grams, grammars, automata), Learning classifiers from attribute value taxonomies and partially specified data; Learning attribute value taxonomies from data; Learning classifiers from sequential and spatial data; Learning relationships from multi-modal data (e.g., text, images), Learning classifiers from distributed data, multi-relational data, and semantically heterogeneous data; Incremental learning, Ensemble methods, multi-agent learning, selected topics in computational learning theory.
  • Semantic Web: Semantic Web: Ontology-based and probabilistic approaches to information integration; description logics, federated data bases - statistical queries against federated databases, knowledge bases - federated reasoning, selective knowledge sharing, services - service composition, substitution, and adaptation; epistemic description logics; secrecy-preserving query answering, representing and reasoning about qualitative preferences.
  • Other Topics of Interest: Biological Computation - Evolutionary, Cellular and Neural Computation, Complex Adaptive Systems, Sensory systems and behavior evolution, Language evolution, Mimetic evolution; Computational Semiotics - Origins and use of signs, emergence of semantics; Computational organization theory; Computational Neuroscience; Computational models of creativity, Computational models of discovery.


Selected Publications:

  • Caragea, C., Caragea, D., Silvescu, A., and Honavar, V. Semi-Supervised Prediction of Protein Subcellular Localization Using Abstraction Augmented Markov Models. , BMC Bioinformatics, Special Issue on Machine Learning in Computational Biology (MLCB), 2010. In press.
  • El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2010). Predicting MHC-II binding affinity using multiple instance regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
  • Towfic, F., VanderPlas, S., Oliver, C.A., Couture, O., Tuggle, C.K., Greenlee, M.H.W., and Honavar, V. (2010). Detection of gene orthology from gene co-expression and protein interaction networks. BMC Bioinformatics, BMC Bioinformatics 2010, 11 (Suppl 3): S7 doi:10.1186/1471-2105-11-S3-S7
  • Bromberg, F., Margaritis, D., and Honavar, V. (2009). Efficient Markov Network Structure Discovery from Independence Tests. Journal of Artificial Intelligence Research. Vol. 35. pp. 449-485.
  • Towfic, F., Greenlee, H., and Honavar, V. (2009). Aligning Biomolecular Networks Using Modular Graph Kernels. In: Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009). Berlin: Springer-Verlag: LNBI Vol. 5724, pp. 345-361.
  • El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition, DOI:10.1002/jmr.893. vol. 21. pp. 243-255.
  • El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). On Evaluating MHC-II Binding Peptide Prediction Methods. PLoS One, 3(9):e3268
  • Peto M., Kloczkowski A., Honavar V., Jernigan R.L. (2008). Use of machine learning algorithms to classify binary protein sequences as highly designable or poorly-designable. BMC Bioinformatics, 9:487
  • Yan, C., Wu, F., Jernigan, R.L., Dobbs, D., Honavar, V. (2008) Analysis of Protein-Protein Interfaces. The Protein Journal 27 :59-70.
  • Andorf, C., Dobbs, D., and Honavar, V. (2007). Exploring Inconsistencies in Large-Scale Protein Function Annotations: A Machine Learning Approach. BMC Bioinformatics.
  • Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D. And Honavar, V. (2007). Glycosylation Site Prediction Using Ensembles of Support Vector Machine Classifiers. BMC Bioinformatics. doi:10.1186/1471-2105-8-438
  • Terribilini, M., Sander, J.D., Lee, J-H., Zaback, P., Jernigan, R.L., Honavar, V. and Dobbs, D. (2007). RNABindR: A Server for Analyzing and Predicting RNA Binding Sites in Proteins. Nucleic Acids Research. Vol. 35. No. 9. pp. doi:10.1093/nar/gkm2, 2007
  • Terribilini, M., Lee, J.H., Yan, C., Jernigan, R., Honavar, V., and Dobbs, D. (2006). Computational Prediction of Protein-RNA Interfaces. RNA Journal. Vol. 12. No. 1450. pp. 1462, 2006.
  • Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D. and Honavar, V. (2006). Identifying amino acid residues involved in protein-DNA interactions from sequence. BMC Bioinformatics. Vol. 7. pp. 262-, 2006.

Vita: Click here to download

Website: Vasant Honavar

Richard Honzatko

Faculty Member

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

Xiaoqiu Huang

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

Matt 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

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:

Vita: Click here to download

Website: Laura Jarboe


*Robert Jernigan

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:
  • Feng, F., Kloczkowski, A., & Jernigan, R.L. ( 2010). Potentials'R'Us web -server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinformatics: 11, 92.

  • Saraswathi, S., Sundaram, S., Sundararajan, N., Zimmermann, M. & Nilsen-Hamilton, M. (2010). ICGA-PSO-ELM approach for Accurate Cancer Classification Resulting in Reduced Gene Sets Involved in Cellular Interface with the Microenvironment. IEEE Transactions in Bioinformatics and Computational Biology. Preprint:

  • Feng, F., Kloczkowski, A., & Jernigan, R.L. ( 2010). Potentials'R'Us web -server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinformatics: 11, 92.

  • Zimmermann, M.T., Towfic, F., Jernigan, R.L., & Kloczkowski, A. (2009) Short Paths in Protein Structure Space Originate in Graph Structure. PNAS: 106, 51, E138.

  • Yang, L., Song, G., & Jernigan, R.L. (2009). Comparisons of Experimental and Computed Protein Anisotropic Temperature Factors. Biophysical Journal: 76, 164-175.

  • Kurkcuoglu O., Kurkcuoglu Z., Doruker P., & Jernigan R.L. (2009). Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins: 75, 837-845.

  • 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.

  • Schuyler, A.D., Jernigan, R.L., Qasba, P.K., Ramakrishnan B., & Chirikjian, G.S. (2009). Iterative cluster-NMA (icNMA): A tool for generating conformational transitions in proteins.  Proteins: 74, 760-776.

  • Yang, L., Song, G., & Jernigan, R.L. (2009). Protein elastic network models and the ranges of cooperativity.  Proc Natl Acad Sci USA: 106, 12347-12352.

  • Feng, Y., Kloczkowski, A., & Jernigan, R.L. (2009). The energy profiles of atomic conformational transition intermediates of adenylate kinase.  Proteins: 77, 551-558.

  • Feng, C., Mukhopadhyay, K., Young, W-B., Jernigan, R.L., & Wu, Z. (2009). Refinement of under-determined loops of human prion protein by database-derived distance constraints.  Int J Data Mining and Bioinformatics: 3, 454-468.

  • Kurkcuoglu, O., Turgut, O.T., Cansu, S., Jernigan, R.L., & Doruker, P. (2009). Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model. Biophys J: 97, 1178-1187.

  • Sun, X., Wu, D., Jernigan, R.L., Wu, Z.  (2009). PRTAD: A database for protein residue torsion angle distributions. Int J Data Mining and Bioinformatics: 3, 469-482.

  • Rashin, A.A., Rashin, A.H.L., & Jernigan, R.L.  (2009). Protein Flexibility: Coordinate uncertainties and interpretation of structural differences. Acta  Crystal: D65, 1140 - 1161.

  • Zimmermann, M., Towfic, F., Jernigan, R.L., & Kloczkowski (2009). Short paths in protein structure space originate in graph structure. Proc Natl Acad Sci USA: A106, E137.

Resume: Click here to download

Website: Robert Jernigan

Douglas Jones

BCB Faculty Member

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

Susan Lamont

BCB Faculty Member

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

  • 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 disease resistance, growth and development.

Selected Publications:

  • Wang, C., Habier, D., Peiris, L., Wolc, A., Kranis, A., Watson, K., Avendano, S.,  Garrick, D., Fernando, R.,  Lamont, S.,  Dekkers, J.  2013 (in press).  Accuracy of genomic prediction using an evenly spaced, low-density SNP panel in broiler chickens. Poultry Sci.
  • 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
  • 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

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:

  • Sen, T.Z., Harper, L.C., Schaeffer, M.L., Andorf, C.M., Seigfried, T.E., Campbell, D.A., & Lawrence, C.J. (2010). Choosing a genome browser for a Model Organism Database: Surveying the Maize community. Database: 2010, baq007, doi:10.1093/database/baq007.

  • Andorf, C.M., Lawrence, C.J., Harper, L.C., Schaeffer, M.L., Campbell, D.A., & Sen, T.Z. (2010). The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps. Bioinformatics: 26, 434-436.

  • Sen, T.Z., Andorf, C.M., Schaeffer, M.L., Harper, L.C., Sparks, M.E., Duvick, J., Brendel, V.P., Cannon, E., Campbell, D.A., & Lawrence, C.J. (2009), MaizeGDB becomes 'sequence-centric' Database 2009:bap020; doi: 10.1093/database/bap020.

  • Yi, G., Luth, D., Goodman, T.D., Lawrence, C.J., & Becraft, P.W. (2009). High-throughput linkage analysis of Mutator insertion sites in maize. Plant Journal: 58, 5, 883-892.

Vita: Click here to download

Website: Carolyn Lawrence

Howard Levine

Education: Ph.D., Cornell, 1969

Research Interests: Modeling of angiogenesis and tumor growth, chemotaxis in biological systems. Mathematical modeling of transport and branching processes in biological systems

  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Mathematical modeling of biological branching processes including angiogenesis, vasculogenesis, neuronal growth, mammary duct development involving cell-cell and intra cellular signal transduction pathways.

Selected Publications:

  • Levine, H. A. and M. Nilsen-Hamilton A mathematical analysis of SELEX, Journal of Computational Biology and Chemistry , 31 (2007) 11-35 K.
  • Boushaba, Levine, H. A and Nilsen-Hamilton, M., A mathematical model for the regulation of metastatic tumor dormancy based on enzyme kinetics, Bull. Math. Biol., 68, 2006, 1-32.
  • Levine, H. A. and Smiley, M. W. , Tucker, A. and Nilsen-Hamilton, M) A mathematical model for the formation of avascular tumors based on the role of the p53 tumor suppressor gene, Cancer Informatics, 2, 2006 , 163-188.
  • Levine, H. A. and M. Nilsen-Hamilton, Angiogenesis-A Biochemical/Mathematical Perspective, Chapter 2., in Tutorials in mathematical biosciences: Cell cycle, proliferation, and cancer (Vol. 3). A. Friedman,ed., Springer-Verlag, Berlin, Heidelberg, New York , 2006.
  • Levine, H. A. , Renclawowicz, J., Singularity formation in chemotaxis - A conjecture of Nagai\jour( SIAM J. Appl. Math., ) 65(1) , 2004, 336-362 Hillen , T. and Levine, H. A. Blow up and pattern formation in hyperbolic models for chemotaxis, ZAMP 54, 2003 839-868.
  • Levine, H. A., Tucker, A. and Nilsen-Hamilton, M., A mathematical model for the role of cell signal transduction in the initiation and inhibition of angiogenesis, Growth Factors, 20(4), 2002, 155-175.
  • Levine, H. A. and Sleeman, B.,D. Modelling Tumour Induced Angiogenesis, Chapter 6, in: Cancer Modelling and Simulation, L. Preziozi, eds., Chapman and Hall/CRC Press, 2003, pp. 147-183. Levine, H. A., Pamuk, S., Sleeman, B. D. and Nilsen-Hamilton, M., Mathematical modeling of capillary formation and development in tumor angiogenesis: penetration into the stroma, Bull. Math. Biol., 63(5), 2001, 801-863.
  • Levine, H. A., S. Pamuk, B. D. Sleeman and Nilsen-Hamilton, M. Mathematical modelling of tumor angiogenesis and the action of angiostatin as a protease inhibitor, J. Theoret. Med. 4(2) 2002 133-145.
  • Levine, H. A., Sleeman, B. D. and Nilsen-Hamilton, M., Mathematical Modeling of the initiation of capillary formation initiating angiogenesis, J. Math. Biol., 42(3), 2001, 195-238.
  • Levine, H. A., Sleeman, B. D. and Nilsen-Hamilton, M., A mathematical model for the roles of pericytes and macrophages in the initiation of angiogenesis: I. The role of protease inhibitors in preventing angiogenesis., Mathematical Biosciences, 168, 2000, 77-115.

Vita: Click here to download

Website: Howard Levine

Peng Liu

BCB Faculty Member

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

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

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

Anastasios Matzavinos

Education: Ph.D., 2004, Dundee (Scotland)

Research Interests: Applied mathematics, mathematical biology, data clustering algorithms.

Selected Publications:

  • Anastasios Matzavinos, Alexander Roitershtein, Blerta Shtylla, Zachary Voller, Sijia Liu, and Mark Chaplain, 2011, Stochastic modelling of chromosomal segregation: Errors can introduce correction. Submitted.
  • .J. Giedt, D.R. Pfeiffer, A. Matzavinos, C.-Y. Kao, B.R. Alevriadou, 2011, Mitochondrial dynamics and motility inside living vascular endothelial cells: Role of bioenergetics. Submitted.  
  • Sijia Liu, Anastasios Matzavinos, and Sunder Sethuraman, 2011, Random walk distances in data clustering and applications. Submitted.  
  • Kelsey Schafer, Sohee Kim, Anastasios Matzavinos, and Jeff Kuret, 2011, Selectivity requirements for diagnostic imaging of neurofibrillary lesions in Alzheimer's disease: a simulation study. To appear in NeuroImage.   [Link]
  • R.J. Giedt, C. Yang, J.L. Zweier, A. Matzavinos, and B.R. Alevriadou, 2011, Mitochondrial fission in endothelial cells following simulated ischemia/reperfusion: Role of nitric oxide and mitochondrial reactive oxygen species. To appear in Free Radical Biology & Medicine.   [Link]
  • Iddo Ben-Ari, Anastasios Matzavinos, and Alexander Roitershtein, 2011, On a species survival model. Electronic Communications in Probability, 16: 226–233.   [Link]
  • I. Ben-Ari, K. Boushaba, A. Matzavinos, and A. Roitershtein, 2011, Stochastic analysis of the motion of DNA nanomechanical bipeds. Bulletin of Mathematical Biology, 73 (8): 1932-1951.   [Link]
  • O. Cominetti, A. Matzavinos, S. Samarasinghe, D. Kulasiri, S. Liu, P.K. Maini, and R. Erban, 2010, DifFUZZY: A fuzzy clustering algorithm for complex data sets. International Journal of Computational Intelligence in Bioinformatics and Systems Biology. 1(4): 402-417.   [PDF]
  • K. Preedy, P.G. Schofield, S. Liu, A. Matzavinos, M. Chaplain, S.F. Hubbard, 2010, Modelling contact spread of infection in host-parasitoid systems: vertical transmission of pathogens can cause chaos. Journal of Theoretical Biology. 262 (3): 441-451.   [Link] Reference [8] is one of the ScienceDirect Top 25 Hottest Articles for October 2009 - September 2010.
  • B. Joshi, X. Wang, S. Banerjee, H. Tian, A. Matzavinos, and M. Chaplain, 2009, On immunotherapies and cancer vaccination protocols: A mathematical modelling approach. Journal of Theoretical Biology, 259 (4): 820-827.   [Link] Part of Ref. [7] appeared in 2008 in the Mathematical Biosciences Institute Technical Report Series (Technical Report No. 75).
  • A. Matzavinos, C.-Y. Kao, J.E.F. Green, A. Sutradhar, M. Miller, and A. Friedman, 2009, Modeling oxygen transport in surgical tissue transfer. PNAS, 106 (29): 12091-12096.   [Link] Links to some press releases on Reference [6]: Science Daily, Math in the News, ISU news release.
  • E.E. Congdon, S. Kim, J. Bonchak, T. Songrug, A. Matzavinos and J. Kuret, 2008, Nucleation dependent tau filament formation: The importance of dimerization and an estimation of elementary rate constants. Journal of Biological Chemistry, 283 (20): 13806-13816.  [Link]
  • A. Matzavinos and H.G. Othmer, 2007, A stochastic analysis of actin polymerization in the presence of twinfilin and gelsolin. Journal of Theoretical Biology, 249 (4): 723-736.  [Link] Reference [4] is one of the ScienceDirect Top 25 Hottest Articles for October 2007 - December 2007.
  • J. Hu, A. Matzavinos, and H.G. Othmer, 2007, A theoretical approach to actin filament dynamics. Journal of Statistical Physics, 128 (1): 111-138.  [Link]
  • A. Matzavinos and M. Chaplain, 2004, Travelling wave analysis of a model of the immune response to cancer. Comptes Rendus Biologies, 327: 995-1008.  [Link]
  • A. Matzavinos, M. Chaplain and V. Kuznetsov, 2004, Mathematical modelling of the spatio-temporal response of cytotoxic T-lymphocytes to a solid tumour. Mathematical Medicine and Biology: A Journal of the IMA, 21: 1-34.  [Link] Reference [1] has been cited as one of the 50 most-frequently cited articles in Math. Med. Biol.

Vita: Click here to download

Website: Tasos Matzavinos


Leslie Miller

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

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

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:

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

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:

  • Nettleton, D. (2009). Testing for the supremacy of a multinomial cell probability. Journal of the American Statistical Association: 104, 1052-1059.

  • Schnable, P.S. et al. (2009). The B73 maize genome: complexity, diversity and dynamics. Science: 326, 1112-1115.

  • Swanson-Wagner, R.A., DeCook, R., Jia, Y., Bancroft, T., Ji, T., Zhao, X., Nettleton, D., & Schnable, P.S. (2009). Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science: 326, 1118-1120.

  • Jia, Y., Lisch, D.R., Ohtsu, K., Scanlon, M.J., Nettleton, D., & Schnable, P.S. (2009). Loss of RNA-dependent RNA Polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes and 24-nt small RNAs. PLoS Genetics: 5, 11, e1000737.

  • Springer, N.M., Ying, K., Fu, Y., Ji, T., Yeh, C.T., Jia, Y., Wu, W., Richmond, T., Kitzman, J., Rosenbaum, H., Iniguez, A.L., Barbazuk, W.B., Jeddeloh, J.A., Nettleton, D., & Schnable, P.S. (2009). Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics: 5, 11, e1000734.

  • Liu, S., Yeh, C.T., Ji, T., Ying, K., Wu, H., Tang, H.M., Fu, Y., Nettleton, D., & Schnable, P.S. (2009). Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genetics: 5, 11, e1000733.

  • 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). 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, 98-111.

  • Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Eudy, D., Pawlowska, T., Ware, D., Janick-Buckner, D., Buckner, B., Timmermans, M.C.P., Schnable, P.S., Nettleton, D., & Scanlon, M.J. (2009). Microdissection of shoot meristem functional domains. PLoS Genetics: 5, 5, e1000476.

  • Schwab, C.R., Baas, T.J., Stalder, K.J., & Nettleton, D. (2009). Results from six generations of selection for intramuscular fat in Duroc swine using real time ultrasound. I. Direct and correlated phenotypic responses to selection. Journal of Animal Science: 87, 2774-2780.

  • Liu, Z., Henderson, A.L., Nettleton, D., Wilson-Welder, J.H., Hostetter, J.M., Ramer-Tait, A., Jergens, A.E., & Wannemuehler, M.J. (2009). Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to Typhlocolitis. Microbes and Infection: 11, 374-383.

  • Li, L. Foster, C., Gan, Q., Nettleton, D., James, M., Myers, A., & Wurtele, E. (2009). Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. The Plant Journal: 58, 485-498.

  • Li, X., Wei, Y., Nettleton, D., & Brummer, E.C. (2009). Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa. BMC Plant Biology: 9, 107.

  • 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.

  • Elling, A.A., Mitreva, M., Gai, X., Martin, J., Recknor, J., Davis, E.L., Hussey, R.S., Nettleton, D., McCarter, J.P., & Baum, T.J. (2009). Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics: 10, article 58.

Vita: Click here to download

Website: Dan Nettleton

*Basil Nikolau

BCB Faculty Member

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

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: Using biochemical, molecular, cellular, and developmental approaches, which include purifying the proteins, cloning the genes, determining their sequences, identifying the relevant regulatory elements, and identifying new transcriptional regulators

Selected Publications:

  • Determan, A.S., Trewyn, B.G., Lin, V.S., Nilsen-Hamilton, M. and Narasimhan, B. (2004) Encapsulation, stabilization, and release of BSA-FITC from polyanhydride microspheres. J. Control. Release 100, 97-109.
  • Nilsen-Hamilton, M., Liu, Q., Ryon, J., Bendickson, L., Lepont, P. and Chang, Q. (2003) Tissue involution and the acute phase response. Ann. NY Acad. Sci. 995, 94-108.
  • Ryon, J., Bendickson, L. and Nilsen-Hamilton, M. (2002) High expression in involuting reproductive tissues of uterocalin/24p3, a lipocalin and acute phase protein. Biochem. J. 367, 271-277.

Vita: Click here to download

Website: Marit Nilsen-Hamilton

Thomas Peterson

BCB Faculty Member

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

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:

  • 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

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

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:

  • Schneider, M.J., Tait, R.G, Jr., Busby, W.D., & Reecy, J.M. (2009). An evaluation of bovine respiratory disease complex incidence in feedlot cattle: Fixed sources of variation and genetic parameter estimates. Journal of Animal Science: 87, 5, 1821-7. Epub 2009 Jan 30.

  • Hu, Z.-L., A.M. Ramos, S.J. Humphray, J. Rogers, J.M. Reecy and M.F.Rothschild. 2011.Use of genomes sequence information for meat quality trait QTL mining for causal genes and mutations on pig chromosome 17. Frontiers in Genetics 2:43. doi: 10.3389/fgene.2011.00043
  • Boddicker, N., E.H. Waide, R.R. Rowland, J.K. Lunney, D.J. Garrick, J.M. Reecy, J.C. Dekkers. 2011. Evidence for a major QTL associated with host response to Porcine Reproductive and Respiratory Syndrome virus challenge. J Anim Sci. 90(6):1733-46. Epub 2011 Dec 28.
  • Hu, Z.-L., J.E. Koltes, C.A. Park, E.R. Fritz and J.M. Reecy. 2011. Bioinformatics approaches to livestock animal genomics research. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2011 6, No. 044
  • Wu, X.-L., D. Gianola, Z.-L. Hu and J.M. Reecy. 2011. Meta-Analysis of Quantitative Trait Association and Mapping Studies using Parametric and Non-Parametric Models. Journal of Biometrics and Biostatistics 2011, S1
  • 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

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

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

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:

  • Hart, E.A., M. Caccamo, J.L. Harrow, S. Humphray, J. G.R. Gilbert, S. Trevanion, T. Hubbard, J. Rogers and M.F. Rothschild. 2007. Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 MB region of pig chromosome 17. Genome Biology 8: R168.
  • Rothschild, M.F., Z.H. Hu and Z. Jiang. 2007. Advances in QTL mapping in pigs. Int. J. Biol. Sci. 3: 192-197.
  • Rothschild, M.F. and G.S. Plastow. 2008. Impact of genomics in animal agriculture and opportunities for animal health. Trends in Biotechnology. 26:21-25.
  • Do, K., S Moon, Z Hu, BH Choi, BW Cho, M F Rothschild, H Kim and  KS Kim.  2008. Development and characterization of in silico SNP map in pigs. Animal Genetics, in press

Vita: Click here to download

Website: Max Rothschild

Donald Sakaguchi

BCB Faculty Member

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:

  • 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

Patrick Schnable

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:

  • Lin Z, X Li, ML Wang, G Bai, Z Peng, J Li, TE Clemente, HN Trick, PS Schnable, MR Tuinstra, TT Tesso, F White, J Yu (2012) Parallel domestication of the SHATTERING1 genes in cereals. Nature Genetics, 44:720-4. (Selected as an Editors' Choice by MaizeGDB, 7/12; "Recommended" by the Faculty of 1000 Biology)
  • Ronin Y, D Mester, D Minkov, R Belotserkovski, BN Jackson, PS Schnable, S Aluru, A Korol (2012) Two-Phase analysis in consensus genetic mapping. G3, 2: 537-549.
  • Liu S, C-T Yeh, HM Tang, D Nettleton, PS Schnable (2012) Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One, 7(5):e36406. (Selected as an Editors' Choice by MaizeGDB, 6/12)
  • Eichten SR, NA Ellis, I Makarevitch, CT Yeh, JI Gent, G Lin, KM McGinnis, X Zhang, PS Schnable, MW Vaughn, RK Dawe, NM Springer (2012) Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genetics, 8(12): e1003127.
  • Zhang X, RN Douglas, J Strable, M Lee, B Buckner, D Janick-Buckner, PS Schnable, MCP Timmermans, MJ Scanlon (2012) PUNCTATE VASCULAR EXPRESSION1 (PVE1) is a novel maize gene required for leaf pattern formation that functions downstream of the ta-siARF pathway. Plant Physiology, 159:1453-62. (Selected as an Editors’ Choice by MaizeGDB, 7/12)
  • Liu S, K Ying, C-T Yeh, J Yang, R Swanson-Wagner, W Wu, T Richmond, DJ Gerhardt, J Lai, N Springer, D Nettleton, JA Jeddeloh, PS Schnable (2012) Changes in genome content generated via segregation of non-allelic homologs. Plant J. 72:390-399. (Recommended by the Faculty of 1000 Plant Biology)
  • Takacs EM, J Li, L Ponnala, D Janick-Buckner, J Yu, GJ Muehlbauer, MCP Timmermans, PS Schnable, Q Sun, D Nettleton, MJ Scanlon (2012) Ontogeny of the maize shoot apical meristem. Plant Cell, 24:3219-34. (Selected as an Editors’ Choice by MaizeGDB; Selected by journal editors for "in brief" highlight; "Recommended" by the Faculty of 1000 Biology)
  • Li X, C Zhu, C-T Yeh, W Wu, EM Takacs, KA Petsch, F Tian, G Bai, ES S. Buckler, GJ Muehlbauer, MCP Timmermans, MG Scanlon, PS Schnable, J Yu (2012) Genic and non-genic contributions to quantitative trait variation in maize as detected via GWAS. Genome Research, 22(12): 2436-2444. (Selected as an Editors' Choice by MaizeGDB, 8/12)
  • Paschold A, Y Jia, C Marcon, S Lund, NB Larson, C-T Yeh, S Ossowski, C Lanz, D Nettleton, PS Schnable, F Hochholdinger (2012) Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Research, 22:2445-2454.
  • 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, in press. (Selected as an Editors' Choice by MaizeGDB)
  • Schnable PS , NM Springer (2013) Progress toward understanding heterosis in crop plants. Annu. Rev. Plant Biol., in press.

Vita: Click here to download

Website: Patrick Schnable

Stephan Schneider

BCB Faculty Member

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.

Taner Sen

BCB Faculty Member

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:

  • Sen, T.Z., Harper, L.C., Schaeffer, M.L., Seigfried, T.E., *Andorf, C.M., & Lawrence, C.J, (2010). Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community. Database: The Journal of Biological Databases and Curation, doi: 10.1093/database/baq007.

  • Andorf, C.M., Harper, L.C., Schaeffer, M.L., Seigfried, T.E., Lawrence, C.J, & Sen, T.Z. (2009). The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps. Bioinformatics: 26, 434-436.

  • Sen, T.Z., *Andorf, C.M., Schaeffer, M.L., Harper, L.C., Sparks, M.E., Duvick, J., Brendel, V.P., Cannon, E., Campbell, D.A., & Lawrence, C.J. (2009). MaizeGDB becomes ‘sequence-centric’. Database: doi: 10.1093/database/bap020.

  • Lawrence, C. J., Harper, L.C., Schaeffer, M.L., Sen, T.Z., Seigfried, T.E., Campell, D.A., “MaizeGDB: the Maize Model Organism Database for Basic, Translational, and Applied Research”, International Journal of Plant Genomics, in press.

  • Sen, T.Z., Kloster, M., Kloczkowski, A., Kolinski, A., Bujnicki, J.M., Jernigan, R.L., “Structure prediction and normal mode analysis of the outer membrane transporter FecA”, Biophysical Journal, 94(7), 2482–2491, 2008.

  • Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M., Jernigan, R.L. “Predicting the order in which contacts are broken during single molecule protein stretching experiments”, Proteins, 71, 45-60, 2008.

  • Cheng, H., Sen, T.Z., Jernigan, R.L., Kloczkowski, A., “Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)”, Bioinformatics, 23(19), 2628-2630, 2007.

  • Peto, M., Sen, T.Z., Jernigan, R.L., Kloczkowski, A., “Generation and enumeration of compact conformations on the 2D triangular and 3D fcc lattices”, Journal of Chemical Physics, 127(4):044101, 2007.

Vita: Click here to download

Website: Taner Z. Sen

Jacqueline Shanks

BCB Faculty Member

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

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

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

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

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

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

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:

  • Travesset, A., & Vangaveti, S. (2009). Correlations at the Stern Layer: Physics or Chemistry? Journal of Chemical Physics: 131, 185102-185112.

  • J. Faraudo and A. Travesset , Phosphatidic Acid Domains in Membranes: effect of Divalent Counterions, Biophys. J.,(in Press)(2007).

  • A. Travesset, Effect of dipolar moments in domain sizes of lipid bilayers and monolayers, J. Chem. Phys. 125 (8), 084905 (2006).

  • W. Bu, D. Vaknin, and A. Travesset, How Accurate Is Poisson-Boltzmann Theory for Monovalent Ions near Highly Charged Interfaces, Langmuir 22, 5673 (2006).

  • M. Bowick, D.R. Nelson, and A. Travesset, Curvature-Induced Defect Unbinding in Toroidal vesicles, Phys. Rev. E 69, 41102 (2004).

  • Bowick and A. Travesset, The Statistical Mechanics of Membranes, Phys. Rep. 344; (2001) 255.

Vita: Click here to download

Website: Alex Travesset

Jeffrey Trimarchi

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.

The primary goal of my research is to understand the gene expression programs that drive the development and diversification of retinal ganglion cells, the major output neurons of the retina. These cells vary extensively in their morphologies and are lost in glaucoma, a leading cause of blindness. To achieve this goal, my lab will first develop a molecular taxonomy of retinal ganglion cells in the mouse by profiling individual, labeled ganglion cells. In addition, we will identify the gene networks present in the progenitor cells that produce the retinal ganglion cells. Once these gene networks have been assembled, gain and loss of function studies will be performed to assess the effects of perturbing these networks on ganglion cell production and survival. These experiments will provide insights into how to generate ganglion cells de novo or perhaps how to maintain the survival of these cells in a disease state.

Selected Publications:

  • Emerson, MM, Surzenko, N, Goetz, JJ, Trimarchi, JM, and Cepko CL. The Otx2 and Onecut factors promote cone photoreceptor and horizontal cell genesis over rod photoreceptors, Dev. Cell., In Press.
  • Mizeracka, K, Trimarchi JM, Stadler, MB, and Cepko, CL. Analysis of gene expression in wildtype and Notch 1 mutant cells by single cell profiling, Dev. Dyn. In Press.
  • 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.

Christopher Tuggle

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

*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.


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. Description:


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 to download

Website: Nicole Valenzuela

*Erik Vollbrecht

BCB Faculty Member

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

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:

  • 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

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

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

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:

  • 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]

  • Schreiber, A.W., Sutton, T., Caldo, R.A., Kalashyan, E., Lovell, B., Mayo, G., Muehlbauer, G.J., Druka, A., Waugh, R., Wise, R.P., Langridge, P. & Baumann, U. (2009). Comparative transcriptomics in the Triticeae. BMC Genomics: 10, 285. [Full Text]

  • Hu, P., Meng, Y., & Wise, R.P. (2009). Functional contribution of chorismate synthase, anthranilate synthase, and cho rismate mutase to penetration resistance in barley-powdery mildew interactions. Molecular Plant-Microbe Interactions: 22, 3, 311-320. [Full Text]]

  • Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P., & Stein, N. (2009). The international barley sequencing consortium—at the threshold of efficient access to the barley genome. Plant Physiology: 149, 142-147. [Full Text]

Vita: Click here to download

Website: Roger Wise

*Zhijun Wu

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

Education: Ph.D., UCLA, 1980

Research Interests: Metabolic networking of acetyl-CoA starch in plants, computational biology

  • Functional and Structural Genomics-- Metabolic networking in plants; evolution of biotin-containing enzymes; RNA and protein profiling analyses
  • Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking--Same as above

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:

  • Hur M, Cambell 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. Natural Product Reports. Feb, DOI: 10.1039/C3NP20111B
  • Yeo YS, S. Nybo E, Chittiboyina AG, Weerasooriya AD, Wang YH, Gongora-Castillo E, Vaillancourt B, Buell CR, DellaPenna D, Celiz MD, Jones AD, Wurtele ES, Ransom N, Dudareva N, Shabaan KA, Tibrewal N, Chandra S, Smillie T, Khan IA, Coates RM, Watt DS, Chappell J. (2012). Functional identification of valerena-1, 10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologially active sesquiterpenes in Valeriana officinalis. J Biol Chem. doi: 10.1074
  • Ngaki MN, Louie GV, RN, Manning G, Pojer F, Fowman ME, Li L, Elise Larsen E, Wurtele ES, Noel JP. (2012). Evolution of the chalcone isomerae fold from fatty acid-binding to stereospecific enzyme. Nature, 485: 530-533. doi: 10.1038/nature11009
  • Wurtele ES, Chappell J, Jones AD, Celiz MD, Ransom N, Hur M, Rizshsky L,Dixon P, Liu J, Widrlechner MP, Nikolau BJ. (2012). Medicinal Plants: A Public Resource for Metaolomics and Hypothesis Development Metabolites. 2(4), 1031-1059; doi: 10.3390/metabo2041031
  • Feng, YP, Hurst J. Almeida-De-Macedo M. Chen X, Li L, Ransom N, Wurtele ES. (2012). A massive human co-expression network and its medical applications. Special Issues: Molecular Networks and Disease. Systems Biology, Chemistry and Biodiversity. May 9 (5): 868-87. doi: 10.1002/cbdv.201100355
  • Oliver, D.J., Nikolau, B.J., & Wurtele, E.S. (2009). Life at the metabolic nexus. Plant Science: 176, 597-601.
  • El Kaissi, M., Jia, M., Dickerson, J., Wurtele, E.S., & Reiners, D. (2009). Reaction centric layout for metabolic networks. Lecture Notes in Computer Science. Springer-Verlag
  • El Kaissi, M., Jia, M., Dickerson, J., Wurtele, E.S., & Reiners, D. (2009).Visualization of gene regulatory networks. Lecture Notes in Computer Science. Springer-Verlag.
  • Senchina, D.S., McCann, D.A., Flinn, G.N., Wu, L., Zhai, Z., Cunnick, J.E., Wurtele, E.S., & Kohut, M.L. (2009). Echinacea tennesseensis phytomedicinal properties vary by plant organ. Phytomedicine: 16, 669-678.
  • Berleant, D., Zhang, L., Ding, J., Cao, T., Xu, J., Fulmer, A., & Wurtele, E.S. (2009). Text Empirics-Based Mining of Biomolecular Interactions from Texts: Theory and Application. BMC Bioinformatics: 11, S18 (software application).
  • Ding, J., Berleant, D., Xu, J., Juhlin, K., Wurtele, E.S., & Fulmer, A. (2009). GeneNarrator: Mining the Literaturome for Relations Among Genes. J Proteomics Bioinform: 2, 360-371.
  • Li, L., Foster, C., Gan, Q., Nettleton, D., James, M.G., Myers, A.M., & Wurtele, E.S. (2009). Identification of the Novel Protein QQS as a component of the starch metabolic network in Arabidopsis leaves. Plant Journal: Online 2/09,
  • Zhai, Z., Solco, A., Wu, L., Wurtele, E.S., Kohut, M.L., Murphy, P.A., & Cunnick, J.E. (2009). Echinacea increases arginase activity and has anti-inflammatory properties in RAW 264.7 macrophage cells indicative of alternative macrophage activation. J Ethnopharmacol: 122, 76-85
  • Birt, D.F., Widrlechner, M.P., Hammer, K.D., Hillwig, M.L., Wei, J., Kraus, G.A., Murphy, P.A., McCoy, J., Wurtele, E.S., Neighbors, J.D., Wiemer, D.F., Maury, W.J., & Price, J.P. (2009). Hypericum in infection: Identification of anti-viral and anti-inflammatory constituents. Pharm Biol: 47, 774-782.
  • LaLone , C.A. , Rizshsky, L., Hammer, K.D., Wu, L., Solco, A.K., Yum, M., Nikolau, B.J., Wurtele, E.S., Murphy, P.A., Kim, M., & Birt, D.F. (2009). Endogenous levels of Echinacea alkylamides and ketones are important contributors to the inhibition of prostaglandin E2 and nitric oxide production in cultured macrophages. J Agric Food Chem: 57, 8820-8830
  • Senchina, D.S., McCann, D.A., Flinn, G.N., Wu, L., Zhai, Z., Cunnick, J.E., Wurtele, E.S., & Kohut, M.L. (2009). Echinacea tennesseensis ethanol tinctures harbor cytokine- and proliferation-enhancing capacities. Cytokine: 46, 267-272
  • Zhai, Z., Haney, D.M., Wu, L., Solco, A.K., Murphy, P.A., Wurtele, E.S, Kohut, M.L., & Cunnick, J.E. (2009). Alcohol extract of Echinacea pallida reverses stress-delayed wound healing in mice. Phytomedicine: 16, 669-678
  • Perera, A., Choi, S.Y., Wurtele, E.S., & Nikolau, B.J. (2009). Quantitative analysis of acyl-coenzyme As in plant tissues by an LC-MS-MS electrospray ionization method. Chromatography B: Available online 1/09.


Vita: Click here to download

Website: Eve Wurtele

*Edward Yu

BCB Faculty Member

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.