Thomas lab

James H. Thomas, Genome Sciences, University of Washington

The research focus in my lab has recently shifted toward molecular evolution, especially the evolution and function of gene families implicated in environmental interactions and morphological diversity. Our work is focused mostly on nematodes and mammals.

jht@u.washington.edu

Specific projects (under development)

• Function and evolution of chemoreceptors in nematodes
• Function and evolution of ubiquitin ligase adapters in nematodes and plants
• Evolution of Krab Zn-finger genes in primates and rodents
• Function and evolution of cytochrome P450 genes in mammals
• Patterns of gene duplication
• Detection and analysis of positive selection
• Concerted evolution
• Systematic proteome annotation (with the MacCoss lab)

Why functional geneticists should care about molecular evolution

• A polemic

Software downloads (Bonsai, Etho, and others)

Selected Publications (full list from PubMed)

Thomas, J.H. 2006. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Manuscript in review. Preprint.

Thomas, J.H. 2006. Concerted evolution of two novel protein families in Caenorhabditis species. In press, Genetics. Preprint.

Choy, R.K.M., J. Kemner, and J.H. Thomas. 2006. Fluoxetine-resistance genes in C. elegans function in the intestine and may regulate lipid metabolism. In press, Genetics.

Thomas, J.H. 2006. Global analysis of homologous gene clusters in C. elegans reveals striking regional cluster domains. Genetics 172, 127-143. Paper.

Robertson, H.M. and J.H. Thomas. 2006. The putative chemoreceptor families of C. elegans. Chapter in WormBook: Online Review of C. elegans Biology, ed. The C. elegans Research Community, WormBook, doi /10.1895/wormbook.1.7.1, http://www.wormbook.org.

Thomas, J.H., J.L. Kelley, H.M. Robertson, K., Ly, and W.J. Swanson. 2005. Adaptive evolution in the SRZ Chemoreceptor families of C. elegans and C. briggsae. PNAS 102, 4476-4481. Paper.

Stewart, M.K., N. Clark, G. Merrihew, E. Galloway, and J.H. Thomas. 2005. High genetic diversity in the chemoreceptor superfamily of C. elegans. Genetics 165, 1985-1996. Paper.

Ailion, M.A. and J.H. Thomas. 2003. Isolation and characterization of high-temperature-induced dauer formation mutants in Caenorhabditis elegans. Genetics 165, 127-144.

Ailion, M. and J.H. Thomas. 2000. Dauer formation induced by high temperatures in Caenorhabditis elegans. Genetics 156, 1047-1067.

Inoue, T. and J.H. Thomas. 2000. Targets of TGF-b signaling in C. elegans dauer formation. Dev. Biol. 217, 192-204.

Birnby, D., E.A. Malone, J.J. Vowels, H. Tian, P. Colacurcio, and J.H. Thomas. 2000. A transmembrane guanylyl cyclase (DAF-11) and Hsp-90 (DAF-21) regulate a common set of chemosensory behaviors in C. elegans. Genetics 155, 85-104.

Swoboda, P., H. Adler, and J.H. Thomas. 2000. The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. elegans. Molec. Cell 5, 411–421.

Schackwitz, W., T. Inoue, and J.H. Thomas. 1996. Sensory neurons function in parallel to regulate development in C. elegans. Neuron 17, 719-728.

Vowels, J.J. and J.H. Thomas. 1994. Multiple chemosensory defects in daf-11 and daf-21 mutants of Caenorhabditis elegans. Genetics 138, 303-316.

Thomas, J.H., D.A. Birnby, and J.J. Vowels. 1993. Evidence for parallel processing of sensory information controlling dauer formation in C. elegans. Genetics 134, 1105-1117.

Vowels, J.J. and J.H. Thomas. 1992. Genetic analysis of chemosensory control of dauer formation in Caenorhabditis elegans. Genetics 130, 105-123.

Thomas, J.H. 1990. Genetic analysis of defecation in Caenorhabditis elegans. Genetics 124, 855-871.

Authored by James H. Thomas, 2/19/2006