PUBLICATIONS (Full Manuscripts)
2008
Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, Thomas WK. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105(27):9272-7, 2008.
Seyfert AL, Cristescu ME, Frisse L, Schaack S, Thomas WK, Lynch M. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics. 178(4):2113-21, 2008.
Bobilya DJ, Gauthier NA, Karki S, Olley BJ, Thomas WK. Longitudinal changes in zinc transport kinetics, metallothionein and zinc transporter expression in a blood-brain barrier model in response to a moderately excessive zinc environment. J Nutr Biochem. 19(2):129-37, 2008.
2007
Ye, W., Giblin-Davis, R.M., Davies, K.A., Purcell, M.F., Scheffer, S.J., Taylor, G.S., Center, T.D., Morris, K., and Thomas, W.K. Molecular Phylogenetics and the Evolution of Host Plant Associations in the Nematode Genus Fergusobia (Tylenchida: Fergusobiinae) Mol. Phylogenet. Evol. 45(1):123-41, 2007.
Ye, W., Giblin-Davis R.M., Braasch, H., Morris, K., and Thomas, W.K., Phylogenetic Relationships Among Bursaphelenchus species (Nematoda: Parastiaphelenchidae) Inferred from Nuclear Ribosomal and Mitochondrial DNA Sequence Data. J. Mol. Evol. 43:1185-1197, 2007.
Faller, Lina (Mentors: R.D. Bergeron and W.K. Thomas) Bioinformatics: Merging Computer Science and Genetics Inquiry Journal (published by UNH) Spring 2007.
2006
Giblin-Davis, R.M., Kanzaki, N., Ye, W., Mundo-Ocampo, M., Baldwin, J.G. and Thomas, W.K. Morphology and Description of Bursaphelenchus platzeri n. sp. (Nematoda: Parastiaphelenchidae), an Associate of Nitidulid Beetles. J. Nematol. 38:150-157, 2006.
Giblin-Davis, R.M., Ye, W., Kanzaki, N., Williams, D., Morris, K., and Thomas W.K., Stomatal Ultrastructure, Molecular Phylogeny, and Description of Parasitodiplogaster laevigata n. sp.(Nematoda: Diplogasteridae), a Parasite of Fig Wasps. J. Nematology 38:137-149, 2006.
Eyualem-Abebe, Baldwin, J.G., Adams, B., Hope, D., Gardner, S., Huettel, R., Mullin, P., Powers, T., Sharma, J., Ye, W. and Thomas W.K. A Position Paper on the Electronic Publication of Nematode Taxonomic Manuscripts. J. Nematol. 38:305-311, 2006.
2005
De Ley, P., De Ley, I.T., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., Burr, J.A.H., Baldwin, J.G. and Thomas, W.K. An Integrated Approach to Fast and Informative Morphological Vouchering of Nematodes for Applications in Molecular Barcoding Philos. Trans. R. Soc. Lond. B. Biol. Sci. B 360:1945-1958, 2005.
Denver, D.R., Feinberg, S., Estes, S., Thomas, W.K. and Lynch, M. Mutations rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegansGenetics 170:107-113, 2005.
Denver, D.R., Morris, K., Streelman, J.T., Kim, S.K., Lynch, M. and Thomas, W.K. The Transcriptional Consequences of Mutation and Natural Selection in Caenorhabditis elegans.Nature Genetics 37:544-548, 2005. (PDF)
2004
Denver, D.R., Morris, K., Lynch, M., and Thomas, W.K. High Mutation Rate and Predominance of Insertions in the Caenorhabditis elegans nuclear genome.Nature 430:679-682, 2004. (PDF)
Denver, D.R., Morris, K., Kewalramani, A., Harris, K.E., Chow, A., Estes, S., Lynch, M., and Thomas, W.K. Abundance, Distribution, and Mutation Rates of HomopolymericNucleotide Runs in the Genome of Caenorhabditis elegans. J. Mol. Evol. 58:584-595, 2004. (PDF)
Estes, S., Phillips, P.C., Denver, D.R., Thomas, W.K., and Lynch, M. Mutation Accumulation in Populations of Varying Size: the Distribution of MutationalEffects for Fitness Correlates in Caenorhabditis elegans J. Mol. Evol. 166: 1269-1279, 2004.
Abebe, E., Grizzle, R.E., Hope, D., and Thomas, W.K. Nematode Biodiversity in the Gulf of Maine, USA, and a Web-Accessible, Relational Database.J. Mar. Biol. Ass. U.K. 84:1159-1167, 2004.
Giblin-Davis, R.M., Scheffer, S.J., Davies, K.A., Taylor, G.S., Curole, J., Center, T.D., Goolsby, J., and Thomas, W.K.,Coevolution Between Fergusobia and Fergusobiba Mutualists. Nematology Monographs & Perspectives 2:407-417., 2004.
2003
Denver, D.R., Morris, K., and Thomas, W.K. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol. Biol. Evol. 20:393-400, 2003.
Giblin-Davis, R.M., Davies, K.A., Morris, K. and Thomas, W.K., Evolution of Parasitism in Insect-transmitted Plant Nematodes. J. Nematology 35:133-141, 2003.
prior to 2003
Denver, D.R., Morris, K., Lynch, M., Vassilieva, L.L. and Thomas, W.K. High Direct Estimate of the Mutation Rate in the Mitochondrial Genome of Caenorhabditis elegans. Science 289:2342-2344, 2000. (PDF)
Félix, M.-A., De Ley, P., Sommer, R.J., Frisse, L., Nadler, S., Thomas, K., Vanfleteren, J., and Sternberg, P.W.Evolution of Vulva Development in the Cephalobina (Nematoda). Dev. Biol. 221:68-6, 2000.
Kaplan, D.T., Thomas, W.K., Frisse, L.M., Sarah, J.L., Stanton, J.M., Speijer, P.R., Marin, D.H., and Opperman, C.H. Phylogenetic Analysis of Geographically Diverse Radopholus similus via rDNA Sequence Reveals a Monomorphic Motif. J. Nematol. 32:134-142, 2000.
Duncan, L.W., Inserra, R.N., Thomas, W.K., Dunn, D., Mustika, I., Frisse, L.M., Mendes, M.L., Morris, K., and Kaplan, D.T. Molecular and Morphological Analysis of Isolates of Pratylenchus coffeae and Closely Related Species. Nematropica 29:61-80, 1999.
Courtright, E.M., Wall Freckman, D., Virginia, R.A., Frisse, L.M., Vida, J.T., and Thomas, W.K., Nuclear and Mitochondrial DNA Sequence Diversity in the Antarctic Nematode Scottnema lindsayae. J. Nematol. 32:143-153, 2000.
Luong, L.T., Platzer, E.G., De Ley, P, Thomas, W.K., Morphological, Molecular, and Biological Characterization of Mehdinema alii (Nematoda: Diplogasterida) from the Decorated Cricket (Gryllodes sigillatus), J. Parasit. 85:1053-1064, 1999.
De Ley, P., Félix, M.-A., Frisse, L.M., Nadler, S.A., Sternberg, P.W., and Thomas, W.K., Molecular and Morphological Characterisation of Two Reproductively Isolated Species with Mirror-image Anatomy (Nematoda: Cephalobidae). Nematology 1:591-612, 1999.
Goldstein, B., Frisse, L.M., and Thomas, W.K., Embryonic Axis Specification in Nematodes: Evolution of the First Step in Development. Curr. Biol. 8:157-160, 1998.
Blaxter, M.L., De Ley, P., Garey, J., Liu, L.X., Scheldemen, P., Vanfleteren, J., Mackey, L.Y., Dorris, M., Frisse, L.M., Vida, J.T., and Thomas, W.K., A Molecular Evolutionary Framework for the Phylum Nematoda. Nature 392:71-75, 1998.
Thomas, W. K., Vida, J.T., Frisse, L.M., Mundo, M., and Baldwin, J.G., DNA Sequences From Formalin-Fixed Nematodes: Integrated Molecular and Morphological Approaches to Taxonomy. J. Nematology 29:250-254, 1997.
Baldwin, J.G., Frisse, L.M., Vida, J.T., Eddleman, C.D., and Thomas, W.K., An Evolutionary Framework for the Study of Developmental Evolution in a Set of Nematodes Related to Caenorhabditis elegans (Nemata: Rhabditina). Mol. Phylogenet. Evol. 8:249-259, 1997.
Baldwin, J.G., Giblin-Davis, R.M., Eddleman, C.D., Williams, D.S., Vida, J.T., Thomas, W.K., Buccal Capsule of Aduncospiculum halicti (Nemata: Diplogasterina): An Ultrastructural and Molecular Phylogenetic Study. Can. J. Zool., 75:407-423, 1997.
Nielsen, J., Tupper, D., and Thomas, W., Mitochondrial DNA Polymorphism in Unique Runs of Chinook Salmon (Oncoryhynchus tshawutscha) From the Sacramento-San Joaquin River Basin. Cons. Biol. 8:882-884, 1994.
Nielsen, J.L., Gan, C. Wright J.M., Morris, D.B. and Thomas, W.K., Biogeographic Distributions of Mitochondrial and Nuclear Markers for Southern Steelhead. Mol. Mar. Biol. Biotech., 3:281-293, 1994.
Nielsen, J.L., Gan, C. and Thomas, W.K., Differences in Genetic Diversity for mtDNA between Hatchery and Wild Populations of Oncorhynchus. Can. J. Fish Aquat. Sci., 51:Suppl. 1, 1994.
Sidow, A. and Thomas, W.K., A Molecular Evolutionary Framework for Eukaryotic Model Organisms. Curr. Biol. 4:596-603, 1994.
Litvaitis, M., Nunn, G., Thomas, W., and Kocher, T. A Molecular Approach for the Identification of Meiofaunal Tubellarians (Platyhelminthes, Turbellaria). Mar. Biol. 120:437-442, 1994.
Janke, A., Feldmaier-Fuchs, G., Thomas, W.K., Von Haeseler, A. and Pääbo, S., The Marsupial Mitochondrial Genome and the Evolution of Placental Mammals. Genetics 137:243-256, 1994.
Zimmer, R., Erdtmann, B., Thomas, W.K. and Quinn, T.W., Phylogenetic Analysis of the Coscoroba coscoroba Using Mitochondrial srRNA Gene Sequences. Mol. Phylogenet. Evol. 3:85-91, 1994.
Thomas, W.K. and Martin, S.L., A Recent Origin of Marmots. Mol. Phylogenet. Evol. 2:330-336, 1993.
Kocher, T.D. and Thomas, W.K., PCR Mediated DNA Sequencing. Meth. Enzym. 224:391-399, 1993.
Thomas, W.K. and Pääbo, S., Diachronic Studies of DNA in Museum Specimens. Meth. Enzym. 224:406-419, 1993.
Prager, E.M, Sage, R.D., Gyllensten, U., Thomas, W.K., Hubner, R., Jones, C.S., Noble, L., Searle, J.B. and Wilson, A.C. Mitochondrial DNA Sequence Diversity and the Colonization of Scandinavia by House Mice from East Holstein. Biol. J. Linn. Soc. 50:85-122, 1993.
Smith, M.F., Thomas, W.K. and Patton, J.L., Mitochondrial DNA-like Sequence in the Nuclear Genome of an Akodontine Rodent. Mol. Biol. Evol. 9:204-215, 1992.
Pääbo, S., Thomas, W.K., Whitfield, K.M., Kumazawa, Y. and Wilson, A.C. Rearrangements of Mitochondrial tRNA Genes in Marsupials. J. Mol. Evol. 33:426-430, 1991.
Thomas, W.K. and Wilson, A.C., Mode and Tempo of Molecular Evolution in the Nematode Caenorhabditis. Genetics 128:269-279, 1991.
Thomas, W.K., Pääbo, S., Villablanca, F.X. and Wilson, A.C. Spatial and Temporal Continuity of Kangaroo Rat Population Shown by Sequencing Mitochondrial DNA from Museum Specimens J. Mol. Evol. 31:101-112, 1990.
Buroker, N.E., Brown, J.R., Gilbert, T.A., O'Hara, P.J., Beckenbach, A.T., Thomas, W.K. and Smith, M.J., Length Heteroplasmy of Sturgeon Mitochondrial DNA: an Illegitimate Elongation Model. Genetics 124:157-163, 1990.
Beckenbach, A.T., Thomas, W.K. and Sohrabi, H., Intraspecific Sequence Variation in the Mitochondrial Genome of Rainbow Trout (Oncorhynchus mykiss). Genome 33:13-15, 1990.
Thomas, W.K., Maa, J. and Wilson, A.C. Shifting Constraints on tRNA Genes during Mitochondrial DNA Evolution in Animals. New Biol. 1:93-100, 1989.
Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X. and Wilson, A.C. Dynamics of Mitochondrial DNA Evolution in Animals: Amplification and Sequencing with Conserved Primers. Proc. Natl. Acad. Sci. USA 86:6196-6200, 1989.
Thomas, W.K. and Beckenbach, A.T., Variation in Salmonid Mitochondrial DNA: Evolutionary Constraints and Mechanisms of Substitution. J. Mol. Evol. 29:233-245, 1989.
Wilson, G.M., Thomas, W.K. and Beckenbach, A.T., Mitochondrial DNA Analysis of Pacific Northwest Populations of Onchorhynchus tshawytscha Can. J. Fish. Aquatic Sci. 44:1301-1305, 1987.
Thomas, W.K. and Beckenbach, A.T., Mitochondrial DNA Restriction Site Variation in the Townsend's Vole, Microtus townsendii Can. J. Zool. 64:2750-2756, 1986.
Thomas, W.K., Withler, R.E. and Beckenbach, A.T., Mitochondrial DNA Analysis of Pacific Salmonid Evolution Can. J. Zool. 64:1058-1064, 1986.
Wilson, G.M., Thomas, W.K. and Beckenbach, A.T., Intra- and Inter-Specific Mitochondrial DNA Sequence Divergence in Salmo: Rainbow, Steelhead and Cutthroat Trouts Can. J. Zool. 63:2088-2094, 1985.
Book Chapters
Giblin-Davis, R.M., Davies, K.A., Taylor, G.S., and Thomas, W.K. “Entomophilic Nematode Models for Studying Biodiversity and Cospeciation.”in Nematology, Advances and Perspectives, Z.X. Chen, S.Y. Chen and D.W. Dickson, eds., pp 492-538, 2003.
Fitch, D.H.A. and Thomas,W.K. “Evolution” in C. elegans II, D. Riddle, T. Blumenthal, B. Meyer, and J. Priess, eds., pp 815-850, 1997.