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Ralph Ackerman

Education: Ph.D., Florida, 1975

Research Interests: Mathematical biology, environmental physiology, sex determination

• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking --Mathematical biology; modeling environmental physiology; sex determination

Description: Current Research: 1) Water exchange by Reptile Eggs during incubation; 2) Temperature Dependent Sex Determination

Research in my laboratory is directed toward analyzing and understanding two processes: 1) transport processes involving the exchange of energy and materials within the organism and between the organism and the environment and 2) biological regulatory processes. Interest in these processes is directed toward understanding how the organism is adapted to its environment. The approach is typically interdisciplinary and employs both theoretical and experimental techniques to generate and test hypotheses. The current direction of activity in the laboratory is toward describing and understanding the environmental physiology of vertebrate embryos, especially reptile and bird embryos.

Vita: Click here to download

Website: Ralph Ackerman

Dean Adams

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

Research Interests:

• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking--Theoretical and empirical studies of phenotypic change in ecology and evolution; statistical shape analysis (morphometrics); community organization and species interactions

Description: In the Adams lab our research is directed towards understanding how ecological and evolutionary forces generate and maintain phenotypic diversity. To do this we integrate computational, mathematical, statistical and quantitative morphological methods to examine ecological hypotheses from an evolutionary perspective. Our empirical work examines patterns of ecological and evolutionary morphology to understand species interactions, microevolution and community organization (largely in Plethodon salamanders). In our theoretical research, we develop new analytical tools for examining patterns of phenotypic variation. Current theoretical research focuses on developing analytical methods for assessing multivariate patterns of phenotypic change, such as are found in studies of plasticity, character divergence (and displacement) biomechanics, ontogenetics, local adaptation, and microevolution, and quantitative genetics.

Selected Publications:

• Adams, D.C. 2008. Phylogenetic meta-analysis. Evolution. 62:567-572.

• Adams, D.C., and J.O. Church. 2008. Amphibians do not follow Bergmann’s rule. Evolution. 62:413-420.
• Adams, D.C. 2007. Organization of Plethodon salamander communities: guild-based community assembly. Ecology. 88:1292-1299.
• Adams, D.C., and M.L. Collyer. 2007. Analysis of character divergence along environmental gradients and other covariates. Evolution.61:510-515.
• Collyer, M.L., and D.C. Adams. 2007. Analysis of two-state multivariate phenotypic change in ecological studies. Ecology. 88:683-692.
• Adams, D.C., M.E. West, and M.L. Collyer. 2007. Location-specific sympatric morphological divergence as a possible response to species interactions in West Virginia Plethodon salamander communities. Journal of Animal Ecology. 76:289-295.
• Adams, D.C., and M.M. Cerney. 2007. Quantifying biomechanical motion using Procrustes motion analysis. Journal of Biomechanics. 40:437-444.
• Maerz, J. C., E. M. Myers, and D. C. Adams. 2006. Trophic polymorphism in a terrestrial salamander. Evolutionary Ecology Research. 8:23-35.
• Adams, D. C. 2004. Character displacement via aggressive interference in Appalachian salamanders. Ecology. 85:2664-2670.
• Adams, D. C., and F. J. Rohlf. 2000. Ecological character displacement in Plethodon: biomechanical differences found from a geometric morphometric study. Proceedings of the National Academy of Sciences, U.S.A. 97:4106-4111.

Vita:Click here to download

Website: Dean Adams

Srinivas Aluru

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:

• P. Ko and S. Aluru, "Space efficient linear time construction of suffix arrays," Journal of Discrete Algorithms, to appear.
• S. J. Emrich, S. Aluru and P.S. Schnable, "Status of maize genome sequencing and assembly projects," AgBiotechNet Journal, to appear.
• P. Ko, M. Narayanan, A. Kalyanaraman, and S. Aluru, "Space-conserving optimal DNA-protein alignment," IEEE Computational Systems Bioinformatics Conference, to appear.
• S. J. Emrich, S. Aluru, Y. Fu, T.J. Wen, M. Narayanan, L. Guo, D.A. Ashlock, and P.S. Schnable, "A Strategy for Assembling the Maize (Zea mays L.) Genome," Bioinformatics, Vol. 20, No. 2, pp. 140-147, 2004.
• S. Rajko and S. Aluru, "Space and time optimal parallel sequence alignments," IEEE Transactions on Parallel and Distributed Systems, Vol. 15, No. 11, 2004.
• S. Aluru, "Suffix Trees and Suffix Arrays," in Handbook of Data Structures and Applications, edited by Sartaj Sahni and Dinesh P. Mehta, CRC Press, 2004.
• S. J. Emrich, S. Aluru, Y. Fu, T.J. Wen, M. Narayanan, L. Guo, D.A. Ashlock, and P.S. Schnable, "A strategy for assembling the maize genome," Plant and Animal Genomes Conference Bioinformatics Workshop, 2004.

Vita: Click here to download

Website: Srinivas Aluru

Amy Andreotti

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

Description:

Selected Publications:

• Min, L., Fulton, D.B. and Andreotti, A.H. (2005) A case study of proline isomerization in cell signaling. Front. Biosci. 10, 385-397.
• Andreotti, A.H. (2003) Native state proline isomerization: an intrinsic molecular switch. Biochemistry 42, 9515-9524.
• Laederach, A., Cradic, K.W., Brazin, K.N., Zamoon, J., Fulton, D.B., Huang, X.Y. and Andreotti, A.H. (2002) Competing modes of self-association in the regulatory domains of Bruton's tyrosine kinase: intramolecular contact versus asymmetric homodimerization. Protein Sci. 11, 36-45.
• Laederach, A., Andreotti, A.H. and Fulton, D.B. (2002) Solution and micelle-bound structures of tachyplesin I and its active aromatic linear derivatives. Biochemistry 41, 12359-12368.
• Watson, R.M., Woody, R.W., Lewis, R.V., Bohle, D.S., Andreotti, A.H., Ray, B. and Miller, K.W. (2001) Conformational changes in pediocin AcH upon vesicle binding and approximation of the membrane-bound structure in detergent micelles. Biochemistry 40, 14037-14046.

Vita: Click here to download

Website: Amy Andreotti

Lyric Bartholomay

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

Research Interests:

• In describing and understanding the interactions between mosquitoes and the pathogens they transmit to prevent transmission of vector-borne diseases, my lab employs bioinformatics/computational biology - we use bioinformatics (EST sequencing, genome mining, etc.) and functional genomics tools (microarrays), in which I was trained in my Doctoral and Postdoctoral work.

Selected Publications:

Vita: Click here to download

Website: New Faculty

William Beavis

Education:

Research Interests:

Selected Publications:

Vita: Click here to download

Website: New Faculty

Madan Bhattacharyya

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: The primary interest of the Bhattacharyya lab is to understand the molecular basis of plant-pathogen interactions

Selected Publications:

• Gao, H., Narayanan, N., Ellison, L., and Bhattacharyya M.K. (2005) Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. . Mol. Plant-Microbe Interact., 18:1035-1045.      
• Sandhu, D., Schallock K.G., Rivera-Velez, N., Lundeen, P., Cianzio, S., and Bhattacharyya, M.K. (2005) Soybean Phytophthora resistance gene Rps8 maps closely to the Rps3 region. . J. Heredity, 96: 536-541.      
• Bhattacharyya, M.K., Narayanan, N. N., Gao, H., Salimath, S.S., Santra, D., Ellison, L., Kasuga, T., Liu, Y., Espinosa, B., Marek, L.F., Shoemaker, R.C., Gijzen, M. and Buzzell, R.I. (2005)Identification of a large cluster of coiled coil-nucleotide binding site-leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean. Theor. Appl. Genet., 111: 75-86.      
• Sandhu, D., Gao, H., Cianzio, S., and Bhattacharyya, M.K. (2004)Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics 168: 2157-2167      
• W-M. Chou, T. Shigaki, C. Dammann, Y-Q. Liu, M. K. Bhattacharyya (2004). Inhibition of Phosphoinositide-Specific Phospholipase C Results in the Induction of Pathogenesis-Related Genes in Soybean. Plant Biol 6: 664-672.    

Vita: Click here to download

Website: Madan Bhattacharyya

Adam Bogdanove

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

Description:

Selected Publications:

• Meyer, D.F., and Bogdanove, A.J. (2008). Genomics-driven advances in Xanthomonas biology. In Plant Pathogenic Bacteria: Genomics and Molecular Biology, R.W. Jackson, ed. (Norwich, UK, Horizon Scientific Press), in press.
• Patil, P.B., Bogdanove, A.J., and Sonti, R.V. (2007) The role of horizontal transfer in the evolution of a highly variable lipopolysaccharide biosynthesis locus in xanthomonads that infect rice, citrus and crucifers. BMC Evol. Biol. 7:243.
• Wang, L. Makino, S., Subedee, A. and Bogdanove, A.J. (2007) Novel candidate virulence factors in rice pathogen Xanthomonas oryzae pv. oryzicola revealed by mutational analysis. Applied Env. Microbiol. 73:8023-8027.
• Nissinen, R.M, Ytterberg, A.J., Bogdanove, A.J., van Wijk, K.J., and Beer, S.V. (2007) Analyses of the secretomes of Erwinia amylovora and selected hrp mutants reveal novel type III secreted proteins and an effect of HrpJ on extracellular harpin levels. Molecular Plant Pathol. 8:55-67.
• Wise, R.P., Moscou, M.J., Bogdanove, A.J., and Whitham, S.A. (2007). Transcript profiling in host-pathogen interactions. Ann. Rev. Phytopathol. 45:329-369.
• Nino-Liu, D. O., Ronald, P. C., and Bogdanove, A. J. (2006) Xanthomonas oryzae pathovars: model pathogens of a model crop. Molecular Plant Pathol. 7:303-324.

Website: Adam Bogdanove

Khalid Boushaba

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

Research Interests: Mathematical Biology, Applied Mathematics and Mathematical Modeling, Partial Differential Equations

Vita: Click here to download

Website: Khalid Boushaba

Volker Brendel

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:

• Wang, B.-B. & Brendel, V. (2006) Genome-wide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103, 7175-7180.
• Wang, B.-B. & Brendel, V. (2006) Molecular characterization and phylogeny of U2AF1 homologs in plants. Plant Physiol. 140, 624-636.
• Gremme, G., Brendel, V., Sparks, M.E. & Kurtz, S. (2005) Engineering a software tool for gene structure prediction in higher organisms. Information Software Technol. 47, 965-978.
• Brendel, V. (2005) Novel tools for plant genome annotation and applications to Arabidopsis and rice. In J.P. Gustafson, R. Shoemaker & J.W. Snape (eds.), Genome Exploitation: Data Mining the Genome, Stadler Genetics Symposia Series, 23rd Symposium, Springer, NY, U.S.A.
• Sparks, M.E. & Brendel, V. (2005) Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics 21, iii20-iii30.
• Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D., Kurtz, S., Lushbough, C. & Brendel, V. (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol. 139, 610-618.
• Pan, X., Stein, L. & Brendel, V. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics 21, 3461-3468.
• Lawrence, C.J., Seigfried, T.E. & Brendel, V. (2005) MaizeGDB - the community resource for access to diverse maize data. Plant Physiol. 138, 55-58.
• Dong, Q., Kroiss, L., Oakley, F.D., Wang, B.-B. & Brendel, V. (2005) Comparative EST analyses in plant systems. In Molecular Evolution: Producing the Biochemical Data, E.A. Zimmer and E.H. Roalson (eds.), Methods Enzymol. 395, 400-418.
• Brendel, V. (2005) Gene structure prediction in plant genomes. In M.J. Dunn, L.B. Jorde, P.F.R. Little and S. Subramaniam (eds.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley & Sons, Chichester, UK. DOI: 10.1002/047001153X.g402303.
• Dong, Q. & Brendel, V. (2005) Computational identification of related proteins: BLAST, PSI-BLAST, and other tools. In J.M. Walker (ed.), The Proteomics Protocols Handbook, Humana Press, U.S.A., pp. 555-570.
• Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. & Brendel, V. (2005) Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends Plant Sci. 10, 9-14.

Website: Volker Brendel

Anne Bronikowski

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:

• Promislow, D.E.L. and Bronikowski, A.M. in press. The Evolutionary Genetics of Senescence. In Evolutionary Genetics: Concepts and Case Studies. Eds. J. Wolf and C. Fox. Oxford University Press, U.K.
• Bronikowski, A.M. and D.E.L. Promislow.   2005.Testing evolutionary theories of aging in wild populations. Trends in Ecology and Evolution 20(6): 271-273 .
• Gammie, S.C., Hasen, N.S., Awad, T.A., Auger, A.P., Jessen, H.M., Panksepp, J.B., and Bronikowski, A.M.  2005. Gene array profiling of large hypothalamic CNS regions in lactating and randomly cycling virgin mice. Molecular Brain Research 139: 201-211.
• Bronikowski, A.M., Carter, P.A., Morgan, T.J., Garland, T. Jr., Ung, N., Pugh, T.D., Weindruch, R. and Prolla, T.A. 2003. Lifelong voluntary exercise in the mouse prevents age-related alterations in gene expression in the heart. Physiological Genomics 12: 129–138.

Vita: Click here to download

Website: Anne Bronikowski

Steve Cannon

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:

• Ameline-Torregrosa C, Wang B-B, O’Bleness M, Deshpande,S, Zhu H, Roe BA, Young ND, Cannon SB (2008) Identification and Characterization of NBS-LRR Encoded Genes in the Model Plant Medicago truncatula Plant Physiology, 146:5-21
• Zhang X-C, Wu X, Findley S, Wan J, Libault M, Nguyen HT, Cannon SB, Stacey G (2007) Characterization of plant LysM domains and molecular evolution and comparative genomics of plant LysM type receptor-like kinases. Plant Physiology 144:623-636.
• Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy JP, Wang X, Mudge J, Vasdewani J, Scheix T, Spannagl M, Nicholson C, Humphray SJ, Schoof H, Mayer KFX, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Ernest F. Retzel, Roe BA, Town CD, Tabata S, Van de Peer Y, ND Young (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. PNAS 103(40):14959-64.
• Mudge J, Cannon SB, Kalo P, Oldroyd GED, Roe BA, Town CD, Young ND (2005) Hypersyntenic Regions in the Genomes of Soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biology, 2005.

Websites: http://soybase.org/ http://medicago.org/

Vita: Click here to download

Website: Steven Cannon

Alicia Carriquiry

Education: Ph.D., Iowa State, 1989

Research Interests: Statistical methods in bioinformatics and biological sciences

• Bioinformatics-- Statistical methods in bioinformatics and biological sciences

Description:

Selected Publications:

• Fernandez, S., Fernando, R., and Carriquiry, A.L. 2001. An algorithm to sample marker genotypes in a pedigree with loops. Case Studies in Bayesian Statistics, Vol. V, Gatsonis, C. et al. ( eds.). Lecture Notes in Statistics, Springer- Verlag. 309-328. Papers\Bioinformatics and Biological Statistics\Fernandez- CaseStudies.pdf
• Fernandez, S. A., Fernando, R. L., and Carriquiry, A. L.. 2001. An algorithm to sample unobservable genotypes in complex pedigrees.  ISBA 2000 Proceedings: Bayesian Methods with Applications to Science, Policy, and Official Statistics.  Italy: European Communities Press. 125-135. Papers\Bioinformatics and Biological Statistics\Fernandez- ROS.pdf
• Fernandez, S. A., Fernando, R. L., Guldbrandtsen, B., Stricker, C., Schelling, M., and Carriquiry, A. L. 2002. Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops. Genetics, Selection, Evolution. 34:537-555.
• Che, P., Love, T.M., Frame, B.R, Wang, K., Carriquiry, A.L., and Howell, S.P. Gene expression changes during germination and maturation of somatic embryos in maize cultures. Plant Molecular Biology.  In press. Papers\Bioinformatics and Biological Statistics\ PlantMolecBiol.pdf

Vita: Click here to download

Website: Alicia Carriquiry

Hui-Hsien Chou

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

Research Interests: Bioinformatics, computational and molecular biology

Description: My research interest has been the development of sophisticated computer science algorithms for efficiently solving large scale biological research problems, e.g., the automatic DNA sequence clean up programs (LUCY1 & 2), an efficient whole-genome oligo microarray design tool (PICKY), and an automatic Perl programming tool (VECT) for biologists. My software tools employ novel approaches to computing and generally provide better results than previous methods. For example, while most microarray design tools are still based on the sequence level comparison 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 the whole genome, and it does so orders of magnitude faster than any other comparable microarray design tools with the same computation depth. My recent focus is on the whole-genome siRNA design using a similar thermodynamic calculation approach and to verify the designs in my molecular biology lab using C. elegans as the model.
 
Ongoing projects: National Institute of General Medical Sciences, Visual Data Extraction and Conversion Programming Tool - The goal of this project is to develop an auto-programming tool for biomedical scientists to help them handle the large amount of data in their research; National Science Foundation Plant Genome Research Program - A Rice Oligonucleotide Array - Rice has become a model for grasses and cereal because of its small genome size, available genome sequence, and ease of transformation. The structural and functional analysis of rice genes has broad practical implications for the other economically important cereals such as corn and wheat. This project will design, manufacture and distribute whole genome rice microarrays to the public.

Selected Publications:

• Scott Emrich, Tsui-Jung Wen, Marna Yandeau-Nelson, Yan Fu, Li Li, Ling Guo, Hui-Hsien Chou, Srinivas Aluru, Daniel Ashlock, and Patrick Schnable. 2007. Nearly identical paralogs (NIPs): implications for maize (Zea mays L.) genome evolution. Genetics In press.
• Philip M. Maher, Hui-Hsien Chou, Elizabeth Hahn, Tsui-Jung Wen, and Patrick S. Schnable. GRAMA:  Genetic Mapping Analysis of Temperature Gradient Capillary Electrophoresis (TGCE) Data. Theoretical and Applied Genetics, 113(1):156162, 2006.
• Hui-Hsien Chou. Vect: an automatic visual Perl programming tool for nonprogrammers. BioTechniques, 38:615621, April 2005.
• Song Li and Hui-Hsien Chou. UBViz: Explore Biochemical Pathways in 3-D Space. BioTechniques, 38:540542, April 2005.
• Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable. Picky: Oligo Microarray Design for Large Genomes. Bioinformatics, 20:28932902, Nov. 2004.
• Song Li and Hui-Hsien Chou. Lucy2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics, 20:28652866, Nov. 2004.

Department Website: Hui-Hsien Chou

Dianne Cook

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:

• Lee, E.-K., Cook, D., Hofmann, H., Wurtele, E., Kim, D., Kim, J., and An, H. (2004) GeneGobi: Visual Data Analysis Tools for Microarray Data, COMPSTAT '04, Aug 22-27, 2004, Prague, Czech Republic, Pages forthcoming.
• Cook, D., Hofmann, H., Lee, E.-K., Yang, H., Nikolau, B. and Wurtele, E. (2004). Visual Methods For Data From Two Factor Single-Replicate Gene Expression Studies, Technical Report 04-05: http://www.stat.iastate.edu/preprint/articles/2004-05.pdf, Department of Statistics, Iowa State University.
• 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.
• Meyer, D. and Cook, D. (2000). Visualization of Data. Current Opinion in Biotechnology, 11:89--96.

Link: http://www.public.iastate.edu/~dicook/GeneGobi/MetNet_GeneGobi.htm

Vita: Click here to download

Website: Dianne Cook

Jack Dekker

Education: Ph.D., Michigan State, 1980

Research Interests: Weed seed behavior as a complex adaptive system, formalizing seed behavior computational models

• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Weedy Setaria spp. as a complex adaptive system; formalizing Setaria seed behavior computational models; emergent behavior of Setaria biogeography arising from seed flavohemoglobin; pleiotropy and emergent behavior

Description: Conduct a research program on weed biology to understand and characterize the most important weedy traits of the worst weeds in Iowa corn and soybean production systems, especially the seed behavior of the weedy foxtails.  Then, to elucidate the biotic and environmental factors regulating their behavior and to use this information to develop improved, sustainable weed management systems

Selected Publications:

• Dekker, J. 2004a. The evolutionary biology ofthe foxtail (Setaria) species-group.  In: Weed Biology and Management; Inderjit (Ed.). Kluwer Academic Publishers, The Netherlands. Pp. 65-113.

Vita: Click here to download

Website: Jack Dekker

Jack Dekkers

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:

• Chakraborty, R., L. Moreau, and J. C. M. Dekkers. 2001. A method to optimize selection on multiple identified quantitative trait loci. Genet. Sel. Evol. (Accepted).
• Malek, M., J.C.M. Dekkers, H.K. Lee, T.J. Baas, and M.F. Rothschild 2001. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mammalian Genome 12:637-645.
• Dekkers, J.C.M., and F. Hospital. 2002. Utilization of molecular genetics in genetic improvement of plants and animals. Nature Reviews: Genetics 3: 22-32.
•  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.
• Habier, D., R.L. Fernando, J.C.M. Dekkers. 2007. The impact of relationship information genome-assisted breeding values. Genetics 177: 23892397

Vita: Click here to download

Website: Jack Dekkers

Julie Dickerson

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

Description:

Selected Publications:

• Yuting Yang*, Levent Engin, Eve Syrkin Wurtele, Carolina Cruz-Neira, Julie A. Dickerson, “Integration of metabolic networks and gene expression in virtual reality,” Bioinformatics, 2005.
• Ding, J., K. Viswanathan, D. Berleant, L. Hughes, E. S. Wurtele, D. Ashlock, J. A. Dickerson, A. Fulmer and P. S. Schnable (2005). "Using the biological taxonomy to access biological literature with PathBinderH." Bioinformatics 21(10): 2560-2562.
• Tang*, L. Shen, J.A. Dickerson, “BarleyExpress: a web-based submission tool for enriched microarray database annotations,” Bioinformatics, 21(3): 399-401, 200.

Vita: Click here to download

Website: Julie Dickerson

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.

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: Our long-term research goals are to understand how proteins and nucleic acids achieve their functional three-dimensional structures and to elucidate rules that dictate interactions between proteins, nucleic acids and other molecules in cells.  In collaboration with several groups on campus, we have begun to integrate computational and experimental approaches to explore sequence-structure-function relationships in macromolecular complexes.  Current areas of focus include: prediction  and validation of ligand binding residues in proteins (for  protein, DNA, RNA and small molecules), rational design of zinc finger DNA binding proteins, prediction of functional effects of SNPs in unannotated proteins.

Selected Publications:

• An engineered zinc finger/target site design tool. Nucleic Acids Res., [Epub ahead of print]. In press.
• Terribilini, M., Sander, J., Lee, J.H., Zaback, P., Jernigan, R., Honavar, V., Dobbs, D. (2007) RNABindR:  A server for analyzing and predicting RNA binding sites in proteins. Nucleic Acids Res., [Epub ahead of print]. In press.
• Andorf, C., Dobbs, D. and Honavar, V. (2007) Exploring inconsistencies in genome-wide protein function annotations. BMC Bioinformatics. In press.
• EL-Manzalawy, Y., Dobbs, D., Honavar, V. (2007) PepMIL: A novel method for predicting flexible length MHC-II binding peptides. BMC Bioinformatics. In press
• Yan, C., Wu, F., Jernigan, R., Dobbs, D. and Honavar, V. (2007) Characterization of protein-protein interfaces. Protein J. In press.

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:

Selected Publications:

• G. Dancik, K.S. Dorman, D.E. Jones (2006), 'An agent-based model for Leishmania infection'
• H. Zhou, K. S. Dorman. (2005), A branching process model of drug resistant HIV. In Deterministic and Stochastic Models for AIDS Epidemics and HIV Infections with Interventions, Hulin Wu and Wai-Yuan Tan, (eds)
• F. Fang, M.A. Suchard, V.N. Minin, K.S. Dorman (2005), 'A Bayesian phylogenetic model for testing recombination event'
• K. S. Dorman, X. Gu (2005), 'Bayesian inference for functional divergence'
• V. N. Minin, K. S. Dorman, M. A. Suchard (2004), 'Bayesian recombination identification: new models for incorporating prior information', Proceedings of the Joint Statistical Meetings, Section on Bayesian Statistical Science

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:

• M. J. Sanderson, A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases. Mol Biol Evol 20: 1036-1042 (2003).
• Y. P. Yuan, O. Eulenstein, M. Vingron and P. Bork, Towards detection of orthologues in sequence databases Bioinformatics, 285-289, 14,3 (1998).
• O. Eulenstein, B. Mirkin and M. Vingron, Duplication-Based Measures of Difference Between Gene- and Species Trees Journal of Computational Biology, 135--148, 5 (1998).

Vita: Click here to download

Website: Oliver Eulenstein

David Fernandez-Baca

Education: Ph.D., University of California, Davis, 1986

Research Interests: Combinatorial algorithms, with emphasis on sensitivity analysis of optimization problems and evolutionary tree construction

Description:

Selected Publications:

• D. Chen, O. Eulenstein, D. Fernández-Baca, and M.J. Sanderson. Minimum flip supertrees: Complexity and algorithms. To appear in IEEE Trans. Bioinformatics and Computational Biology.
• D. Fernández-Baca and B. Venkatachalam. Parametric sequence alignment. To appear in Handbook of Computational Molecular Biology (S. Aluru, ed.), Chapman and Hall/CRC Press Computer and Information Science Series, 2005, in press.
• F. Sun, D. Fernández-Baca, and W. Yu. Inverse parametric sequence alignment. Journal of Algorithms, 53(1):36--54 (2004).
• D. Chen, O. Eulenstein, and D. Fernández-Baca. Rainbow: A toolbox for phylogenetic supertree construction and analysis. Bioinformatics.

Vita: Click here to download

Website: David Fernández-Baca

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:

Vita: Click here to download

Website: Rohan Fernando

Shashi Gadia

Education: Ph.D., Illinois, Urbana-Champaign, 1977

Research Interests: Relational, object-oriented, and XML modeling for storage, query, and analysis

• Bioinformatics-- Relational, object-oriented, and XML modeling for storage, query, analysis, and exchange of genetic, temporal, spatial, and scientific-beliefs data
• Functional and Structural Genomics-- Same as above
• Genome Evolution-- Same as above

Description: Temporal, spatial, belief, security, stastical and incomplete data; database models, type hierarchy, languages, user interfaces, optimization, implementation and access methods; pattern matching in spatio-temporal data

Selected Publications:

Vita: Click here to download

Website: Shashi Gadia

M. H. West Greenlee

Education: Ph.D., Iowa State, 1999

Research Interests: The molecular basis of neural differentiation

Description:

Selected Publications:

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

Description:

Selected Publications:

• Gao X, Vander Velden KA, Voytas DF and Gu X* (2005) SplitTester: software to identify domains responsible for functional divergence in protein family BMCBioinformatics 2005, 6:137
• Gu, X*, Huang, W., Xu, D., Zhang, H.(2005) GeneContent: software for whole-genome phylogenetic analysis. Bioinformatics 21(8):1713-1714 .
• Sen, T*, Kloczkowski, A., Jernigan, R., Yan, C., Honavar, V., Ho, K., Wang, C., Ihm, Y. Cao, H., Dobbs, D.,Gu, X. (2004) Prediction of binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics. 5:205.

Vita: Click here to download

Website: Xun Gu

Mark Hargrove

Education: Ph.D., Rice, 1995

Research Interests: Structural biology, heme protein structure-function, X-ray crystallography

• Macromolecular Structure and Function-- Heme protein structure and function; X-ray crystallography

Description: The structure, function, folding, and expression of heme proteins. Heme proteins exhibit marked differences in reactivity toward diatomic ligands such as O2, CO, and NO, all of which are important biological molecules. However, unlike most enzymatic reactions which rely on the exact shape and charge distribution of the substrate molecule to determine specificity, selective recognition of small diatomic ligands by heme proteins occurs after the heme-ligand complex is formed

Selected Publications:

• Hargrove, M.S.(2005) Ligand binding with stopped-flow rapid mixing. Methods Mol. Biol. 305,323-342.

Vita: Click here to download

Website: Mark Hargrove

Kai-Ming Ho

Education: Ph.D., Berkeley, 1978

Research Interests: Protein structure prediction

• Macromolecular Structure and Function-- Protein structure prediction

Description:

Selected Publications:

Vita: Click here to download

Website: Kai-Ming Ho

Vasant Honavar

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

Research Interests: Bioinformatics and computational systems biology, artificial intelligence, computational systems biology, data mining and machine learning, databases and knowledge bases, information integration, semantic web, e-science

• Bioinformatics--Ontology-driven and probabilistic approaches to integrative and collaborative analysis of disparate biological data sets; description logics, ontology design, ontology tools, semantic web for life sciences including semantics based data integration, web services.
• Macromolecular Structure and Function--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
• Computational Systems Biology-Qualitative, probabilistic, and dynamic modeling, simulation, and inference of protein-protein interaction networks, genetic regulatory networks, signal transduction networks and metabolic pathways; Biological Computation Evolutionary, Cellular and Neural Computation.
• Data Mining and Machine Learning- Statistical, information theoretic, linguistic and structural approaches to machine learning, Learning and refinement of Bayesian networks, causal networks, Markov networks and Markov random fields, decision networks, neural networks, support vector machines, kernel classifiers, multi-relational models, language models (n-grams, grammars, automata), 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, spectral clustering, selected topics in computational learning theory.
• Semantic Web for e-science: Ontology-based user and query-centric approaches to information integration and acquisition of sufficient statistics for learning from data under different access and resource constraints from heterogeneous, distributed, autonomous, ubiquitous information sources, sensor networks, peer-to peer networks; description logics, ontology design, ontology tools, ontology-extended information sources, ontology-extended workflow components, ontology-extended agents and services, web service composition.

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

• How can we query and use information from autonomous, heterogeneous, distributed, autonomous data and knowledge sources?
• How can we build useful predictive models from large, distributed, semantically heterogeneous, autonomous data sources?
• How can we develop software environments for collaborative development, sharing, and use of large, complex, knowledge bases?
• How can we develop sophisticated machine learning algorithms for knowledge acquisition from richly structured data (sequences, images, graphs, text, etc.)
• How can we support the design, assembly and execution of complex web services using autonomously developed components?
• How can we represent and manipulate scientific knowledge in a form that lends itself to automated processing by the computer and at the same time, is comprehensible by, and communicable to humans?
• How can we develop information processing models of perception, learning, inter-agent communication, multi-agent interaction, coordination, and organization?
• How is information encoded, stored, retrieved, decoded, and used in macromolecular, neural, and cognitive systems?
• How can we discover the relationships between macromolecular sequence, structure, expression, interaction and macromolecular function?
• How can we construct accurate predictive models of signaling networks involved in cellular development, differentiation, and biological function?
• How can we model complex systems at multiple levels of abstraction in space and time?
• How can we automate scientific discovery?

Selected Publications:

• Andorf, C., Silvescu, A., Dobbs, D., and Honavar, V. (2007) Detecting Inconsistencies in Gene Ontology Protein Function Annotations: A MachineLearning Approach. BMC Bioinformatics. In press.
• Bao, J., Slutzki, G., and Honavar, V. (2007). A Semantic Importing Approach to Reusing Knowledge from Multiple Autonomous Ontology Modules. In: Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-2007).
• Bao, J., Slutzki, G. and Honavar, V. Privacy-Preserving Reasoning on the Semantic Web. ACM/WIC/IEEE International Conference on Web Intelligence, San Jose, CA, In press, 2007.
• Bao, J., Slutzki, G., and Honavar, V. Distributed Reasoning with Modular ALC Ontologies (ALCP). Web Intelligence and Agent Systems. Vol. In press, 2007.
• Caragea, C., Sinapov, J., Terribilini, M., Dobbs, D. and Honavar, V. Assessing the Performance of Macromolecular Sequence Classifiers. IEEE Conference on Bioinformatics and Bioengineering, In press.
• Dunn-Thomas, T., Dobbs, D.L., Sakaguchi, D. Young, M.J. Honavar, V. Greenlee, H. M. W. (2007). Proteomic Differentiation Between Murine Retinal and Brain Derived Progenitor Cells. Stem Cells and Development.  In press.
• El-Manzalawy, Y., Dobbs, D. and Honavar, V.  (2007) PepMIL: A Novel Method for Predicting Flexible Lengths MHC-II binding Peptides. In press. 2007.
• Hecker, L., Alcon, T., Honavar, V., Greenlee, H. (2007). Querying multiple large-scale gene expression datasets from the developing retina using a seed network to prioritize experimental targets. To appear.
• Pathak, J., Basu, S., and Honavar, V. (2007). On Context-Specific Substitutability of Web Services. Proceedings of the IEEE International Conference on Web Services, IEEE. 2007.
• 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
• Wu, F., Towfic, F., Dobbs, D. and Honavar, V. (2007) Analysis of Protein Protein Dimeric Interfaces. IEEE International Conference on Bioinformatics and Biomedicine, San Jose, In press, 2007.
• Yan, C., Wu, F., Jernigan, R.L., Dobbs, D., Honavar, V. (2007) Analysis of Protein-Protein Interfaces. Proteins. In press.
• Bao, J., Caragea, D., and Honavar, V. (2006). A Tableau-based Federated Reasoning Algorithm for Modular Ontologies. ACM / IEEE / WIC Conference on Web Intelligence, Hong Kong, pp. 404-410.
• Bao, J., Hu, Z., Caragea, D., Reecy, J., and Honavar, V. (2006). A Tool for Collaborative Construction of Large Biological Ontologies. Fourth International Workshop on Biological Data Management (BIDM 2006), Krakov, Poland, IEEE Press.  pp. 191-195.
• Bao, J., Caragea, D., and Honavar, V. (2006). Modular Ontologies - A Formal Investigation of Semantics and Expressivity. In Proceedings of the First Asian Semantic Web Conference, Beijing, China, Springer-Verlag  Lecture Notes in Computer Science, Vol. 4185, pp. 616-631. Best paper award.
• Caragea, D., Zhang, J., Pathak, J., and Honavar, V. (2006). Learning Classifiers from Distributed, Ontology-Extended Data Sources. Proceedings of the 8th International Conference on Data Warehousing and Knowledge Discovery (DaWaK 2006), Krakov, Poland, Lecture Notes in Computer Science. Berlin: Springer. Vol. 4081. pp. 363-373
• Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2006).  Selecting and Composing Web Services Through Iterative Reformulation of Functional Specifications.  Proceedings of the IEEE International Conference on Tools With Artificial Intelligence (ICTAI 2006), Washington, DC, IEEE. Best Paper Award.
• Terribilini, M., Lee, J-H., Yan, C., Honavar, V. and Dobbs, D. (2006). Identifying Interactions in Recalcitrant Proteins. Predicted Protein and RNA binding sites in REV proteins of HIV and EIAV agree with experimental data. In: Proceedings of the Pacific Symposium on Biocomputing, Hawaii, World Scientific. Vol. 11. pp. 415-426.
• 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.
• Zhang, J., Silvescu, A., Kang, D-K., and Honavar, V. (2006). Learning Compact and Accurate Naive Bayes Classifiers from Attribute Value Taxonomies and Partially Specified Data. Knowledge and Information Systems. Vol. 9. No. 2. pp. 157-179, 2006.
• Caragea, D., Zhang, J., Bao, J., Pathak, J., and Honavar, V. (2005). Algorithms and Software for Collaborative Discovery from Autonomous, Semantically Heterogeneous, Distributed, Information Sources. Invited paper. In: Proceedings of the Conference on Algorithmic Learning Theory. Lecture Notes in Computer Science. Vol. 3734. Berlin: Springer-Verlag. pp. 13-44.
• Lonosky, P.,  Zhang, X., Honavar, V., Dobbs, D., Fu, A., and Rodermel, S. (2004) A Proteomic Analysis of Chloroplast Biogenesis in Maize.  Journal of Plant Physiology. Vol. 134, pp. 560-574, 2004. Yan, C., Dobbs, D., and Honavar, V. (2004).
• A Two-Stage Classifier for Identification of Protein-Protein Interface Residues. Bioinformatics. 20. pp. i371-378, 2004. (Also presented at the Conference on Intelligent Systems in Computational Biology, 2004)
• Silvescu, A. and Honavar, V. (2001). Temporal Boolean Network Models of Genetic Networks and Their Inference from Gene Expression Time Series. Complex Systems. Vol. 13. No. 1. pp. 56-78.

Vita: Click here to download

Website: Vasant Honavar

Mei Hong

Education: Ph.D., Berkeley, 1996

Research Interests: Solid-state NMR studies of the structure and dynamics of membrane proteins and fibrous biopolymers

• Macromolecular Structure and Function-- Determination of the structure and dynamics of membrane-bound proteins and fibrous biopolymers by solid-state NMR

Description: To elucidate the structure and dynamics of membrane proteins, fibrous protein aggregates, and other insoluble macromolecules important in biology

Selected Publications:

• M. Tang, A.J. Waring, and M. Hong, "Intermolecular Packing and Alignment of a β-Hairpin Peptide from 2D Solid-State NMR", J. Am. Chem. Soc. , 2005, in press.
• W. Luo, X.L. Yao and M. Hong, "Evidence of Large Structure Rearrangement of Colicin Ia Channel Domain Due to Membrane Binding from 2D 13C Spin Diffusion NMR", J. Am. Chem. Soc., 2005, 127, 6402-8.

Vita: Click here to download

Website: Mei Hong

Richard Honzatko

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:

• Huang, X. and Madan, A. (1999) CAP3: A DNA Sequence Assembly Program, Genome Research, 9: 868-877.
• 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., 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.
• Ye, L. and Huang, X. (2005) MAP2: Multiple Alignment of Syntenic Genomic Sequences. Nucleic Acids Research, 33: 162-170.
• Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997) A Tool for Analyzing and Annotating Genomic Sequences. Genomics, 46: 37-45.
• 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.
• Huang, X. and Brutlag, D.L. (2007) Dynamic Use of Multiple Parameter Sets in Sequence Alignment,
  Nucleic Acids Research, 35: 678-686.

Vita: Click here to download

Website: Xiaoqiu Huang

Fred Janzen

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:

• Krenz, J. G., G. J. P. Naylor, H. B. Shaffer, and F. J. Janzen. 2005. Molecular phylogenetics and evolution of turtles. Molecular Phylogenetics and Evolution 37:178-191.
• Kuo, C.-H., and F. J. Janzen. 2004. Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata). Conservation Genetics 5:425-437.
• Kuo, C.-H., and F. J. Janzen. 2003. BottleSim: a bottleneck simulation program for long-lived species with overlapping generations. Molecular Ecology Notes 3:669-673. (Software available at http://www.arches.uga.edu/~chkuo/setsoft.html)
• Kolbe, J. J., and F. J. Janzen. 2002. Spatial and temporal dynamics of turtle nest predation: edge effects. Oikos 99:538-544.
• Janzen, F. J., and H. S. Stern. 1998. Logistic regression for empirical studies of multivariate selection. Evolution 52:1564-1571. (Software available at http://www.public.iastate.edu/~fjanzen/software/regress.htm)
• Schwanz, L. E., and F. J. Janzen. 2008. Climate change and temperature-dependent sex determination: can individual plasticity in nesting phenology prevent extreme sex ratios? Physiological and Biochemical Zoology 81:accepted pending revision.
• St. Juliana, J. R., and F. J. Janzen. 2007. Can natural phenotypic variances be estimated reliably under homogeneous laboratory conditions? Journal of Evolutionary Biology 20:1406-1414.

Vita: Click here to download

Website: Fred Janzen

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:
• Sen TZ and Jernigan RL Optimizing cutoff distances and spring constants for the Gaussian Network Model of ATP-binding proteins, in “Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems,” 2006, Eds. I. Bahar and Q. Cui, Chapman and Hall/CRC, Boca Raton, pp 171-186.
• Kurkcuoglu O, Jernigan RL and Doruker P Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks, Biochemistry, 2006;45:1173-1182.
• Song G and Jernigan RL An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins, 2006;63:197-209.
• Terribilini M, Lee, JH, Yan C, Jernigan RL, Honavar V and Dobbs D (2006) Prediction of Protein-RNA Interfaces. RNA, 2006; 12: 1450-1462.
• Sen TZ, Feng Y, Garcia JV, Kloczkowski A and Jernigan RL The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J. Chem. Thy. Comput., 2006; 2, 696-704.
• Sen TZ, Kloczkowski A and Jernigan RL A DNA-Centric Look at Protein-DNA Complexes. Structure, 2006; 14:1341-2.
• Jernigan RL and Kloczkowski Packing regularities in biological structures relate to their dynamics. Methods Mol Biol, 2006; 350:251-76.
• Sen TZ, Kloczkowski A and Jernigan RL Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics. 2006; 7:355.
• Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D and Honavar V Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006;7:262.
• Sen TZ, Cheng H, Kloczkowski A and Jernigan RL A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Sci, 2006; 15:2499-2506.
• Terribilini M, Lee JH, Yan C, Jernigan RL, Carpenter S, Honavar V, and Dobbs D Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data. Pac. Symp. Biocomp. 2006;415-26.
• Pokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL and Kolinski A Ideal Amino Acid Exchange Forms for Approximating Substitution Matrices. Proteins, in press. Peto M, Kloczkowski A and Jernigan, RL. Shape-dependent designability studies of lattice proteins. J. Phys.: Cond. Matter, in press.

Vita: Click here to download

Website: Robert Jernigan

Douglas Jones

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

Description:

Selected Publications:

Vita: Click here to download

Website: Doug Jones

Suresh Kothari

Education: Ph.D., Purdue, 1977

Research Interests: Parallel and distributed computing and its applications in science and engineering. Specific topics of interest are: tools for parallelization of legacy codes, parallel performance models, and distributed processing systems

• Bioinformatics--Parallel and distributed computing; neural networks

Description:

Selected Publications:

Vita: Click here to download

Website: Suresh Kothari

Susan Lamont

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:

• Ye, X., Brown, S.R., Nones, K., Coutinho, L.L., Dekkers, J.C.M. and Lamont. S.J. 2007. Associations of myostatin gene polymorphisms with performance and mortality traits in broiler chickens. Genet. Sel. Evol. 39: 73-89.
• Zhou, H., Deeb, N., Evock-Clover, C., Mitchell, A., Ashwell, C. and Lamont, S.J. 2007. Genome-wide Linkage Analysis to identify chromosomal regions affecting phenotypic traits in the chicken. III. Skeletal integrity. Poultry Sci. 86:255-266.
• Zhou, H., Evock-Clover, C., McMurtry, J.P., Ashwell, C. and Lamont, S.J. 2007. Genome-wide Linkage Analysis to identify chromosomal regions affecting phenotypic traits in the chicken. IV. Metabolic traits. Poultry Sci. 86:267-276.
• Abasht, B. Dekkers, J.C.M, and Lamont, S.J. 2006. Review of quantitative trait loci Identified in the chicken. Poultry Sci. 85:2079-2096.
• Cheeseman, J.H., Kaiser, M.G., Ciraci, C., Kaiser, P. and Lamont, S.J. 2006. Breed effect on early cytokine mRNA expression in spleen and cecum of chickens with and without Salmonella enteritidis infection. Devel. Comp. Immunol. 31: 52-60.
• Hangalapura, B. N., Kaiser, M. G., van der Poel, J.J., Parmentier, H. K., and Lamont, S. J. 2006. Cold stress equally enhances in vivo pro-inflammatory cytokine gene expression in chicken lines divergently selected for antibody responses. Develop. Comp. Immunol. 30:503-511.
• Hasenstein, J.R., Zhang, G., and Lamont, S.J. 2006. Analyses of five gallinacin genes and the Salmonella enterica serovar enteritidis response in poultry. Infection & Immunity 74:3375-3380.
• Kaiser, M.G., J.H. Cheeseman, Kaiser, P., and Lamont, S.J. 2006. Cytokine expression in chicken peripheral blood mononuclear cells after in vitro exposure to Salmonella enterica serovar Enteritidis. Poultry Sci 85:1907-1911. Lamont, S.J. 2006. Perspectives in chicken genetics and genomics. Poultry Sci. 85:2048-2049.
• Wick, G., Andersson, L., Hala, K., Gershwin, M. E., Selmi, C.F., Erf, G. F., Lamont, S.J., and Sgonc, R. 2006. Avian models with spontaneous autoimmune diseases. Pp. 71-117. In: Advances in Immunology. F.W. Alt, Ed. Elsevier/Academic Press, San Diego, CA
• McElroy, J.P., Kim, J.J., Harry, D.E., Brown, S.R., Dekkers, J.C., and Lamont, S.J. 2006. Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens. Poultry Sci. 85:593-605.
• McElroy, J.P., Zhang, W., Koehler, K.J., Lamont, S.J., and Dekkers, J.C.M. 2006. Comparison of methods for analysis of selective genotyping survival data. Genetics Selec. Evol. 38:637-655.
• Soller, M., Weigend, S., Romanov, M.N., Dekkers, J.C.M., and Lamont, S.J. 2006. Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance. Poultry Sci. 85:2061-2078.
• Ye, X., Avendano, S., Dekkers, J.C.M. and Lamont, S.J. 2006. Association of twelve immune-telated genes with performance of three broiler lines in two different hygiene environments. Poultry Sci. 85:1555-1568.
• Ye, X., McLeod, S., Elfick, D., Dekkers, J.C.M., and Lamont, S.J. 2006. Rapid identification of single nucleotide polymorphisms and estimation of allele frequencies using sequence traces from DNA pools. Poultry Science 85: 1165-1168.
• Zhou, J., Deeb, N., Ashwell, C.M., and Lamont, S.J. 2006. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain. Poultry Sci. 85:1700-1711.
• Zhou, J., Deeb, N., Ashwell, C.M., and Lamont, S.J. 2006. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. II. Body composition. Poultry Sci. 85: 1712-1721.

Website: Susan Lamont

Dennis Lavrov

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

Description:

Selected Publications:

• Lavrov, D. V. 2007. Key transitions in animal evolution: a mitochondrial DNA perspective.  Integrative and Comparative Biology. 47:734-743.
• Haen, K. M., Lang, B. F., Pomponi, S. A. and Lavrov D. V. 2007. Mitochondrial genomes of the glass sponges Iphiteon panicea and Sympagella nux (Hexactinellida, Plakinidae): an evidence of the bilaterian affinity or an example of parallel evolution? Molecular Biology and Evolution. 24:1518-1527.
• Wang, X. and D. V. Lavrov 2007. Mitochondrial Genome of the Demosponge Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals  Molecular Biology and Evolution.  24: 363-373.
• Lavrov, D. V. and B. F. Lang, 2005.  Transfer RNA gene recruitment in mitochondrial DNA.  Trends in Genetics.  21:129-133.
• Lavrov D.V. and Lang B.F. 2005 Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements Systematic Biology 54:651-659.
• Lavrov D.V., Forget L., Kelly, M., and Lang B.F. 2005 Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution Mol. Biol. Evol. 22:1231-1239.

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. http://www.lawrencelab.org

Selected Publications:

• L.D. Stein, W.D. Beavis, D.D. Gessler, E. Huala, C.J. Lawrence, D. Main, L.A. Mueller, S.Y. Rhee, and D.S. Rokhsar, Save our data!, The Scientist 20(4):24-25, 2006.
• Lawrence, C.J. and Walbot, V. Maize as a model for bioenergy production from fuelstock grasses. The Plant Cell 19(7):2091-2094. 2007.
• Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D.,  Lawrence, C.J., Lushbough, C., and Brendel, V. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Research 36(Database issue):D959-965. 2008.
• Lawrence, C.J. MaizeGDB, the maize genetics and genomics database. In Plant bioinformatics, D. Edwards (Editor) for the series Methods in Molecular Biology. pp. 331-345. Humana Press, Totowa, New Jersey, USA. 2007.
• Lawrence, C.J. and Walbot, V. Reply: specific reasons to favor maize in the U.S. Plant Cell 19(10):2973. 2007.
• Lawrence, C.J. and Ware, D. Databases and data mining. In The maize handbook, S. Hake and J. Bennetzen (Editors), Springer. Accepted October 15, 2007.
• Harper, L.C., Sen, T.Z., and Lawrence, C.J. Plant cytogenetics in genome databases. In: Plant cytogenetics: genome structure and chromosome function. J. Birchler and H. Bass (Editors), Springer.  Accepted October 30, 2007.

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

Charles Link Jr.

Education: M.D., Stanford, 1985

Research Interests: Evaluation of cancer causes using high through-put genomic applications

• Functional and Structural Genomics-- Dr. Link's laboratory is interested in developing and applying high through-put genomic applications to evaluate the root causes of human cancer. This requires approaches to interface biological data with computers and to process and sort information in a useful way to advance the understanding of gene function in cancer cells

Description:

Selected Publications:

Vita: Click here to download

Website: Charles Link, Jr.

Peng Liu

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.

Publications:

• 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

Gustavo MacIntosh

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

Research Interests: Gene expression and metabolic changes during plant defense responses to pests; functional genomics of plant nucleases.

• Macromolecular Structure and Function-- Gene expression and metabolic changes during plant defense responses to pests; functional genomics of plant nucleases.

Description:

Selected Publications:

Vita: Click here to download

Website: Gustavo MacIntosh

Roger Maddux

Education: Ph.D., Berkeley, 1978

Research Interests: Relation algebras, logic, combinatorics, mathematical ecology

• Mathematical Biology-- species-area relationships

Description:

Selected Publications:

Vita: Click here to download

Website: Roger Maddux

Surya Mallapragada

Education: Ph.D., Purdue University, 1996

Research Interests: Designing polymers with tailored micro/nanostructures

• Macromolecular Structure and Function-- Our research program is focused on designing polymers with tailored micro/nanostructures, both at the surface as well as in the bulk, with relevance to technological and bioengineering applications. Fundamental investigations of molecular attributes, as well as studies of macroscopic performance are linked together to investigate the relationship between the two

Description:

Selected Publications:

Vita: Click here to download

Website: Surya Mallapragada

John Mayfield

Education: Ph.D., Pittsburgh, 1968

Research Interests: The goal of my research is to develop a generalized theory of evolution that relates naturally to fundamental mathematical and physical concepts of complexity.

• Genome Evolution-- Evolutionary theory; molecular genetics

Selected Publications:

• John E. Mayfield (2007) Minimal History, a Theory of Plausible Explanation. Complexity (in press)
• John E. Mayfield. (2006) Evolution as Computation. Evolutionary Theory (in press)

Vita: Click here to download

Website: John Mayfield

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

Description:

Selected Publications:

Vita: Click here to download

Website: Leslie Miller

Allen Miller

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

Description:

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:

• Chung BY-W, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105, 5897-5902.
• Treder K, Pettit Kneller EL, Allen EM, Wang Z, Browning KS, Miller WA (2008) The 3’ cap-independent translation element of Barley yellow dwarf virus binds eIF4F via the eIF4G subunit to initiate translation. RNA 14, 134-147.
• Miller WA, Wang Z, Treder K (2007) The amazing diversity of cap-independent translation elements in the 3’-untranslated regions of plant viral RNAs. Biochemical Society Transactions 35, 1629-1633.

Vita: Click here to download

Website: W. Allen Miller

Chris Minion

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:

• Menon, S. A. M., J. Wannemuehler, G. G. Mahairas, and F. C. Minion. 2002. Mycobacterial ESAT-6 protein enhances mouse interferon- responses to Mycoplasma hyopneumoniae P71 protein. J. Interf. Cytok. Res. 22:807-813.
• Minion, F.C., S.A. Menon, G.G. Mahairas, and M.J. Wannemuehler. 2003. Enhanced murine antigen-specific IFN- g responses using mycobacterial ESAT-6 sequences in DNA vaccines. Infect. Immun. 71:2239-2242.
• Matic, J.N., J.L. Wilton, R.J. Towers, A.L. Scarman, F.C. Minion, M.J. Walker and S.P. Djordjevic . 2003. The pyruvate dehydrogenase complex of Mycoplasma hyopneumoniae contains a novel lipoyl domain arrangement. Gene 319:99-106.
• Djordjevic, S. P., S. J. Cordwell, M. A. Djordjevic, J. Wilton, and F. C. Minion. 2004. Proteolytic processing of the Mycoplasma hyopneumoniae cilium adhesin. Infect. Immun. 72:2791-2802.
• Minion, F. C., E. L. Lefkowitz, M. L. Madsen, B J. Cleary, S. M. Swartzell, and G. G. Mahairas. 2004. The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J. Bacteriol. 186:7123-7133.
• Adams, C., J. Pitzer, and F. C. Minion. 2005. In vivo expression analysis of the P97 and P102 paralog families of Mycoplasma hyopneumoniae. Infect. Immun. 73:7784-7787.
• Madsen, M. L., D. Nettleton, E. L. Thacker, R. Edwards, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays. Infect. Immun. 74: 167-174.
• Jenkins, C., J. L. Wilton, F. C. Minion, L. Falconer, M. J. Walker, and S. P. Djordjevic. 2006. Two domains within the Mycoplasma hyopneumoniae cilium adhesin bind heparin. Infect. Immun. 74:481-487.
• Burnett, T.A., K. Dinkla, M. Rohde, G.S. Chhatwal, M. Srivastava, S.J. Cordwell, S. Geary, F. C. Minion,. M. J. Walker, S. P. Djordjevic. 2006. P159 is a proteolytically processed, surface adhesin of Mycoplasma hyopneumoniae: defined domains of P159 bind heparin and promote adherence to eukaryotic cells. Mol. Microbiol. 60:669-686.
• Madsen, M. L., D. Nettleton, E. L. Thacker, and F. C. Minion. 2006. Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152:937-944.
• Schafer, E. R., M. J. Oneal, M. L. Madsen, F. C. Minion. 2007. Global transcriptional analysis of Mycoplasma hyopneumoniae following exposure to hydrogen peroxide. Microbiol. 153:3785-3790.
• Madsen, M. L., M. J. Oneal, S. W. Gardner, E. L. Strait, D. Nettleton, E. L. Thacker, and F. C. Minion. 2007.Array-based genomic comparative hybridization of field strains of Mycoplasma hyopneumoniae. J. Bacteriol. 189:7977-7982.
• Vicca, J., D. Maes, T. Stakenborg, P. Butaya, F. Minion, J. Peeters, A. De Kruif, A. Decostere, and F. Haesebrouck. 2007. Resistance mechanism against fluoroquinolones in Mycoplasma hyopneumoniae field isolates. Microb. Drug Resist. 13:166-170.
• Madsen, M. L., S. Puttamreddy, E. L. Thacker, M. D. Carruthers, F. C. Minion. 2008. Transcriptome changes in Mycoplasma hyopneumoniae during infection. Infect. Immun. 76:658-663.
• Chang, L.-J., W.-H. Chen, F. C. Minion and D. Shiuan. 2008. Mycoplasmas regulate the expression of heat shock protein genes through CIRCE-HrcA interactions. Biochem. Biophys. Res. Commun. 367:213-218.

Vita: Click here to download

Website: Chris Minion

Kirk Moloney

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

Alan Myers

Education: Ph.D., Duke, 1983

Research Interests: mRNA and polypeptide profiling, predictions and modeling of protein structures

• Functional and Structural Genomics-- Gene identification in nucleotide sequence databases, mRNA and polypeptide profiling, predictions and modeling of protein structures, and global analysis of metabolism
• Macromolecular Structure and Function-- Same as above

Description:

Selected Publications:

• Zhang, X., Myers, A.M. and James, M.G. (2005) Mutations affecting starch synthase III in Arabidopsis alter leaf starch structure and increase the rate of starch synthesis. Plant Physiol. 138,663-674.
• Morell, M.K. and Myers, A.M. (2005) Towards the rational design of cereal starches. Curr. Opin. Plant Biol. 8, 204-210.
• Zhang, X., Colleoni, C., Ratushna, V., Sirghie-Colleoni, M., James, M.G. and Myers, A.M. (2004) Molecular characterization demonstrates that the Zea mays gene sugary2 codes for starch synthase isoform SSIIa. Plant Mol. Biol. 54, 865-879.

Vita: Click here to download

Website: Alan Myers

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

Description:

Selected Publications:

• Nettleton, D. (2006). A Discussion of statistical methods for design and analysis of microarray experiments for plant scientists. The Plant Cell. 18 2112-2121.
• Wang, D., Nettleton, D. (2006). Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling. Biometrics. 62 504-514.
• Nettleton, D., Hwang, J.T.G., Caldo, R.A., Wise, R.P. (2006). Estimating the number of true null hypotheses from a histogram of p-values. Journal of Agricultural, Biological, and Environmental Statistics. 11 337-356.

Vita: Click here to download

Website: Dan Nettleton

Basil Nikolau

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

Description:

Selected Publications:

• Dietrich, C.R., Perera, M.A., M, D.Y.-N., Meeley, R.B., Nikolau, B.J.and Schnable, P.S. (2005) Characterization of two GL8 paralogs reveals that the 3-ketoacyl reductase component of fatty acid elongase is essential for maize (Zea mays L.) development. Plant J. 42,844-861.
• Fatland, B.L., Nikolau, B.J. and Wurtele, E.S. (2005) Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-Citrate lyase in Arabidopsis. Plant Cell 17, 182-203. Yandeau-Nelson, M.D., Zhou, Q., Yao, H., Xu, X., Nikolau, B.J. and Schnable, P.S. (2005) MuDR transposase increases the frequency of meiotic crossovers in the vicinity of a Mu insertion in the maize a1 gene. Genetics 169, 917-929.
• Sluszny, C., Yeung, E.S. and Nikolau, B.J. (2005) In-situ probing of the biotic-abiotic boundary of plants by laser desorption/ionization time-of-flight mass spectrometry. J. Am. Soc. Mass. Spectrom. 16, 107-115.

Vita: Click here to download

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

Lisa K. Nolan

Education: D.V.M..,University of Georgia, Athens, 1988; Ph.D., University of Georgia, Athens, 1992

Research Interests: We employ functional and structural genomics approaches to understand the molecular pathogenesis of E. coli-caused diseases of humans and animals

Description: Our research explores the molecular basis of virulence and resistance of E. coli-caused diseases of humans and animals and exploits the knowledge gained to better control these diseases. We combine pan-genome approaches with classic bacteriology to identify molecular mechanisms underlying E. coli virulence and resistance. In particular, we focus on the E. coli that are responsible for such extraintestinal diseases, as human urinary tract infections and neonatal meningitis and avian colisepticemia and cellulitis. We also use genomic approaches to look for relationships between pathogenic E. coli of food animals and human disease, and we explore the contributions of plasmids to the pathogenesis and evolution of extraintestinal pathogenic E. coli and Salmonella.

Selected Publications:

• Johnson, T.J., Siek, K.E., Johnson, S., and Nolan, L.K. 2006. Complete Sequence of a ColV Plasmid and Prevalence of Selected Plasmid-Encoded Virulence Genes among Avian Escherichia coli Strains. J Bacteriol. 188: 745-758.
• Kariyawasam, S., Johnson, T.J., and Nolan, L.K. 2006. pap Operon of Avian Pathogenic Escherichia coli Strain O1 is Located on a Novel Pathogenicity Island. Infect Immun. 74: 744-749.
• Skyberg, J.A., Logue, C.M., and Nolan, L.K. 2006. Virulence Genotyping of Salmonella spp. with Multiplex PCR. Avian Dis. 50: 77-81.
• Q. Li, J.A. Skyberg, M.K. Fakhr, J.S. Sherwood, L.K. Nolan, and C.M. Logue. 2006. Antimicrobial Susceptibility and Characterization of Salmonella Isolated from Processed Bison Carcasses. Appl Environ Microbiol. 72: 3046-3049.
• Lynne, A.M., Foley, S.L., and Nolan, L.K. 2006. Immune Response to Recombinant Escherichia coli Iss in Poultry. Avian Dis. 50: 273-276.
• Skyberg, J.A., Siek, K.E., Doetkott, C., and Nolan, L.K. 2006. Biofilm formation on Plastic Surfaces by Escherichia coli Isolated from Sick and Healthy Poultry. J Appl Microbiol. 102: 548-554.
• Lynne, A. M., Foley, S.L., and Nolan, L.K. 2006. Characterization of Monoclonal Antibodies to Avian Escherichia coli Iss. Avian Dis. 50: 445-449.
• Johnson, T.J., Johnson, S.J., and Nolan, L.K. 2006. Complete DNA Sequence of a ColBM Plasmid Occurring in an Extraintestinal Pathogenic Escherichia coli Isolate and Its Prevalence among Other E. coli Isolates. J Bacteriol. 188: 5975-5983.
• Kariyawasam, S., Johnson, T.J., DebRoy, C., and Nolan, L.K. 2006. Occurrence of Pathogenicity Island APEC-O1 Genes Among Escherichia coli Implicated in Avian Colibacillosis. Avian Dis. 50: 405-410.
• *Skyberg, J.A., Johnson, T.J., Johnson, J.R., Clabots, C., Logue, C.M., and Nolan, L.K. 2006. Acquisition of Avian Pathogenic Escherichia coli Plasmids by a Commensal E. coli Isolate Enhances Its Abilities to Kill Chick Embryos, Grow in Human Urine, and Colonize the Murine Kidney. Infect Immun. 74: 6287-6292.
• Kariyawasam, S., Johnson, T.J., Siek, K.E., and Nolan, L.K. 2006. Unique DNA Sequences of Avian Pathogenic Escherichia coli Isolates as Determined by Genomic Suppression Subtractive Hybridization. FEMS Microbiol Lett. 262: 193-200.
• Lynne, A.M., Skyberg, J.A., Logue, C.M., and Nolan, L.K. 2007 (Online 2006). Detection of Iss and Bor on the Surface of Escherichia coli. J Appl Microbiol. 102: 660-666.
• Johnson, T.J., Wannemuehler, Y., Scaccianoce, J., Johnson, S.J., and Nolan, L.K. 2006. Complete DNA Sequence of an Avian Pathogenic Escherichia coli IncHI2 Plasmid Reveals Striking Similarities to Serratia marcescens Plasmid R478. Antimicrob Agents Chemother. 50: 3929-3933.
• Johnson, T.J., Kariyawasam, S., Wannemuehler, Y., Mangiamele, P., Johnson, S.J., Doetkott, C., Skyberg, J.A., Lynne, A.M., and Nolan, L.K. 2007. Genome Sequence of Avian Pathogenic Escherichia coli Strain O1:K1:H7 Shares Strong Similarities with Human ExPEC Genomes . J Bacteriol. 189: 3228-3236.
• Johnson, T.J., Wannemuehler, Y.M., Johnson, S.J., Logue, C.M., White, D.G., Doetkott, C., and Nolan, L.K. 2007. Plasmid Replicon Typing of Commensal and Pathogenic Types of Escherichia coli. Appl Environ Microbiol. 73:1976-1983.
• Lynne, A.M., Skyberg, J.A., Logue, C.M., and Nolan, L.K. 2007. Characterization of a Series of Transconjugant Mutants of an Avian Pathogenic Escherichia coli Isolate for Resistance to Serum Complement. Avian Dis. 51:771-776.
• Trampel, D.W., Wannemuehler, Y., and Nolan, L.K. 2007. Characterization of APEC from Peritonitis Lesions in Commercial Laying Hens. Avian Dis. 51:840-4.
• Kariyawasam, S., Scaccianoce, J., and Nolan, L.K. 2007. Common and Specific Virulence-Associated Markers of Avian and Human Extraintestinal Pathogenic Escherichia coli as Determined by Genomic Subtractive Hybridization. BMC Microbiol. 7:81-88.
• Skyberg, J., Johnson, T.J., and Nolan, L.K. 2008. Mutational and Transcriptional Analyses of an Avian Pathogenic Escherichia coli ColV Plasmid. BMC Microbiol.8:24.
• Johnson, T.J., Wannemuehler, Y.M., and Nolan, L.K. 2008. Evolution of the iss Gene in Escherichia coli. Accepted by Appl Environ Microbiol.

Vita: Click here to download

Website: Lisa K. Nolan

Jean Peccoud

Education: Ph.D., Grenoble, 1991

Research Interests

• Calibration of genetic parts Modularity of artificial gene networks Portability of artificial gene networks across biological species
• Genetic properties of gene networks

• Bioinformatics-- Genetic properties and evolution of molecular networks, design of artificial gene networks, numerical methods for simulating molecular networks

Selected Publications:

• Dellabona P, Peccoud J, Kappler J, Marrach P, Benoist C, Mathid D (1990) Superantigens interact with MHC class II molecules outside of the antigen groove. Cell 62: 1115-1121.
• Peccoud J, Jacob C (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J. 71: 101-108.
• Goss PJ, Peccoud J (1998) Quantitative modeling of stochastic systems in molecular biology using stochastic Petri nets. Proc. Natl. Acad. Sci. U.S.A. 95: 6750-6755.
• Peccoud J, Velden KV, Podlich DW, Winkler CR, Arthur WL, Cooper M (2004) The selective values of alleles in a molecular network model are context dependent. Genetics 166: 1715-1725.

Description:

Jean Peccoud received his Ph.D. in molecular biology and bioinformatics from the University of Grenoble, France, in 1991. Prior to joining VBI, he was responsible for a research program at Pioneer Hi-Bred International that focused on gene and regulatory network discovery, the design of DNA transformation vectors, and the development of methods to analyze the genetic properties of gene networks. As an associate professor in the Department of Genetics, Development & Cell Biology at Iowa State University, he collaborated with the Bioinformatics and Computational Biology program since 2003. From 2000-2001, Dr. Peccoud founded and oversaw the operations of e-NoteBooks, Inc. (Seattle, WA), a support company for the technical computing industry, which sold its assets to The MathWorks, Inc. (Natick, MA) and BetterVIEW Consulting (Vancouver, BC). From 1994-1999, Jean Peccoud held a series of research positions at the Institut National de la Sant et de la Recherche Mdicale (INSERM) in Grenoble, France, and in the Department of Electrical Engineering at the University of Washington in Seattle.

Vita: Click here to download

Website: GDCB -- Jean Peccoud; VBI Website -- https://www.vbi.vt.edu/article/articleview/371

Thomas Peterson

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

Research Interests: Transposons elements, genome rearrangements

• Functional and Structural Genomics-- Characterization and prediction of gene regulatory regions; computational reduction of primary genomic sequence data to composite elements; computational analysis of regulatory information encoded in DNA base modifications, e.g. methylation

Description:

Selected Publications:

• Cocciolone, S.M., Nettleton, D., Snook, M.E., and T. Peterson. 2005. Transformation of maize with the p1 transcription factor directs production of silk maysin, a corn earworm resistance factor, in concordance with a hierarchy of floral organ pigmentation. Plant Biotechnology Journal 3: 225-235.
• Zhang, F. and T. Peterson. 2005. Comparisons of maize pericarp color 1 alleles reveal paralogous gene recombination and an organ-specific enhancer region. The Plant Cell 17: 903 ­ 914.
• Zhang, J. and T. Peterson. 2005. A Segmental Deletion Series Generated by Sister Chromatid Transposition of Ac Transposable Elements in Maize. Genetics 2005: doi: 10.1534/genetics.104.035576.
• Boddu, J., Sangar, V., Jiang, C., Olson, T., Peterson, T., and S. Chopra. Comparative structural and functional characterization of sorghum and maize duplications containing orthologous Myb transcription regulators of 3-deoxyflavonoid biosynthesis. (Plant Mol. Biol., accepted).
• Zhang, F. and T. Peterson. Gene conversion between direct non-coding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.) Genetics, in press
• Zhang, J., Zhang, F., and T. Peterson. Transposition of Reversed Ac Element Ends Generates Novel Chimeric Genes in Maize. PLoS Genetics, in press.

Vita: Click here to download

Website: Agronomy: Thomas Peterson; GDCB Page

Gregory Phillips

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

Description:

Selected Publications:

• 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

Edward Pollak

Education: Ph.D., Columbia, 1964

Research Interests: Effects on populations of selection and finite population size

• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Mathematical, population and quantitative genetics, focusing on how the genetic composition of populations is influenced by selection, migration, systems of mating and finite population size

Description:

Selected Publications:

• Pollak, E.(2000) The effective population size of some age structured populations.Mathematical Biosciences, 168:39-56.
• Wang, Y. and Pollak,E. (2000) The effective number of a population that varies cyclically in size. I. Discrete generations. Mathematical Biosciences 166:1-21.
• Wang, Y. and Pollak, E. (2002) The effective number of a population That varies cyclically in size. II. Overlapping generations. Mathematical Biosciences, 179:161-181.
• Pollak, E. (2006) Genealogical theory for random mating populations with two sexes. Mathematical Biosciences, 202,133-155.
• Pollak, E. (2007) Coalescent theory for a completely random mating monoecious population. Mathematical Biosciences, 205: 315-324.

Vita: Click here to download

Stephen Proulx

Education: University of Utah, Department of Biology, May 2000

Research Interests:

• Genome Evolution-- Much of my current work is focused on understanding the evolutionary forces that structure genomes. Do genomes evolve to be robust? How do multi-gene families form? What evolutionary forces act to shape the machinery of DNA replication, transcription, and translation? My research has shown that environmental and ecological context play a surprisingly large role in the evolution of these basic genomic features
• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking-- Same as above

Description:

Selected Publications:

• Proulx, S.R. , Promislow, D.E.L. and Phillips, P.C. 2005, Network thinking in ecology and evolution. Trends in Ecology and Evolution, 20(6):345-353.
• Day, T., Proulx, S.R. , 2004. A general theory for the evolutionary dynamics of virulence, The American Naturalist, 163(4):E40-E63.

Vita: Click here to download

Website: Stephen Proulx

Krishna Rajan

Education: Sc.D., MIT, 1978.

Research Interests: Linking bioinformatics with materials informatics.

Vita: Click here to download

Website: http://mse.iastate.edu/cosmic/why2.html

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:

• Zhi-Liang, H., E.R. Fritz, and J.M. Reecy. 2006. AnimalQTLdb: A Livestock QTL Database Tool Set for Positional QTL Information Mining and Beyond. Nucleic Acid Research Database issue doi:10.1093/nar/gkl946. Nucleic Acid Research 35(Database issue):D604-9.
• Zhi-Liang, H., and J.M. Reecy. 2007. Animal QTLdb: Beyond a Repository – A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome 18(1):1-4.
• Tuggle, C.K., J.C.M. Dekkers, and J.M. Reecy. 2006. Integration of structural and functional Genomics. Animal Genetics 37:(Supplement 1):1-6.
• Tantia, M.S., R.K. Vijh, S.T. Bharani Kumar, B. Mishra, and J.M. Reecy. 2006. Comparative analysis of GDF 8 (myostatin) in Bos indicus and Bos Taurus. DNA Sequence 17(4):311-3.
• Bao, J., Z. Hu, D. Caragea, J.M. Reecy, and V. Honavar. A Tool for Collaborative Construction of Large Biological Ontologies. Fourth International Workshop on Biological Data Management (BIDM 2006), Krakov, Poland, IEEE Press. pp. 191-195
• Steelman, C. A., J.C. Recknor, D. Nettleton, and J.M. Reecy. 2006. Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy. FASEB Journal 20(3):580-582. Epub 2006 Jan 19.
• Steelman, C.A., J.C. Recknor, D. Nettleton, and J.M. Reecy. 2006. Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy. FASEB J. published Jan 19, 2006, doi:10.1096/fj.05-5125fje.

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:

• 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

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

Description:

Selected Publications:

Vita: Click here to download

Website: Steve Rodermel

Max Rothschild

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

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

Description:

Selected Publications:

• Grozdanic, S.D., Ast, A.M., Lazic, T., Kwon, Y.H., Kardon, R.H., Betts, D.M., Sonea, I.M. and Sakaguchi, D.S. (2006) Morphological integration and functional assessment of transplanted neural progenitor cells in healthy and acute ischemic rat eyes. Experimental Eye Research. 82 (4): 597-607.
• Ostojic, J., Sakaguchi, D.S., de Lathouder, Y., Hargrove, M.S., Trent, J.T. III., Kwon, Y.H., Kardon, R.H., Kuehn, M.H., Betts, D.M., and Grozdanic, S.D. (2006) Neuroglobin and Cytoglobin: Oxygen binding proteins in retinal neurons. Investigative Ophthalmology and Visual Science. 47(3): 1016-1023.
• Recknor, J.B., Sakaguchi, D.S., Mallapragada, S.K. (2006) Directed growth and selective differentiation of neural progenitor cells on micropatterned polymer substrates. Biomaterials. 27(22): 4098-4108.
• Eucher, J.N., Uemura, E., Sakaguchi, D.S., and Greenlee, M.H.W. (2007) Amyloid-beta peptide affects mitochondrial function but not differentiation of embryonic and adult rat hippocampal progenitor cells. Experimental Neurology. 203(2):486-92.

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.

Description:

Selected Publications:

• Emrich SJ, L Li, TJ Wen, MD Yandeau-Nelson, Y Fu, L Guo, HH Chou, S Aluru, DA Ashlock, PS Schnable (2007) Nearly identical paralogs (NIPs) and implications for maize genome evolution. Genetics, 175(1): 429-439.
• Ohtsu K, M Smith, SJ Emrich, LA Borsuk, R Zhou, T Chen, X Zhang, M Timmermans, J Beck, B Buckner, D Janick-Buckner, D Nettleton, MJ Scanlon, PS Schnable (2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).  Plant J, 52(3):391-404.
• Barbazuk WB, SJ Emrich, HD Chen, PS Schnable (2007) SNP discovery via 454 transcriptome sequencing.  Plant J, 51: 910-918.
• Emrich SJ, WB Barbazuk, L Li, PS Schnable (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing.  Genome Research, 17: 69-73.
• Swanson-Wagner R, Y Jia, R DeCook, LA Borsuk, D Nettleton, PS Schnable (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci, in press.
• Fu Y, SJ Emrich, L Guo, TJ Wen, S Aluru, DA Ashlock, PS Schnable (2005) Quality assessment of maize assembled genomic islands (MAGIs) and experimental verification of predicted novel genes. Proceedings Natil Acad Sci, 102:12282-12287.

Vita: Click here to download

Website: Patrick Schnable

Taner Sen

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:

• 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

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

Description:

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

Randy Shoemaker

Education: Ph.D., Iowa State, 1984

Research Interests: Genome evolution, organization and function; plant nutrition, disease resistance, seed composition and plant development.

Description: The Shoemaker laboratory focuses on legume biology. The group has two main foci; plant genomics and bioinformatics. The group currently is a key member of the multi-agency team assembling and analyzing the whole genome sequence of soybean. These efforts are facilitating studies of genome evolution, evolution of function, and evolution of polyploids. The biology of legumes is being explored through current projects on iron acquisition and utilization, disease resistance, seed composition and developmental ontology.

Selected Publications:

• Charlson, D., R. Shoemaker.  Evolution of Iron Acquisition in Higher Plants.  2006. Journal of Plant Nutrition 29:1109-1125.
• Shoemaker, R. Schlueter, J., and Doyle, J. 2006. Paleopolyploidy and gene duplication in soybean and other legumes. Current Opinions in Plant Biology 9:104-109.
• Schlueter, J.A., Scheffler, B.E., Schlueter, S.D. and Shoemaker, R.C., 2006 Sequence conservation of homeologous BACs and expression of homeologous genes in soybean (Glycine max L. Merr). Genetics. 174:1017-1028.
• Jackson, S.A., Rokhsar, D., Stacey, G., Shoemaker, R., Schmutz, J., and Grimwood, J. Toward a reference sequence of the soybean genome: a multiagency effort. 2006. The Plant genome 1: 55-61.
• Schlueter, J.A., Sanders, I.F., Deshpande, S., Yi, J., Siegfried, M., Roe, B.E., Schlueter, S.D., Scheffler, B.E., and Shoemaker, R.C., 2007 The FAD2 family of soybean: insights into the structural and functional divergence of a paleopolyploid genome. The Plant Genome. 1:14-26.
• O'Rourke, J.A., Graham, M.A., Vodin, L., Gonzalez, D. O., Cianzio, S.R., and Shoemaker, R.C.. 2007. Recovering from Iron Deficiency Chlorosis in near-isogenic lines of soybeans: A microarray study. Plant Phys. And Biochemistry 45:287-292.
• O'Rourke, J.A., Charlson, D.V., Gonzalez, D.O., Vodkin, L., Graham, M., Cianzio, S., Grusak, M. and Shoemaker, R.C. Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. Biomed Central (BMC) Genomics.
• Schlueter, J., Lin, J.-Y., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O'Bleness, M., Roe, B., Nelson R., Scheffler, B., Jackson, S. and Shoemaker, R. Gene duplication and paleopolypoloidy in soybean and the implications for whole genome sequencing. Biomed Central (BMC) Genomics 8:330.
• Randy Shoemaker, David Grant, Terry Olson, Wesley C. Warren, Rod Wing, Yeisoo Yu, HyeRan Kim, Perry Cregan, Bindu Joseph, Montona Futrell-Griggs, Will Nelson, Jon Davito, Jason Walker, John Wallis, Colin Kremitski, Debbie Scheer, Sandy Clifton, Tina Graves, Henry Nguyen, Xiaolei Wu, Mingcheng Luo, Jan Dvorak, Rex Nelson, Steven Cannon, Jeff Tomkins, Jeremy Schmutz, Gary Stacey, and Scott Jackson. 2008. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps. Genome (In Press).

Website: Randy Shoemaker

Pranav Shrotriya

Education: Ph.D., University of IL, Champaign-Urbana, 2001

Research Interests: To understanding the influence of ligand/receptor binding on as surface stress development. We want to utilize this understanding for development of surface stress sensors for detection of chemical and biological species.

Selected Publications:

• P. Shrotriya, S. M. Allameh, J. Lou, T. Buchheit, and W. O. Soboyejo, “On the measurement of the plasticity length scale parameter in LIGA nickel foils,” Mechanics of Materials, vol. 35, pp. 233-243, 2003
• J. Lou, P. Shrotriya, T. Buchheit, D. Yang, and W. O. Soboyejo, “Nanoindentation study of plasticity length scale effects in LIGA Ni Microelectromechanical systems structures,” Journal of Materials Research, vol. 18, pp. 719-728, 2003
• S. M. Allameh, P. Shrotriya, A. Butterwick, S. B. Brown, and W. O. Soboyejo, “Surface topography evolution and fatigue fracture in polysilicon MEMS structures,” Journal of Microelectromechanical Systems, vol. 12, pp. 313-324, 2003

Website: Pranav Shrotriya

Michael Smiley

Education: Ph.D., Michigan, 1980

Research Interests:

• Mathematical Biology, Computational Modeling, and Metabolic and Developmental Networking

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 http://la-press.com/). Vita: Click here to download

Website: Michael Smiley

Jonathan Smith

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

Description:

Selected Publications:

• Guang Song and Robert L. Jernigan, "vGNM: a Better Model for Understanding the Dynamics of Proteins in Crystals" Journal of Molecular Biology, 2007, to appear.
• 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, 2007, to appear.
• Guang Song and Robert L. Jernigan, "An Enhanced Elastic Network Model to Represent the Motions of Domain-Swapped Proteins," Proteins, 63(1):197-209, 2006.
• Guang Song and Nancy M. Amato, "A Motion Planning Approach to Folding: From Paper Craft to Protein Folding, " IEEE Transactions on Robotics and Automation, 20(1):60-71, 2004.
• Nancy M. Amato, Ken A. Dill, and Guang Song, "Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures," Journal of Computational Biology, 10(3-4):239-256, 2003. Featuring selected papers from RECOMB 2002.
• Guang Song and Nancy M. Amato, "Using Motion Planning to Study Protein Folding Path-ways," in Proceedings the 5th ACM International Conference on Computational Molecular Biology (RECOMB), pp. 287-296, April 2001, Montreal, Canada.

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

Description:

Selected Publications:

Vita: Click here to download

Website: Xueyu Song

Bo Su

Education: Ph.D., Northwestern University, 1999

Research Interests: Nonlinear Partial Differential Equations: Mathematical Biology, Calculus of Variations, Free Boundary Problems, Homogenization, Fluid Mechanics. Mathematical Modeling in Biology.

Vita: Click here to download

Website: Bo Su

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:

• 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

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:

• 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).
• Zhao, S.-H. J. Recknor, J.K. Lunney, D. Nettleton, D. Kuhar, S. Orley, H. Dawson, C. K Tuggle. 2005. Validating a first-generation porcine oligonucleotide microarray for transcriptional profiling in the pig. Genomics 86:618-625.
• Abbott, M.A., and C.K. Tuggle. 2005. Ectopic HOXA5 expression results in abnormal differentiation, migration and p53-independent cell death of superficial dorsal horn neurons. Brain Res. Dev. Brain Res. 159:87-97.
• Caetano, A.R., Edeal, J.B., Burns, K., Johnson, R.K., C.K. Tuggle. Pomp D. 2005. Physical Mapping of Genes in the Porcine Ovarian Transcriptome. Animal Genetics 36:322-330.
• Joksimovic, M., Jeannotte, L., C.K. Tuggle. 2005. Dynamic expression of murine HOXA5 protein in the central nervous system. Mechanisms of Development-Gene Expression Patterns 5: 792-800.
• Tuggle, C.K., J.A. Green, C. Fitzimmons, R. Woods, R.S. Prather, S. Malchenko, M.B. Soares, T. Kucaba, K. Crouch, C. Smith, D. Tack, N. Robinson, B. O'Leary, T. Scheetz, T. Casavant, D. Pomp. J.B. Edeal, Y. Zhang, M.F. Rothschild, K. Garwood, and W. Beavis. 2003. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm. Genome 14:565-579.

Vita: Click here to download

Website: Christopher Tuggle

Nicole Valenzuela

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:

Description:

• 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.
• Valenzuela, N. and Shikano T. 2007. Embryological ontogeny of Aromatase gene expression in Chrysemys picta and Apalone mutica turtles: comparative patterns within and across temperature-dependent and genotypic sex-determining mechanisms. Development, Genes and Evolution 217: 5562.
• 25. Valenzuela, N., LeClere A., and Shikano T. 2006. Comparative expression of steroidogenic factor 1 in Chrysemys picta and Apalone mutica turtles with environmental and genotypic sex determination. Evolution and Development 8 (5): 424-432.
• Ezaz T., Valenzuela, N., Gruetzner F., Miura I., Burke R., Georges, A. and Graves J.M. 2006. Cryptic XY sex chromosome system in a GSD turtle, Chelodina longicollis (Chelidae, Reptilia). Chromosome Research  14:139-150.
• Devon E. Pearse, A.D. Arndt, N.Valenzuela, B.A. Miller, V. Cantarelli, J.W. Sites, Jr. 2006. Estimating population structure under non-equilibrium conditions in a conservation context: Continent-wide population genetics of the giant Amazon river turtle Podocnemis expansa (Chelonia; Podocnemidae). Molecular Ecology 15: 985-1006.
• Valenzuela, N. and V. Lance, Eds. 2004. Temperature Dependent Sex Determination in Vertebrates. Smithsonian Books. Washington D.C.
• Valenzuela, N., D.C. Adams, and F.J. Janzen. 2003. Pattern does not equal process: Exactly when is sex environmentally determined? American Naturalist 161 (4): 676-683.

Vita: Click here to download

Website: Nicole Valenzuela

Daniel Voytas

Education: Ph.D., Harvard, 1990

Research Interests: Transposable elements and genome organization

• Genome Evolution-- Genomic organization of transposable elements and consequences for genome evolution; evolutionary relationships among transposable elements; predicting function of transposable element proteins

Description:

Selected Publications:

• Dai, J., Xie, W., Brady, T.L. and Voytas, D.F.  Phosphorylatoin regulates integration of the yeast Ty5 retrotransposon into heterochromatin.  Mol. Cell.  In press.
• Wright DA, Townsend FA, Winfrey RJ Jr, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005). High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. Nov;44(4):693-705.
• Havecker ER, Gao X, Voytas DF (2005). The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, ineract with a family of proteins to dynein light chain 8. Plant Physiol. Oct;139(2):857-68.
• Gao X, Vander Velden KA, Voytas DF, Gu X (2005). SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics. Jun 1;6(1):137.
• Gao X, Voytas DF (2005). A eukaryotic gene family related to retroelement integrases. Trends Genet. Mar;21(3):133-7.

Vita: Click here to download

Website: Daniel Voytas

Jonathan F. Wendel

Education: Ph.D., North Carolina, 1983

Research Interests:

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

Selected Publications:

• Grover, C. E., H. Kim, R. A. Wing, A. H. Paterson, and J. F. Wendel. 2007. Microcolinearity and genome size evolution in the AdhA region of diploid and polyploid cotton (Gossypium). The Plant Journal (in press).
• Udall, J. A., F. Cheung, A. W. Woodward, J. M. Swanson, L. Flagel, R. Hovav, R. A. Rapp, D. Nettleton, J. J. Lee, A. R. Gingle, C. Town, Z. J. Chen, and J. F. Wendel. 2007. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics (in press).
• Fortune, P. M., K. A. Schierenbeck, A. K. Ainouche, J. Jacquemin, J. F. Wendel, and M.L. Ainouche. 2007. Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae). Molecular Phylogenetics and Evolution (in press).
• Adams, K. L. and J. F. Wendel. 2006. Allele-specific, bi-directional silencing of an alcohol dehydrogenase gene in different organs of interspecific cotton hybrids. Genetics 17: 2139-2142.
• Udall, J. A., J. Swanson, K. Haller, R.A. Rapp, M. Sparks, J. Hatfield, Y. Yu, Y. Wu, A.B. Arpat, B.A. Sickler, T.A. Wilkins, J.-Y. Guo, X.-Y. Chen, E. Taliercio, R. Turley, C. Dowd, H. McFadden, N. Klueva, P. Payton, R. Allen, D. Zhang, C. Haigler, C. Wilkerson, J. Suo, S.R. Schulze, M.L. Pierce, M. Essenberg, H. Kim, D.J. Llewellyn, E.S. Dennis, D. Kudrna, R. Wing, A.H. Paterson, C. Soderlund, and J.F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16: 441-450.
• Álvarez, I. and J. F. Wendel. 2006. Ancient interspecific introgression and modern genetic differentiation within Gossypium aridum (Malvaceae) and its relatives. Evolution 60: 505-517.
• Udall, J. A., J. M. Swanson, D. Nettleton, R. J. Percifield, and J. F. Wendel. 2006. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173: 1823-1827.
• Keyte, A. L., R. Percifield, B. Liu, and J. F. Wendel. 2006. Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). Journal of Heredity 97: 444-450.
• Hawkins, J. S., H. Kim, J. D. Nason, R. A. Wing, and J. F. Wendel. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 16: 1252-1261.
• Udall, J. A. and J. F. Wendel. 2006. Polyploidy and crop improvement. The Plant Genome, a Supplement to Crop Science 46: S3-14.
• Adams, K. L. and J. F. Wendel. 2005. Novel patterns of gene expression in polyploid plants. Trends in Genetics 21: 539-543. Rapp, R. and J. F. Wendel. 2005. Epigenetics and plant evolution. New Phytologist 168: 81-91.

Vita: Click here to download

Website: Jonathan F. Wendel

Stephen Willson

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:

• 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 through analysis of GeneChip profiling experiments
• Genome Evolution-- automated annotation of complex LTR retrotransposons and repeated regions in maize and other cereals, nuclear-mitochondrial interactions.

Description:

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:

• Kronmiller, BA and RP Wise. 2008. TEnest: Automated chronological annotation and visualization of maize nested transposable elements. Plant Physiology: 45-59 . [Cover article]
• Wise, RP, M Moscou, SA Whitham, AJ Bogdanove. 2007. Transcript Profiling in Host – Pathogen Interactions. Annual Review of Phytopathology 45: 329-369.
• Potokina, E, A Druka, ZW Luo, R Wise, R Waugh, and MJ Kearsey. 2007. eQTL analysis of 16,000 barley genes reveals a complex pattern of genome wide transcriptional regulation. Plant Journal: 53(1): 90-101.
• Wise, RP, RA Caldo +, L Hong +, L Shen, JA Dickerson. 2007. BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens. Pages 347-363 In Methods in Molecular Biology, Vol. 406, Plant Bioinformatics - Methods and Protocols. Edwards, D. ed. Humana Press, Totowa, NJ. 2007.
• Caldo RA, D Nettleton, J Peng, and RP Wise. 2006. Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant-Microbe Interactions 19(9): 939-947.
• Druka, A, G Muehlbauer, I Druka, R Caldo, U Baumann, N Rostoks, A Schreiber, R Wise, T Close, A Kleinhofs, A Graner, A Schulman, P Langridge, K Sato, P Hayes, J McNicol, D Marshall and R Waugh. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics 6: 202-211.

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

Description:

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 (http://metnet.vrac.iastate.edu/), and 2) the elucidation of the metabolic networks associated with the two-carbon activated molecule, acetyl-CoA.

Selected Publications:

• Fatland B, Nikolau BJ, Wurtele ES. 2005. Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-citrate lyase in Arabidopsis. Plant Cell. 2005 Jan; 17(1):182-203. Epub 2004 Dec 17.
• Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Raoul Bino R, Hall R, Kopka J, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wurtele ES, Kell DB. 2005. A proposed framework for the description of plant metabolomics experiments and their results.  Nature Biotech 22 (January Issue).
• J. A. Dickerson, P. Du, E. Wurtele, J. Li. 2004. Fuzzy modeling of metabolic maps in MetNetDB. NAFIPS04.

Link: http://metnet.vrac.iastate.edu/

Vita: Click here to download

Website: Eve Wurtele

Edward Yu

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

Description:

Selected Publications:

• 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-
  593.
• 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.
  374:591-603.
• 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