Thomas, James

TitlePhysicist Staff Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentNuclear Science
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    Collapse Research 
    Collapse Research Activities and Funding
    Proteogenomic Analysis of C. elegans
    NIH/NIGMS R21GM074787May 1, 2006 - Apr 30, 2009
    Role: Principal Investigator
    NIH/NIMH R01MH058916Aug 1, 1998 - Jul 31, 2002
    Role: Principal Investigator
    NIH/NIGMS R01GM048700Aug 1, 1993 - Feb 28, 2005
    Role: Principal Investigator
    NIH/NINDS R01NS030187Jan 1, 1992 - Jan 31, 2004
    Role: Principal Investigator
    NIH/NIGMS R01GM039868Jun 1, 1988 - Aug 31, 1992
    Role: Principal Investigator
    Training Program in Genetics General and Medical
    NIH/NIGMS T32GM007735Jul 1, 1979 - Jun 30, 2010
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Smukowski Heil C, Burton JN, Liachko I, Friedrich A, Hanson NA, Morris CL, Schacherer J, Shendure J, Thomas J, Dunham MJ. Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C. Yeast. 2018 01; 35(1):71-84. PMID: 28892574.
      View in: PubMed
    2. Coyan GN, Moncure M, Thomas J, Wood JG. Induced hypothermia during resuscitation from hemorrhagic shock attenuates microvascular inflammation in the rat mesenteric microcirculation. Shock. 2014 Dec; 42(6):518-24. PMID: 25046540; PMCID: PMC4236241.
    3. Schneider SE, Thomas J. Accidental genetic engineers: horizontal sequence transfer from parasitoid wasps to their Lepidopteran hosts. PLoS One. 2014; 9(10):e109446. PMID: 25296163; PMCID: PMC4190172.
    4. Schwartz JJ, Roach DJ, Thomas J, Shendure J. Primate evolution of the recombination regulator PRDM9. Nat Commun. 2014 Jul 08; 5:4370. PMID: 25001002; PMCID: PMC4110516.
    5. Lachowiec J, Lemus T, Thomas J, Murphy PJ, Nemhauser JL, Queitsch C. The protein chaperone HSP90 can facilitate the divergence of gene duplicates. Genetics. 2013 Apr; 193(4):1269-77. PMID: 23410833; PMCID: PMC3606102.
    6. Santoni de Sio FR, Barde I, Offner S, Kapopoulou A, Corsinotti A, Bojkowska K, Genolet R, Thomas J, Luescher IF, Pinschewer D, Harris N, Trono D. KAP1 regulates gene networks controlling T-cell development and responsiveness. FASEB J. 2012 Nov; 26(11):4561-75. PMID: 22872677; PMCID: PMC4894473.
    7. Santoni de Sio FR, Massacand J, Barde I, Offner S, Corsinotti A, Kapopoulou A, Bojkowska K, Dagklis A, Fernandez M, Ghia P, Thomas J, Pinschewer D, Harris N, Trono D. KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function. Blood. 2012 May 17; 119(20):4675-85. PMID: 22452978; PMCID: PMC3683646.
    8. Emerson RO, Thomas J. Gypsy and the birth of the SCAN domain. J Virol. 2011 Nov; 85(22):12043-52. PMID: 21865395; PMCID: PMC3209298.
    9. George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas J. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res. 2011 Oct; 21(10):1686-94. PMID: 21795384; PMCID: PMC3202285.
    10. Thomas J, Schneider S. Coevolution of retroelements and tandem zinc finger genes. Genome Res. 2011 Nov; 21(11):1800-12. PMID: 21784874; PMCID: PMC3205565.
    11. Mattioli LF, Thomas J, Holloway NB, Schropp KP, Wood JG. Effects of intragastric fructose and dextrose on mesenteric microvascular inflammation and postprandial hyperemia in the rat. JPEN J Parenter Enteral Nutr. 2011 Mar; 35(2):223-8. PMID: 21378252.
      View in: PubMed
    12. Jafari G, Burghoorn J, Kawano T, Mathew M, Mörck C, Axäng C, Ailion M, Thomas J, Culotti JG, Swoboda P, Pilon M. Genetics of extracellular matrix remodeling during organ growth using the Caenorhabditis elegans pharynx model. Genetics. 2010 Nov; 186(3):969-82. PMID: 20805556; PMCID: PMC2975278.
    13. Mattioli LF, Holloway NB, Thomas J, Wood JG. Fructose, but not dextrose, induces leukocyte adherence to the mesenteric venule of the rat by oxidative stress. Pediatr Res. 2010 Apr; 67(4):352-6. PMID: 20032812.
      View in: PubMed
    14. Thomas J, Emerson RO, Shendure J. Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One. 2009 Dec 30; 4(12):e8505. PMID: 20041164; PMCID: PMC2794550.
    15. Thomas J, Emerson RO. Evolution of C2H2-zinc finger genes revisited. BMC Evol Biol. 2009 Mar 04; 9:51. PMID: 19261184; PMCID: PMC2667407.
    16. Emerson RO, Thomas J. Adaptive evolution in zinc finger transcription factors. PLoS Genet. 2009 Jan; 5(1):e1000325. PMID: 19119423; PMCID: PMC2604467.
    17. Mahoney TR, Luo S, Round EK, Brauner M, Gottschalk A, Thomas J, Nonet ML. Intestinal signaling to GABAergic neurons regulates a rhythmic behavior in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2008 Oct 21; 105(42):16350-5. PMID: 18852466; PMCID: PMC2570992.
    18. Thomas J, Robertson HM. The Caenorhabditis chemoreceptor gene families. BMC Biol. 2008 Oct 06; 6:42. PMID: 18837995; PMCID: PMC2576165.
    19. Reiner DJ, Ailion M, Thomas J, Meyer BJ. C. elegans anaplastic lymphoma kinase ortholog SCD-2 controls dauer formation by modulating TGF-beta signaling. Curr Biol. 2008 Aug 05; 18(15):1101-9. PMID: 18674914; PMCID: PMC3489285.
    20. Biron D, Wasserman S, Thomas J, Samuel AD, Sengupta P. An olfactory neuron responds stochastically to temperature and modulates Caenorhabditis elegans thermotactic behavior. Proc Natl Acad Sci U S A. 2008 Aug 05; 105(31):11002-7. PMID: 18667708; PMCID: PMC2504807.
    21. Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas J, MacCoss MJ. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res. 2008 Oct; 18(10):1660-9. PMID: 18653799; PMCID: PMC2556273.
    22. Thomas J. Genome evolution in Caenorhabditis. Brief Funct Genomic Proteomic. 2008 May; 7(3):211-6. PMID: 18573804.
      View in: PubMed
    23. Smith ED, Tsuchiya M, Fox LA, Dang N, Hu D, Kerr EO, Johnston ED, Tchao BN, Pak DN, Welton KL, Promislow DE, Thomas J, Kaeberlein M, Kennedy BK. Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. Genome Res. 2008 Apr; 18(4):564-70. PMID: 18340043; PMCID: PMC2279244.
    24. Inoue T, Ailion M, Poon S, Kim HK, Thomas J, Sternberg PW. Genetic analysis of dauer formation in Caenorhabditis briggsae. Genetics. 2007 Oct; 177(2):809-18. PMID: 17660533; PMCID: PMC2034645.
    25. Sengupta P, Thomas J. From eye of newt to chemical structure. Nat Chem Biol. 2007 Jul; 3(7):368-9. PMID: 17576419.
      View in: PubMed
    26. Thomas J. Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet. 2007 May 11; 3(5):e67. PMID: 17500592; PMCID: PMC1866355.
    27. Pierce GE, Thomas J, Fenton JR. Novel repair of venous aneurysms secondary to arteriovenous dialysis fistulae. Vasc Endovascular Surg. 2007 Feb-Mar; 41(1):55-60. PMID: 17277244.
      View in: PubMed
    28. Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas J, Moerman DG. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res. 2007 Mar; 17(3):337-47. PMID: 17267812; PMCID: PMC1800925.
    29. McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas J, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D. Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol. 2007; 8(7):R132. PMID: 17612391; PMCID: PMC2323215.
    30. Zhao Z, Thomas J, Chen N, Sheps JA, Baillie DL. Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in caenorhabditis species. Genetics. 2007 Mar; 175(3):1407-18. PMID: 17194779; PMCID: PMC1840077.
    31. Kaeberlein TL, Smith ED, Tsuchiya M, Welton KL, Thomas J, Fields S, Kennedy BK, Kaeberlein M. Lifespan extension in Caenorhabditis elegans by complete removal of food. Aging Cell. 2006 Dec; 5(6):487-94. PMID: 17081160.
      View in: PubMed
    32. Wheeler JM, Thomas J. Identification of a novel gene family involved in osmotic stress response in Caenorhabditis elegans. Genetics. 2006 Nov; 174(3):1327-36. PMID: 16980399; PMCID: PMC1667073.
    33. Harris J, Lowden M, Clejan I, Tzoneva M, Thomas J, Hodgkin J, Ahmed S. Mutator phenotype of Caenorhabditis elegans DNA damage checkpoint mutants. Genetics. 2006 Oct; 174(2):601-16. PMID: 16951081; PMCID: PMC1602097.
    34. Thomas J. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res. 2006 Aug; 16(8):1017-30. PMID: 16825662; PMCID: PMC1524861.
    35. Kraemer BC, Burgess JK, Chen JH, Thomas J, Schellenberg GD. Molecular pathways that influence human tau-induced pathology in Caenorhabditis elegans. Hum Mol Genet. 2006 May 01; 15(9):1483-96. PMID: 16600994.
      View in: PubMed
    36. Thomas J. Concerted evolution of two novel protein families in Caenorhabditis species. Genetics. 2006 Apr; 172(4):2269-81. PMID: 16415360; PMCID: PMC1456376.
    37. Robertson HM, Thomas J. The putative chemoreceptor families of C. elegans. WormBook. 2006 Jan 06; 1-12. PMID: 18050473; PMCID: PMC4781013.
    38. Reiner DJ, Weinshenker D, Tian H, Thomas J, Nishiwaki K, Miwa J, Gruninger T, Leboeuf B, Garcia LR. Behavioral genetics of caenorhabditis elegans unc-103-encoded erg-like K(+) channel. J Neurogenet. 2006 Jan-Jun; 20(1-2):41-66. PMID: 16807195.
      View in: PubMed
    39. Thomas J. Analysis of homologous gene clusters in Caenorhabditis elegans reveals striking regional cluster domains. Genetics. 2006 Jan; 172(1):127-43. PMID: 16291650; PMCID: PMC1456141.
    40. Vancura RW, Thomas J, Jewell WR, Damjanov I. Bilateral oncocytic malignant melanoma in axillary lymph nodes without evidence of an extranodal primary. Ultrastruct Pathol. 2005 Sep-Oct; 29(5):399-404. PMID: 16257866.
      View in: PubMed
    41. Choy RK, Kemner JM, Thomas J. Fluoxetine-resistance genes in Caenorhabditis elegans function in the intestine and may act in drug transport. Genetics. 2006 Feb; 172(2):885-92. PMID: 16118202; PMCID: PMC1456238.
    42. Cuff RF, Thomas J. Recurrent symptomatic aortic sac seroma after open abdominal aortic aneurysm repair. J Vasc Surg. 2005 Jun; 41(6):1058-60. PMID: 15944610.
      View in: PubMed
    43. Efimenko E, Bubb K, Mak HY, Holzman T, Leroux MR, Ruvkun G, Thomas J, Swoboda P. Analysis of xbx genes in C. elegans. Development. 2005 Apr; 132(8):1923-34. PMID: 15790967.
      View in: PubMed
    44. Thomas J, Kelley JL, Robertson HM, Ly K, Swanson WJ. Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12):4476-81. PMID: 15761060; PMCID: PMC555475.
    45. Cuff RF, Thomas J. Pediatric blunt carotid injury from low-impact trauma: a case report and review of the literature. J Trauma. 2005 Mar; 58(3):620-3. PMID: 15761361.
      View in: PubMed
    46. Li J, Brown G, Ailion M, Lee S, Thomas J. NCR-1 and NCR-2, the C. elegans homologs of the human Niemann-Pick type C1 disease protein, function upstream of DAF-9 in the dauer formation pathways. Development. 2004 Nov; 131(22):5741-52. PMID: 15509773.
      View in: PubMed
    47. Stewart MK, Clark NL, Merrihew G, Galloway EM, Thomas J. High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans. Genetics. 2005 Apr; 169(4):1985-96. PMID: 15520260; PMCID: PMC1449585.
    48. McElwee JJ, Schuster E, Blanc E, Thomas J, Gems D. Shared transcriptional signature in Caenorhabditis elegans Dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance. J Biol Chem. 2004 Oct 22; 279(43):44533-43. PMID: 15308663.
      View in: PubMed
    49. Petersen CI, McFarland TR, Stepanovic SZ, Yang P, Reiner DJ, Hayashi K, George AL, Roden DM, Thomas J, Balser JR. In vivo identification of genes that modify ether-a-go-go-related gene activity in Caenorhabditis elegans may also affect human cardiac arrhythmia. Proc Natl Acad Sci U S A. 2004 Aug 10; 101(32):11773-8. PMID: 15280551; PMCID: PMC511051.
    50. Ailion M, Thomas J. Isolation and characterization of high-temperature-induced Dauer formation mutants in Caenorhabditis elegans. Genetics. 2003 Sep; 165(1):127-44. PMID: 14504222; PMCID: PMC1462745.
    51. Kraemer BC, Zhang B, Leverenz JB, Thomas J, Trojanowski JQ, Schellenberg GD. Neurodegeneration and defective neurotransmission in a Caenorhabditis elegans model of tauopathy. Proc Natl Acad Sci U S A. 2003 Aug 19; 100(17):9980-5. PMID: 12872001; PMCID: PMC187908.
    52. Lakso M, Vartiainen S, Moilanen AM, Sirviö J, Thomas J, Nass R, Blakely RD, Wong G. Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alpha-synuclein. J Neurochem. 2003 Jul; 86(1):165-72. PMID: 12807436.
      View in: PubMed
    53. McElwee J, Bubb K, Thomas J. Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16. Aging Cell. 2003 Apr; 2(2):111-21. PMID: 12882324.
      View in: PubMed
    54. Schafer JC, Haycraft CJ, Thomas J, Yoder BK, Swoboda P. XBX-1 encodes a dynein light intermediate chain required for retrograde intraflagellar transport and cilia assembly in Caenorhabditis elegans. Mol Biol Cell. 2003 May; 14(5):2057-70. PMID: 12802075; PMCID: PMC165097.
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