PUBLICATIONS (Refereed Journal articles)

1.                  Wilson G.M., Thomas W.K., and Beckenbach, A.T., 1985. Intra‑ and inter‑specific mitochondrial DNA sequence divergence in Salmo: rainbow, steelhead and cutthroat trout. Can. J. Zool., 63(9): 2088-2094, doi:10.1139/z85-307

2.                  Thomas W.K., Withler R.E., and Beckenbach A.T. 1986. Mitochondrial DNA analysis of Pacific salmonid evolution. Can. J. Zool., 64(5): 1058-1064, 10.1139/z86-158.

3.                  Thomas W.K. and Beckenbach A.T., 1986. Mitochondrial DNA restriction site variation in the Townsend's vole, Microtus townsendii. Can. J. Zool., 64(12): 2750-2756, doi: 10.1139/z86-399

4.                  Wilson G.M., Thomas W.K., and Beckenbach, A.T. 1987. Mitochondrial DNA analysis of Pacific northwest populations of Onchorhynchus tshawytscha, Can. J. Fish. Aquatic Sci., 44(7): 1301-1305, doi:10.1139/f87-153

5.                  Thomas W.K. and Beckenbach A.T. 1989.  Variation in Salmonid Mitochondrial DNA: Evolutionary Constraints and Mechanisms of Substitution. J. Mol. Evol. 29(3):233‑245,doi:10.1007/BF02100207

6.                  Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X. and Wilson A.C. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. PNAS 86(16): 6196–6200 doi:10.1073/pnas.86.16.6196

7.                  Thomas W.K., Maa J., and Wilson A.C. 1989. Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals.  New Biol. 1(1):93-100.

8.                  Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Villablanca F.X., Wilson A.C., 1989. Dynamics of mitochondrial-DNA evolution in animals: Amplification and sequencing with conserved primers. PNAS 86:6196-6200.

9.                  Beckenbach A.T., Thomas W.K., and Sohrabi H. 1990. Intraspecific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss)," Genome. 33(1):13-15.

10.              Buroker N.E., Brown J.R., Gilbert T.A., O'Hara P.J., Beckenbach A.T., Thomas W.K. and Smith M.J. 1990. Length heteroplasmy of sturgeon mitochondrial DNA:  an Illegitimate Elongation Model. Genetic. 124(1):157-63.

11.              Thomas W.K., Pääbo S., Villablanca F.X. and Wilson A.C. 1990.  Spatial and temporal continuity of kangaroo rat population shown by sequencing mitochondrial DNA from museum specimens.  J. Mol. Evol. 31(2):101‑112, doi:10.1007/BF02109479

12.              Thomas W.K., and Wilson A.C. 1991. Mode and tempo of molecular evolution in the nematode Caenorhabditis. Genetics. J Mol Evol. 31(2):101-12.

13.              Pääbo S., Thomas W.K., Whitfield K.M., Kumazawa Y. and Wilson A.C. 1991. Rearrangements of mitochondrial tRNA genes in marsupials.  J. Mol. Evol. 33(5):426‑430, doi:10.1007/BF02103134

14.              Smith M.F., Thomas W.K. and Patton J.L. 1992. Mitochondrial DNA‑like sequence in the nuclear genome of an Akodontine rodent. Genetics 128(2):269-79.

15.              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. 1993.  Mitochondrial DNA Sequence Diversity and the Colonization of Scandinavia by House Mice from East Holstein.  Biol. J. Linn. Soc. 50(2):85‑122, doi:10.1111/j.1095-8312.1993.tb00920.x.

16.              Thomas, W.K. and Pääbo, S. 1993. Diachronic studies of DNA in museum specimens. Methods in Enzymology 224:406‑419, doi:10.1016/0076-6879(93)24031-0

17.              Kocher T.D. and Thomas W.K. 1993. PCR Mediated DNA sequencing. Methods in Enzymology  224:391‑399. 

18.              Thomas W.K. and Martin S.L. 1993. A recent origin of marmots. Molecular Phylogenetics and Evolution 2(4):330‑336, doi:10.1006/mpev.1993.1032

19.              Nielsen J.L., Gan C., Wright J.M., Thomas W.K. 1994. Phylogeographic patterns in California steelhead as determined by mtDNA and microsatellite analyses. CalCOFI Rep. 35:90-92.

20.              Zimmer R., Erdtmann B., Thomas W.K. and Quinn T.W. 1994. Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences. Mol. Phylogenet. Evol. 3(2):85‑91, doi:10.1006/mpev.1994.1011

21.              Janke A., Feldmaier‑Fuchs G., Thomas W.K., Von Haeseler A. and Pääbo S., 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137(1):243‑256.

22.              Litvaitis M., Nunn G., Thomas W., and Kocher T. 1994. A molecular approach for the identification of meiofaunal tubellarians (Platyhelminthes, Turbellaria).  Marine Biology 120(3): 437‑442, doi:10.1007/BF00680218

23.              Sidow A. and Thomas W.K. 1994. A molecular evolutionary framework for eukaryotic model organisms. Curr. Biol. 4(7):596‑603, doi:10.1016/S0960-9822(00)00131-7

24.              Nielsen J.L., Gan C. and Thomas, W.K. 1994. Differences in genetic diversity for mtDNA between hatchery and wild populations of Oncorhynchus.  Can. J. Fish Aquat. Sci., 51:209-297, doi:10.1139/f94-316

25.              Nielsen J.L., Gan C., Wright J.M., Morris D.B., and Thomas W.K. 1994. Biogeographic distributions of mitochondrial and nuclear markers for southern steelhead. Mol. Mar. Biol. Biotech., 3:281-293.

26.              Nielsen J., Tupper D., and Thomas W. 1994. Mitochondrial DNA polymorphism in unique runs of chinook salmon (Oncoryhynchus tshawutscha) from the Sacramento‑San Joaquin river basin," Conserv. Biol. 8(3):882‑884, doi:10.1046/j.1523-1739.1994.08030863-11.x

27.              Lamont M.M., Vida J.T., Harvey J.T., Jeffries S., Brown R., Huber H.H., Delong R., Thomas W.K. 1996. Genetic substructure of the pacific harbor seal (Phoca vitulina richardsi) off Washington, Oregon, and California. Marine Mammal Science, 12(3), 402-413 doi:10.1111/j.1748-7692.1996.tb00593.x.

28.              Baldwin J.G., Giblin‑Davis R.M., Eddleman C.D., Williams D.S., Vida J.T., Thomas W.K. 1997. Buccal Capsule of Aduncospiculum halicti (Nemata: Diplogasterina): An Ultrastructural and Molecular Phylogenetic Study. Can. J. Zool., 75:407-423, doi:10.1139/z97-051

29.              Baldwin J.G., Frisse L.M., Vida J.T., Eddleman C.D., and Thomas W.K. 1997. 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, doi:10.1006/mpev.1997.0433

30.              Thomas W.K., Vida J.T., Frisse L.M., Mundo M., and Baldwin J.G. 1997. DNA sequences from formalin-fixed Nematodes: integrated molecular and morphological approaches to taxonomy, J. Nematology. 29(3):250-4.

31.              Blaxter M.L., De Ley P., Garey J., Liu L.X., Scheldeman P., Vierstraete A., Vanfleteren J. R., Mackey L.Y., Dorris M., Frisse L.M., Vida J.T., Thomas W.K. 1998.  A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75, doi:10.1038/32160

32.              Goldstein B., Frisse L.M., and Thomas, W.K. 1998.  Embryonic axis specification in nematodes: evolution of the first step in development. Curr. Biol. 8(3):157-160, doi:10.1016/S0960-9822(98)70062-4

33.              Luong L.T., Platzer E.G., De Ley P., Thomas W. K. 1999. Morphological, molecular, and biological characterization of Mehdinema alii  (Nematoda: Diplogasterida) from the decorated cricket (Gryllodes sigillatus). J. Parasitol. 85(6), 1053-1064, doi:10.2307/3285668

34.              De Ley P., Félix M.A., Frisse L.M., Nadler S.A., Sternberg P.W., Thomas W.K. 1999. Molecular and morphological characterization of two reproductively isolated species with mirror-image anatomy (Nematoda: Cephalobidae). Nematology 1(6):591-612, doi:10.1163/156854199508559   

35.              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. 1999. Molecular and morphological analysis of isolates of Pratylenchus coffeae and closely related species.  Nematropica 29:61-80.

36.              Courtright E.M., Wall Freckman D., Virginia R.A., Frisse L.M., Vida J.T., and Thomas W.K. 2000. Nuclear and mitochondrial DNA sequence diversity in the Antarctic nematode Scottnema lindsayae. J. Nematol. 32:143-153.

37.              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. 2000. Phylogenetic analysis of geographically diverse Radopholus similus via rDNA sequence reveals a monomorphic motif.  J. Nematol. 32:134-142.

38.              Félix M.-A., De Ley P., Sommer R.J., Frisse L., Nadler S., Thomas K., Vanfleteren J., and Sternberg P.W. 2000. Evolution of vulva development in the Cephalobina (Nematoda). Dev. Biol. 221(1):68-86, doi:10.1006/dbio.2000.9665

39.              Denver D.R., Morris K., Lynch M., Vassilieva L.L. and Thomas W.K. 2000. High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289(5488):2342-2344, doi:10.1126/science.289.5488.2342

40.              Dolinski C., Baldwin J.G., Thomas W.K. 2001. Comparative survey of early embryogenesis of Secernentea (Nematoda), with phylogenetic implications. Can. J. Zool. 79(1):82-94. doi:10.1139/cjz-79-1-82

41.              Denver D.R., Morris K., Thomas W.K. 2003. Phylogenetics in Caenorhabditis elegans: An analysis of divergence and outcrossing. Mol. Biol. Evol., 20(3), 393-400. doi:10.1093/molbev/msg044

42.              Giblin-Davis R.M., Davies K.A., Morris K., Thomas W.K. 2003. Evolution of parasitism in insect-transmitted plant-parasitic nematodes. J Nematol. 35(2): 133–141.

43.              Abebe E., Grizzle R.E., Hope D., Thomas W.K. 2004. Nematode diversity in the Gulf of Maine, USA, and a Web-accessible, relational database. J. Mar. Biol. Assoc. U.K. 84(06):4714.1-4714.9, doi:10.1017/S0025315404010604h

44.              Estes S., Phillips P.C., Denver D.R., Thomas W.K., and Lynch M. 2004.  Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Genetics 166:1269-1279, doi:10.1534/genetics.166.3.1269 

45.              Denver D.R., Morris K., Lynch M., and Thomas W.K. 2004. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome.  Nature 430:679-682, doi:10.1038/nature02697

46.              Denver D.R., Morris K., Kewalramani A., Harris K., Chow A., Estes S., Lynch M., Thomas W.K. 2004.  Abundance, distribution, and mutation rates, of homopolymeric, nucleotide runs in the genome of Caenorhabditis elegans. J. Mol. Evol. 58(5):584-595, doi:10.1007/s00239-004-2580-4

47.              Giblin-Davis R.M., Scheffer S.J., Davies K.A., Taylor G.S., Curole J., Center T.D., Goolsby J. and Thomas W.K. 2004.  Coevolution between Fergusobia and Fergusonina mutualists. Nematology Monographs and Perspectives 2:407-417

48.              Denver D.R., Morris K., Streelman J.T., Kim S.K., Lynch M., and Thomas W.K. 2005. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genetics 37(5):544-548, doi:10.1038/ng1554

49.              Giblin-Davis R.M., Hazir S., Center B.J., Ye W., Keskin N., Thorp R., and Thomas W.K. 2005. Bursaphelenchus anatolius n. sp. (Nematoda: Parasitaphelenchidae), an associate of bees in the genus Halictus. J. Nematol. 37(3):336-342.

50.              Denver D.R., Feinberg S., Estes S., Thomas W.K. and Lynch, M. 2005. Mutations rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans. Genetics 170(1):107-113, doi:10.1534/genetics.104.038521

51.              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. 2005. An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding.  Philos. Trans. R. Soc. Lond. B. Biol. Sci. 360(1462):1945-1958, doi:10.1098/rstb.2005.1726

52.              Bird D.M., Blaxter M.L., McCarter J.P., Mitreva M., Sternberg P.W., Thomas W.K. 2005. A white paper on nematode comparative genomics.  J. Nematol. 37(4):408-416.

53.              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. 2006. A position paper on the electronic publication of nematode taxonomic manuscripts. J. Nematol. 38:305-311, doi:10.1073/pnas.0235779100.

54.              Giblin-Davis R.M., Ye W., Kanzaki N., Williams D., Morris K., and Thomas W.K. 2006. Stomatal ultrastructure, molecular phylogeny, and description of Parasitodiplogaster laevigata n. sp. (Nematoda: Diplogasteridae), a parasite of fig wasps.  J. Nematology 38(1):137-149.

55.              Giblin-Davis R.M., Kanzaki N., Ye W., Mundo-Ocampo M., Baldwin J.G. and Thomas W.K. 2006. Morphology and description of Bursaphelenchus platzeri n. sp. (Nematoda: Parastiaphelenchidae), an associate of nitidulid beetles. J. Nematol. 38(1):150-157.

56.              Giblin-Davis, R. M., N. Kanzaki, W. Ye, B. J. Center, and W. K. Thomas. 2006. Morphology and systematics of Bursaphelenchus gerberae n. sp. (Nematoda: Parasitaphelenchidae), a rare associate of the palm weevil, Rhynchophorus palmarum in Trinidad.  Zootaxa 1189:39-53.

57.              Kulkarni S., Bergeron R.D., and Thomas W.K. 2006. Multiple assembly viewer with enhanced navigation (MAVEN): interactive display of multiple genome assemblies. Eurographics/IEEE-VGTC Symposium on Visualization. Technical Report.

58.              Ye W., Giblin-Davis R.M., Davies K.A., Purcell M.F., Scheffer S.J., Taylor G.S., Center T.D., Morris K., Thomas W.K. 2007.  Molecular phylogenetics and the evolution of host plant associations in the nematode genus Fergusobia (Tylenchida: Fergusobiinae)” Mol. Phylogenet. Evol. 45(1):123-141, doi:http://dx.doi.org/10.1016/j.ympev.2007.02.027

59.              Mundo-Ocampo, M., Lambshead, P. J. D., Debenham, N., King, I. W., De Ley, P., Baldwin, J. G., De Ley I.T., Rocha-Olivares A., Waumann D., Thomas, W.T., Packer M., Boucher, G. 2007. Biodiversity of littoral nematodes from two sites in the Gulf of California. Hydrobiologia, 586(1), 179-189. doi:10.1007/s10750-006-0624-z

60.              Ye W., Giblin-Davis R.M., Braasch, H., Morris K. and Thomas W.K. 2007. Phylogenetic relationships among Bursaphelenchus species (Nematoda: Parasitaphlenchidae) inferred from nuclear ribosomal and mitochondrial DNA sequence data. Mol. Phylogenet. Evol. 43(3):1185-1187.

61.              Porazinska D.L., Giblin-Davis  RM., Powers T.O., Kanzaki N., Ye W., Morris K., Thomas W.K. 2007. 454 pyrosequencing for metagenomic analysis of nematode diversity. J. Nematology 39: 90.

62.              Zeng Y., Giblin-Davis R.M., Ye W., Bélair G., Boivin G., and Thomas W.K. 2007.  Bradynema listronoti n. sp. (Nematoda: Allantonematidae), a parasite of the carrot weevil Listronotus oregonensis (Coleoptera: Curculionidae) in Quebec. Canada Nematology 9(5): 605-623, doi:10.1163/156854107782024749

63.              Hazir, C., Giblin-Davis R. M., Keskin N., Ye W., Kanzaki N., Center B. J., Hazir S.,. Kaya H. K, Thomas W. K. 2007. Bursaphelenchus debrae n. sp. (Nematoda: Parasitaphelenchidae), an associate of the bee Halictus brunnescens in Turkey. Nematology 9(6):777-789, doi:10.1163/156854107782331270

64.              Bobilya D.J., Gauthier N.A., Karki S., Olley B.J., Thomas W.K. 2008. 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):129-137, doi:10.1016/j.jnutbio.2007.06.014

65.              Seyfert A.L., Cristescu M.E.A., Frisse L., Schaak S., Thomas W.K., and Lynch M.2008. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178(4):2113-2121, doi:10.1534/genetics.107.081927

66.              Lynch M., Sung W., Morris K., Coffey N., Landry C.R., Dopman E.B., Dickinson W.J., Okamoto K., Kulkarni S., Hartl D.L., Thomas W.K. 2008.  A genome-wide view of the spectrum of spontaneous mutations in yeast. PNAS 105(27):9272-9288.  doi:10.1073/pnas.0803466105 

67.              Brites D., McTaggart S., Morris K., Anderson J., Thomas K., Colson I., Fabbro T., Little T.J., Ebert D., Du Pasquier L. 2008. The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. Mol Biol Evol. 25:1429-39. Epub, doi:10.1093/molbev/msn087

68.              Zhao Z., Ye W., Giblin-Davis R.M., Li D., Thomas W.K., Davies K.A., Riley I.T. 2008. Morphological and molecular analysis of six aphelenchoids from Australian conifers and their relationship to Bursaphelenchus (Fuchs, 1937). Nematology  10:663-678, doi:10.1163/156854108785787299 

69.              Gulcu B., Hazir S., Giblin-Davis R.M., Ye W., Kanzaki N., Mergen H., Keskin N., Thomas W.K. 2008. Molecular variability of Schistonchus caprifici (Nematoda: Aphelenchoididae) from Ficus carica in Turkey. Nematology 10(5):639-649, doi:10.1163/156854108785787244.

70.              Porazinska D.L., Giblin-Davis R.M., Faller L. , Farmerie W. , Kanzaki N., Morris K., Powers T.O., Tucker A.E., Sung W., and Thomas W.K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol. Ecol. Res.  9:1439-1450, doi:10.1111/j.1755-0998.2009.02611.x

71.              Kanzaki, N., Giblin-Davis R.M., Davies K., W Ye., Center B.J., Thomas W.K. 2009. Teratodiplogaster fignewmani gen. nov. sp.  (Nematoda: Diplogastridae) from the synconia of Ficus racemosa in Australia. Zool. Sci. 26(8)569-578, doi:10.2108/zsj.26.569

72.              Li W., Tucker A.E., Sung W., Thomas W.K., and Lynch M.  2009.  Extensive, recent intron gains in Daphnia populations. Science. 326(5957)1260-1262, doi:10.1126/science.1179302

73.              Davies K.A., Ye W., Giblin-Davis R.M., Thomas W.K. 2009. Ficotylus congestae n. gen., n. sp. (Anguinata), from Ficus congesta (Moraceae) sycones in Australia. Nematology 11(1):63-75, doi:10.1163/156854108X398426

74.              Denver D.R., Dolan P.C., Wilhelm L.J., Sung W., Lucas-Lledó W.I., Howe D.K., Lewis S.C., Okamoto K., Thomas W.K., Lynch M., Baer C.F. 2009. A genome-wide view of Caenorhabditis elegans base-substitution mutation processes.  PNAS 106(38):16310-16314, doi:10.1073/pnas.0904895106

75.              Sung W., Porazinska D., Creer S., Giblin-Davis R.M., and Thomas W.K. 2009.  Octupus: a package for defining “Operational Clustered Taxonomic Units from Parallel-Tagged Ultra-Sequencing”. J. Nematology 41:383

76.              Abebe E., Jumba M., Bonner K., Gray V., Morris K., Thomas, W.K. 2010.  An entomopathogenic Caenorhabditis briggsae. J. Exp. Biol. 213: 3223-3229, doi:10.1242/jeb.043109

77.              Bik H.M., Thomas W.K., Lunt D.H., and Lambhead P.J. 2010. Low Endemism, continued deep-shallow interchanges, and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida). BMC Evol. Biol. 10:389, doi:10.1186/1471-2148-10-389  

78.              Bik H.M., Lambshead P.J., Thomas W.K., Lunt D.H. 2010.  Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades. BMC Evol. Biol. 10:353, doi:10.1186/1471-2148-10-353

79.              Kanzaki, N., Giblin-Davis R. M., Zeng Y., Ye W, Center B. J., Thomas W. K. 2010. Acrostichus puri n. sp. (Nematoda: Diplogastridae), a phoretic associate of Augochlora pura mosieri Cockerell (Hymenoptera: Halictidae). Nematology 12(1):49-64. doi:10.1163/156854109X448339

80.              Hazir, C., Giblin-Davis R.M., Keskin N., Ye W., Hazir S., Scheuhl E, Thomas W. K. 2010. Diversity and distribution of nematodes associated with wild bees in Turkey. Nematology 12(1):65-80. doi:10.1163/156854109X448348.

81.              Kanzaki, N., Giblin-Davis R.M., Wcislo W.T., Zeng Y., Ye W., Center B. J.,. Esquivel A., Thomas W.K. 2010. Acrostichus megaloptae n. sp. (Nematoda: Diplogastridae), a phoretic associate of Megalopta spp. (Hymenoptera: Halictidae) in Central America. Nematology 12(3):453-468, doi:10.1163/138855409X12559479585089

82.              Creer S., Fonseca V.G., Porazinska, D.L., Giblin-Davis, R.M., Sung W., Power D.M., Packer M., Carvalho G R., Blaxter M.L., Lambshead P.J.D., and Thomas W.K. 2010.  Ultrasequencing of the meiofaunal biosphere: practice, promises and pitfalls. Mol. Ecol. 19 (Suppl. 1):4-20, doi:10.1111/j.1365-294X.2009.04473.x

83.              Davies K.A., Ye W., Giblin-Davis R.M., Taylor G.S., Scheffer S., Thomas W.K. 2010. The nematode genus Fergusobia (Nematoda: Neotylenchidae): molecular phylogeny, descriptions of clades and associated galls, host plants and Fergusonina fly larvae.  Zootaxa 2633: 1–66.

84.              Porazinska, D., R. M. Giblin-Davis, W. Sung, and W. K. Thomas. 2010. Linking operational clustered taxonomic units (OCTU) from parallel ultrasequencing (PUS) to nematode species. Zootaxa 2427: 55-63.

85.              Fonseca V.G., Carvalho G.R., Sung W., Johnson H.F., Power D.M., Neill S.P., Packer M., Blaxter M.L., Lambshead P.J., Thomas W.K., Creer S. 2010. Second-generation environmental sequencing unmasks marine metazoan biodiversity.  Nat. Comm. 1(7):98, doi:10.1038/ncomms1095

86.              Davies, K. A., Giblin-Davis R.M., Ye W., Taylor G. S., Thomas W.K. 2010. Nematodes from galls on Myrtaceae. I. Fergusobia/Fergusonina galls on Corymbia spp., with re-description of F. magna and notes on its phylogenetic relationships. Zootaxa 2634:25-40.

87.              Porazinska D.L., Giblin-Davis R.G., Esquivel A., Powers T.O., Sung W., Thomas W.K. 2010. Ecometagenetics confirm high tropical rainforest nematode diversity.  Mol. Ecol.  19: 5521-5530, doi:10.1111/j.1365-294X.2010.04891.x

88.              Porazinska D.L., Sung W., Giblin-Davis R.M., and Thomas, W.K.  2010. Reproducibility of Read Numbers in High-Throughput Sequencing Analysis of Nematode Community Composition and Structure. Mol. Ecol. Res. 10:666-676, doi:10.1111/j.1755-0998.2009.02819.x

89.              Sung W., Tucker A., Bergeron R.D., Lynch M., and Thomas W.K. 2010. Simple sequence repeat variation in the Daphnia pulex genome.  BMC Genomics 11:691, doi:10.1186/1471-2164-11-691

90.              Colbourne J.K., Pfrender M.E., Gilbert D., Thomas W.K., Tucker A., Oakley T.H., Tokishita S., Aerts A., Arnold G.J., Basu M.K., Bauer D.J., Caceres C.E., Carmel L., Casola C., Choi J.H., Detter J., Dong Q., Dusheyko S., Eads B.D., Frohlich T., Geiler-Samerotte K.A., Gerlach D., Hatcher P., Jogdeo S., Krijgsveld J., Kriventseva E.V., Kultz D., Laforsch C., Lindquist E., Lopez J., Manak J.R., Muller J., Pangilinan J., Patwardhan R.P., Pitluck S., Pritham E.J., Rechtsteiner A., Rho M., Rogozin I.B., Sakarya O., Salamov A., Schaack S., Shapiro H., Shiga Y., Skalitzky C., Smith Z., Souvorov A., Sung W., Tang Z., Tsuchiya D., Tu H., Vos H., Wang M., Wolf Y., Yamagata H., Yamada T., Ye Y., Shaw J.R., Andrews J., Crease T.J., Tang H., Lucas S.M., Robertson H.M., Bork P., Koonin E.V., Zdobnov E.M., Grigoriev I.V., Lynch M., Boore J.L. 2011. The ecoresponsive genome of Daphnia pulex. Science, 331(6017):555-561, doi:10.1126/science.1197761

91.              Abebe E., Abebe-Akele F., Morrison J., Cooper V., and Thomas W.K. 2011. An insect pathogenic symbiosis between a Caenorhabditis and Serratia. Virulence 2:158-161, doi:10.4161/viru.2.2.15337

92.              Solorzano E., Okamoto K., Datla P., Sung W., Bergeron R.D. Thomas W.K. 2011. Shifting patterns of natural variation in the nuclear genome of Caenorhabditis elegans. BMC Evol. Biol., 11:168. doi:10.1186/1471-2148-11-168

93.              Walker C.W., Van Beneden R.J., Muttray A.F., Böttger S.A., Kelley M.L., Tucker A.E., Thomas W.K. 2011. P 53 Superfamily proteins in marine bivalve cancer and stress biology. Adv. Mar. Biol. 59:1-36, doi:10.1016/b978-0-12-385536-7-.00001.7

94.              Abebe E., Mekete T., Thomas, W.K. 2011. A critique of current methods in nematode taxonomy. African Journal of Biotechnology, Vol.10(3), pp. 312-323,  doi:10.5897/ajb10.1473

95.              Bell, D., Thomas, W. K., Murtagh, K., Glover, W. 2011.  Albert Crewe's Dream Realized: Sequencing DNA with STEM. Microscopy and Microanalysis 17 (S2):1276-1277. doi:10.1017/S1431927611007252.

96.              Abebe, E., Bonner, K., Gray, V., Thomas, W.K. 2011. Response to 'bugs don't make worms kill'. J Exp Biol, 214, 1053-1054 doi: 10.1242/​jeb.053827

97.              Gao, H., Green, S. J., Jafari, N., Kingham, B., Kiss, A., Lyons, R., Thomas, W. K. 2012. Next-generation sequencing: An exclusive Q&A with our expert panel. Genetic Engineering and Biotechnology News, 32(8), 30-33. doi:10.1089/gen.32.8.13

98.              Wang Q., Arighi C.N., King B.L., Polson S.W., Vincent J., Chen C., Huang H., Kingham B.F., Page S.T., Rendino M.F., Thomas W.K., Udwary D.W., Wu, C. H. 2012. Community annotation and bioinformatics workforce development in concert-Little Skate Genome Annotation Workshops and Jamborees. Database, 2012:bar064. doi:10.1093/database/bar064

99.              Anderson J.L., Taylor R.L., Smith E.C., Thomas W.K., Smith, S.C. 2012. Differentially expressed genes in aortic smooth muscle cells from atherosclerosis-susceptible and atherosclerosis-resistant pigeons. Poultry Science, 91(6), 1315-1325. doi:10.3382/ps.2011-01975

100.          Turlapati S.A., Minocha R., Bhiravarasa P.S., Tisa L.S., Thomas W.K., Minocha S.C. 2012. Chronic N-amended soils exhibit an altered bacterial community structure in Harvard Forest, MA, USA., doi: 10.1111/1574-6941.12009

101.          Bik H.M., Sung W., De Ley P., Baldwin J.G., Sharma J., Rocha-Olivares A., Thomas W.K. 2012.  Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol Ecol. 21(5): 1048–1059. doi: 10.1111/j.1365-294X.2011.05297.x

102.          Bik, H.M., Halanych, K.M., Sharma, J., Thomas, W.K. 2012. Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill. PLoS ONE 06/2012; 7(6):e38550. doi:10.1371/journal.pone.0038550

103.          Bik H.M., Porazinska D.L., Creer S., Caporaso J.G., Knight R., Thomas W.K. 2012. Sequencing our way towards understanding global eukaryotic biodiversity.  Trends in Ecol. Evol. 27(4): 233–243, doi:10.1016/j.tree.2011.11.010

104.          Bell D.C., Thomas W.K., Murtagh K.M., Dionne C.A., Graham A., Anderson J., and Glover W.R. 2012. DNA base identification by electron microscopy. Microsc Microanal. 18(5):1049-53. doi:10.1017/S1431927612012615.

105.          Bik H.M. and Thomas W. K. 2012. Metagenomics will highlight and drive links to taxonomic data: Reply to Murray. Trends in Ecology and Evolution, 27(12), 652-653. doi:10.1016/j.tree.2012.09.005

106.          Sung W., Tucker A., Doak T.G., Choi E., Thomas W.K. and Lynch M. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. PNAS 109:19339-19344 doi:10.1073/pnas.1210663109

107.          Davies K., Giblin-Davis R.M., Ye W., Taylor G., Thomas K. 2012. Nematodes from galls on Myrtaceae. II. Fergusobia/Fergusonina from small axillary bud (‘stem’) and leaf (‘pea’) galls in Australia with descriptions of two new species. Zootaxa 3415:1-22, DOI: doi.org/10.11646/zootaxa.3741.1.5

108.          Davies K., Giblin-Davis R.M., Ye W., Taylor G., Thomas K. 2012. Nematodes from galls on Myrtaceae. III. Fergusobia from flower bud and stigma galls on Eucalyptus, with descriptions of four new species. Zootaxa 3532:1-36

109.          Porazinska D.L., Giblin-Davis R.M., Powers T.O., Thomas, W.K. 2012. Nematode spatial and ecological patterns from tropical and temperate rainforests. PLoS One. 2012; 7(9): e44641. Published online 2012 September 11. doi:10.1371/journal.pone.0044641

110.          Porazinska D.L., Giblin-Davis R.M., Sung W. and Thomas W.K. 2012. The nature and frequency of chimeras in eukaryotic metagenetic samples. J. Nematology 44(1): 18-25.

111.          Vaughn R., Garnhart N., Garey J.R., Thomas W.K. Livingston B.T. 2012. Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii. EvoDevo 3:19 doi:10.1186/2041-9139-3-19

112.          Gout, J. -F., Thomas, W. K., Smith, Z., Okamoto, K., & Lynch, M. 2013. Large-scale detection of in vivo transcription errors. PNAS, 110(46), 18584-18589. doi:10.1073/pnas.1309843110

113.          Davies K.A., Giblin-Davis R.M., Ye W., Lisnawita L., Taylor G.S., Thomas W.K. 2013. Nematodes from galls on Myrtaceae. V. Fergusobia from large multilocular shoot bud galls from Angophora and Eucalyptus in Australia, with descriptions of six new species. Zootaxa 3741(1):101-140. DOI: http://dx.doi.org/10.11646/zootaxa.3741.1.3

114.          Davies K.A., Giblin-Davis R.M., Ye W., Taylor G.S., Thomas W.K. 2013 . Nematodes from galls on Myrtaceae. IV. Fergusobia from flat leaf galls on Eucalyptus and Corymbia, with descriptions of two new species. Zootaxa, 3741(1), 151-171. doi:10.11646/zootaxa.3741.1.5

115.          Schiffer P.H., Kroiher M., Kraus C., Koutsovoulos G.D., Kumar S., Camps J.I.R., Nsah N.A., Stappert D., Morris K., Heger P., Altmüller J., Frommolt P., Nürnberg P., Thomas W.K., Blaxter M.L., Schierenberg E. 2013. The genome of Romanomermis culicivorax: Revealing fundamental changes in the core developmental genetic toolkit in Nematoda. BMC Genomics, 14(1):923, doi:10.1186/1471-2164-14-923

116.          Gaspar J.M. and Thomas W.K. 2013. Assessing the consequences of denoising marker-based metagenomic data. PLoS One 8(3): e60458. doi:10.1371/journal.pone.0060458.

117.          Bik H.M., Fournier D., Sung W., Bergeron R.D., Thomas W.K. 2013. Intra-Genomic Variation in the Ribosomal Repeats of Nematodes. PLoS ONE 8(10): e78230. doi: 10.1371/journal.pone.0078230

118.          Davies K.A., Bartholomaeus F., Giblin-Davis R.M., Ye W., Taylor G.S., Thomas W.K. 2014. Nematodes from galls on Myrtaceae. VIII. Fergusobia from small galls on shoot buds, with descriptions of four new species. Zootaxa, 3857, 1-40. doi:10.11646/zootaxa.3857.1.1

119.          Fonseca V.G., Carvalho G.R., Nichols B., Quince C., Johnson H.F., Neill S.P., Lambshead P.J.D., Thomas W.K., Creer S., Power D.M. 2014. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography 23(11):1293-1302. doi:10.1111/geb.12223

120.          Ghazal S., Hurst IV S.G., Morris K., Abebe-Akele F., Thomas W.K., Badr U.M., Hussein M.A., AbouZaied M.A., Khalil K.M., Tisa L. S. 2014. Draft genome sequence of Photorhabdus luminescens Strain BA1, an entomopathogenic bacterium Isolated from nematodes found in Egypt. Genome Announc. 2(2): e00396-14. doi:10.1128/genomeA.00396-14

121.          Hurst IV S. G., Oshone R., Ghodhbane-Gtari F., Morris K., Abebe-Akele F., Thomas W.K., Ktari A., Salem K., Gtari M., Tisa L. S., Mansour S. 2014. Draft Genome Sequence of Frankia sp. strain Thr, a nitrogen-fixing Actinobacterium isolated from the root nodules of Casuarina cunninghamiana grown in egypt. Genome Announcements, 2(3):e00493-14. doi:10.1128/genomea.00493-14

122.          Ghodhbane-Gtari, F., Hurst IV S.G., Oshone R., Morris K., Abebe-Akele F., Thomas W.K., Ktari A., Salem K., Gtari M. Tisa L.S. 2014. Draft Genome Sequence of Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing Actinobacterium isolated from the root nodules of Casuarina glauca grown in Tunisia. Genome announcements, 2(3):e00520-14. doi:10.1128/genomea.00520-14

123.          Morgan M.J., Bass D., Bik H., Birky C.W., Blaxter M., Crisp M.D., Creer S., Derycke S., Fitch D., Fontaneto D., Hardy C.M., King A.J., Kiontke K.C., Moens T., Pawlowski J.W., Porazinska D., Tang C.Q. Thomas, W.K., Yeats D.K., Creer, S. 2014. A critique of Rossberg et al.: Noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proc. R. Soc. B: 281: 20133076. doi:10.1098/rspb.2013.3076.

124.          Davies K.A., Ye W., Giblin-Davis R.M., Taylor G.S., Hodda M., Thomas, W. K. 2014. Nematodes from galls on Myrtaceae. VII. Fergusobia from 'leafy' leaf bud galls in Australia, with re-description of Fergusobia tumifaciens (Currie 1937) Wachek 1955 and descriptions of Fergusobia planchonianae n. sp. and Fergusobia viminalisae n. sp. Zootaxa, 3856(4), 529-554. doi:10.11646/zootaxa.3856.4.4

125.          Fonseca V.G., Carvalho G.R., Nichols B., Quince C., Johnson H.F., Neill S.P., Lambshead P.J.D., Thomas W.K., Power D.M., Creer S. 2014. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Global Ecology and Biogeography, 23(11): 1293-1302. doi:10.1111/geb.12223

126.          Lallias D., Hiddink J.G., Fonseca V.G., Gaspar J.M., Sung W., Neill S.P., Barnes N., Ferrero T., Hall N., Lambshead P.J.D., Packer M., Thomas W.K., Creer S. 2014. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. The ISME journal 2014:1-14. doi:10.1038/ismej.2014.213

127.          Davies K.A., Ye W., Giblin-Davis R.M., Taylor G.S., Purcell M., Thomas W.K. 2014. Nematodes from galls on Myrtaceae. IX. Fergusobia rosettae n. sp. on Melaleuca quinquenervia and F. tolgaensis n. sp. on Syzygium luehmannii, from Queensland. Zootaxa  3889(2):214-236. doi: 10.11646/zootaxa.2889.2.3.

128.          Gaspar J.M., Thomas W.K. 2015. FlowClus: efficiently filtering and denoising pyrosequenced amplicons. BMC Bioinformatics 16:105 doi:10.1186/s12859-015-0532-1

129.          Kovach, Adrienne I., Walsh, Ramsdell Jordan, Thomas, W. Kelley, 2015. Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone. Ecology and Evolution. doi: 10.1002/ece3.1514


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