Biological Sciences

Michael A. Thomas, Ph.D.

Michael A. Thomas

Associate Professor of Bioinformatics

Education

Biographical Sketch

Dr. Thomas has been an Assistant Professor of Bioinformatics since the summer of 2003. He obtained his Ph.D. at Penn State University in 2000, working with Dr. Bruce McPheron's insect evolution group. His training was in entomology and molecular evolutionary genetics. He trained in bioinformatics at the Bioinformatics Research Center of the Medical College of Wisconsin's Human and Molecular Genetics Group from 2000-2003.

Dr. Thomas's group develops genomic approaches to studying complex evolutionary problems, specializing in detecting adaptive evolutionary changes. Projects involve examining the fates of duplicated genes, identifying genes involved with key evolutionary innovations, and determining the adaptive significance of genome processes involving functional modifications, such as alternative splicing and RNA editing. Other projects in the lab examine new methods for environmental genomic prospecting using an approach called "metagenomic bootstrapping", created by Mitch Day, a student in the Thomas lab.

Teaching

Publications

Marden, J.H., B.C. O'Donnell, M.A. Thomas, and J.Y. Bye, 2000. Surface-skimming locomotion in modern stoneflies and mayflies: a taxonomically diverse and finely graded series of mechanical intermediates between swimming and flying. Physiological and Biochemical Zoology 73:751-764.

Thomas, M.A., K.A. Walsh, M.R. Wolf, B.A. McPheron, and J.H. Marden, 2000. Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior. Proceedings of the National Academy of Science 97: 13178-13183.

Marden, J.H., and M.A. Thomas, 2003 Rowing locomotion by an adult stonefly that retains abdominal gills. The Biological Journal of the Linnaean Society 79: 341-349.

Thomas, M.A. and M. Joseph, 2003. Variation in the Evolutionary Dynamics of Human Genes by Molecular Function and Cellular Component. Proceedings of the 7th World Multiconference on Systemics, Cybernetics and Informatics.

Thomas, M.A., C.-F. Chen, M.I. Jensen-Seaman, P.J. Tonellato, and S.N. Twigger, 2003. Evolution of rat inbred strains. Mammalian Genome 14:61-64.

Thomas, M.A, B. Weston, M. Joseph, W. Wu, A. Nekrutenko, and P.J. Tonellato, 2003. Evolutionary dynamics of cancer-related genes. Molecular Biology and Evolution 20: 964-968.

Michael I. Jensen-Seaman, Terrence S. Furey, Bret A. Payseur, Yontao Lu, Krishna M. Roskin, Chin-Fu Chen, Michael A. Thomas, David Haussler, and Howard J. Jacob. 2004. Comparative Recombination Rates in the Rat, Mouse, and Human Genomes. Genome Research 14: 528-538.

Rebecca Klaper and Michael A. Thomas. 2004. At the Crossroads of Genomics and Ecology: The Promise of a Canary on a Chip. BIOLcience 54: 403-412.

Tadashi Imanishi, ...Michael A. Thomas, ...Takashi Gojobori, (& 148 co-authors), 2004. Integrative Annotation of 23,149 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology 2: 1-21.

Michael A. Thomas & Rebecca D. Klaper. 2004. Genomics for the ecological toolbox. Trends in Ecology & Evolution 19: 439-445.

Michael A. Thomas, Mitch Day, and Luobin Yang. 2005. Computational Options for Bioinformatics Research in Evolutionary Biology. In Proc. 2005 International Conference on Computer Science.


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