Robert Holt Publications

Robert Holt Complete Bibliography
  1. Branton WG, Lu JQ, Surette MG, Holt RA, Lind J, Laman JD, Power C. Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis. Sci Rep, 2016 Nov 28;6:37344. PMID: 27892518
  2. Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. PloS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016. PMID: 27632164
  3. Jspeert H, Rozmus J, Schwarz K, Warren RL, van Zessen D, Holt RA, Pico-Knijnenburg I, Simons E, Jerchel I, Wawer A, Lorenz MR, Patıroğlu T, Akar HH, Leite R, Verkaik NS, Stubbs AP, van Gent DCC, van Dongen JJM, and van der Burg M. XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination.  Blood, 2016 Aug 4;128(5):650-9. PMID: 27281794
  4. Martin SD, Brown SD, Wick DA, Nielsen JS, Kroeger DR, Twumasi-Boateng K, Holt RA, Nelson BH. Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines. PLoS One. 2016 May 18;11(5):e0155189. doi: 10.1371/journal.pone.0155189. eCollection 2016. PMID: 27192170
  5. De Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D’Souza CA, Kaspieva O, Laprise S, Mclnerny SC, Swanson-Newman MI, Wong K, Yang GS, Zhou M, Jones SJM, Holt RA, Asokan A, Goldowitz D, Wasserman WW, Simpson EM. rAAV-Compatible MiniPromoters for Restricted Expression in the Brain and Eye. Molecular Brain. 2016 May 10;9(1):52. doi: 10.1186/s13041-016-0232-4. PMID: 27164903
  6. The Cancer Genome Atlas Research Network. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. PMID: 26536169. 
  7. Brown SD, Raeburn LA, Holt RA. Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Med. 2015 Nov 30;7(1):125. doi: 10.1186/s13073-015-0248-x. PMID: 26620832. PMCID: PMC4666197
  8. Martin SD, Coukos G, Holt RA, Nelson BH. Targeting the undruggable: Immunotherapy meets personalized oncology in the genomic era. Ann Oncol. 2015 Dec;26(12):2367-74. doi: 10.1093/annonc/mdv382. PMID: 26371284. 
  9. Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025. PMID: 26544944
  10. Holt RA. Immunogenomics: a foundation for intelligent immune design. Genome Med. 2015 Nov 19;7(1):116. doi: 10.1186/s13073-015-0247-y. PMID: 26582413
  11. The Cancer Genome Atlas Research Network.  Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. doi: 10.1016/j.cell.2015.09.033. PMID: 26451490
  12. The Cancer Genome Atlas Research Network. Comprehensive, Integrative Genomic Analysis of Diffuse Lower Grade GliomasThe New England Journal of Medicine. 2015 Jun 25;372(26):2481-98. PMID: 26061751.
  13. The Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. PMID: 26091043. 
  14. Gibb EA, Warren RL, Wilson GE, Brown SD, Robertson G, Morin GB and Holt RAActivation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinomaGenome Medicine.  2015 Mar 5;7(1):22. PMID:25821520. 
  15. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129. PMID: 25631445.
  16. Watson C, Steinberg KM, Graves T, Warren R, Malig M, Schein J, Wilson R, Holt R, Eichler E, Breden F. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes and Immunity.  2015 Jan;16(1):24-34. doi: 10.1038/gene.2014.56. PMID: 25338678. 
  17. The Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell. 2014 Oct 23;159(3):676-90. PMID: 25417114.
  18. The Cancer Genome Atlas Research Network. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-30. PMID: 25155756. 
  19. The Cancer Genome Atlas Research Network. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. PMID: 25313082. 
  20. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. PMID: 25079317. 
  21. The Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14;158(4):929-44. PMID: 25109877. 
  22. The Cancer Genome Atlas Research Network.  Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 July 31; 511(7511):543-50. PMID: 25079552
  23. Sharma G and Holt RA. T-cell epitope discovery technologies. Human Immunology. 2014 Jun;75(6):514-519. PMID: 24755351.
  24. Brown SD, Warren RL, Gibb E, Martin SD, Nelson BH, Holt RA.  Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.  Genome Research. 2014 May;24(5):743-50. PMID: 24782321. 
  25. The Cancer Genome Atlas Research Network.  Comprehensive molecular characterization of urothelial bladder carcinoma.  Nature. 2014 March 20; 507(7492):315-322. PMID: 24476821. PMCID: PMC3962515 
  26. McKinnon ML, Rozmus J, Fung SY, Hirschfeld AF, Del Bel KL, Thomas L, Marr N, Martin SD, Marwaha AK, Priatel KK, Tan R, Senger C, Tsang A, Prendiville J, Junker AK, Seear M, Schultz KR, Sly LM, Holt RA, Patel MS, Friedman JM, Turvey SE.  Combined immunodeficiency associated with homozygous MALT1 mutations. J Allergy Clin Immunol. 2014 May;133(5):1458-1462.e1-7. PMID: 24332264.
  27. De Leeuw CN, Dyka FM, Boye SL, Laprise S, Zhou M, Chou AY, Boretta L, McInerny SC, Banks KG, Portales-Casamar E, Swanson MI, D’Souza CA, Boye SE, Jones SJM, Holt RA, Goldowitz D, Hauswirth WW, Simpson EM.  Targeted CNS Delivery using human MiniPromoters and demonstrated compatibility with adeno-associated viral vectors. Molecular Therapy – Methods and Clinical Development. 2014 Jan 8;1:5. PMID: 24761428. 
  28. Bosdet I, Docking R, Butterfield Y, Mungall A, Zeng T, Coope R, Yorida E, Chow K, Young S, Hirst M, Birol I, Moore R, Jones S, Holt R, Karsan A.  A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations. Journal of Molecular Diagnostics. 2013 Nov;15(6):796-809. PMID: 24094589. 
  29. Woodsworth DJ, Castellarin M, Holt RASequence analysis of T-cell repertoires in health and diseaseGenome Medicine. 2013 Oct 30;5(10):98. PMID: 24172704. 
  30. Schmouth JF, Castellarin M, Laprise S, Banks KG, Bonaguro RJ, McInerny SC, Borretta L, Amirabbasi M, Korecki AJ, Portales-Casamar E, Wilson G, Dreolini L, Jones SJM, Wasserman WW, Goldowitz D, Holt RA, Simpson EM.  Non-coding regulatory regions of human brain genes delineated by BAC knock-in miceBMC Biology.  2013 Oct 14;11(1):106. PMID: 24124870
  31. The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26;45(10):113-20.doi:10.1038/ng.2764. PMID: 24071849.
  32. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff R, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhsi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Narnoud N, Rogic S, Lim E, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA.  Mutational and structural analysis of diffuse large B-cell lymphoma using whole genome sequencingBlood. 2013 Aug 15;122(7):1256-65. PMID: 23699601. 
  33. The Cancer Genome Atlas Research Network.  Comprehensive molecular characterization of clear cell renal cell carcinomaNature.  2013 Jul 4;499(7456):43-9. PMID: 23792563. PMCID: PMC3771322. Citations: 40
  34. Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, Allen-Vercoe E, Holt RACo-occurrence of anaerobic bacteria in colorectal carcinomas.   Microbiome. 2013 May 15;1(1):16. PMID: 24450771. 
  35. Reinke SN, Resch L, Maingat F, Branton W, Jackson A, Saxinger L, Holt RA, Slupsky C, Marrie T, Sykes BD, Power C.  Metagenomic and metabolomic characterization of rabies encephalitis – new insights into the treatment of an ancient disease.  Journal of Infectious Diseases.  2013 May 1;207(9):1451-6. PMID: 22927447.
  36. The Cancer Genome Atlas Research Network.  The Genomic and Epigenomic Landscape of Adult de novo Acute Myeloid LeukemiaNew England Journal of Medicine  2013 May 30;368(22):2059-74. PMID: 23634996.
  37. The Cancer Genome Atlast Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA.  Integrated Genomic Characterization of Endometrial Carcinoma.  Nature. 2013 May 2;497(7447):67-73. PMID: 23636398. PMCID: PMC3704730. 
  38. Castellarin M, Milne K, Zeng T, Tse K, Mayo M, Zhao YJ, Webb JR, Watson PH, Nelson BH, Holt RAClonal evolution of high-grade serous ovarian carcinoma from primary to recurrent diseaseJournal of Pathology. 2013 Mar;229(4):515-24. PMID: 22996961.
  39. Watson CT, Steinberg KM, Huddleston J, Sudmant P, Warren RL, Malig M, Schein J, Willsey JA, Joy JB, Scott JK, Graves, Wilson RK, Holt RA, Eichler EE, Breden F.  Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.  American Journal of Human Genetics.  2013 Apr 4;92(4):530-46. PMID: 23541343. 
  40. Branton WG, Ellestad KK, Maingat F, Wheatley BM, Rud E, Warren RL, Holt RA, Surrete MG, Power C.  Brain Microbial Population in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status.  PLoS One.  2013; 8(1): e54673. PMID: 23355888. 
  41. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RADerivation of HLA types from shotgun sequence datasets.  Genome Medicine. 2012 Dec 10;4(12):95. PMID: 23228053. 
  42. The Cancer Genome Atlas Research Network.  Comprehensive molecular portraits of human breast tumours.  Nature. 2012 Oct 4;490(7418):61-70. PMID: 23000897.
  43. The Cancer Genome Atlas Research Network.  Comprehensive genomic characterization of squamous cell lung cancers.  Nature.  2012 Sep 27;489(7417):519-25. PMID: 22960745.
  44. Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Aug 2; 488(7409):49-56. PMID: 22832581.
  45. The Cancer Genome Atlas Research Network.  Comprehensive molecular characterization of human colon and rectal cancer.  Nature.  2012 Jul 18; 487 (7407):330-7. PMID: 22810696.
  46. Schmouth JF, Banks KG, Mathelier A, Gregory-Evans CY, Castellarin M, Holt RA, Gregory-Evans K, Wasserman WW, Simpson EM.  Retina restored and brain abnormalities ameliorated by single-copy knock-in of human NR2E1 in null mice.  Molecular Cell Biology.  2012 Apr;32(7):1296-311. PMID: 22290436. 
  47. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Research. 2012 Feb;22(2):299-306. PMID: 22009989. 
  48. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt RA, Schein J, Horsman DE, Moore RA, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA.  Frequent mutation of histone-modifying genes in non-Hodgkin lymphomaNature. 2011 Jul 27 ;476(7360):298-303. PMID: 21796119. 
  49. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chenard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissuesPLoS One. 2011;6(5):e19838. PMID: 21603639. 
  50. Warren RL, Holt RA Targeted assembly of short sequence reads.  PLoS One. 6(5):e19816.11 May 2011. PMID: 21589938.
  51. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T- cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Research. 21(5):790-7. 2011 May. PMID: 21349924.
  52. Bhat RK, Ellestad KK, Wheatley BM, Warren R, Holt RA, Power C. Age- and disease-dependent HERV-W envelop allelic variation in brain: association with neuroimmune gene expression. PLoS One. 6(4):e19176. 2011 Apr 29. PMID: 21559469. 
  53. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Massoumi Alamouti S, Tsui CK, Docking TR, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJM, Bohlmann J, Breuil C.  Genome and transcriptome analyses of the mountain pine beetle fungal symbiont Grosmannia clavigera, a lodgepole pine pathogenGenome.  108(6):2504-9. 2011 February 8. PMID: 21262841.
  54. D’Souza CA, Kronstad JW, Taylor G, Warren R, Hao H, Yuen M, Hu G, Jung WH, Sham A, Kidd S, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich J, Fraser J, Meyer W, Carter D, Schein J, Krzywinski M, Kwong Chung KJ, Varma A, Wang J, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt RA, Birren BW, Galagan JE and Cuomo CA. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio. 8;2(1) e00342-10. 2011 February. PMID: 21304167. 
  55. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. New England Journal of Medicine. 364(8):730-9. 24 February 2011. PMID: 21345102. 
  56. Horspool DR, Coope RJ and Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Research Notes. 3(1):291. 2010 November 9. PMID: 21062485.
  57. Hesse-Orce U, Diguistini S, Keeling CI, Wang Y, Li M, Henderson H, Docking R, Liao NY, Robertson G, Holt RA, Jones SJ, Bohlmann J, Breuil C. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. BMC Genomics. 4;11(1):536. 2010 October 4. PMID: 20920358.
  58. Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JC, Chopra V, Docking TR, Dreolini L, D'Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu M, McConechy M, McLeod AJ, Milisavljevic M, Mis J, O'Connor K, Palma B, Palmquist DL, Schmouth JF, Swanson MI, Tam B, Ticoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BK, Wong SH, Wong TY, Yang GS, Ypsilanti AR, Jones SJ, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proceedings of the National Academy of Sciences. 21;107(38):16589-94. 2010 September 21. PMID: 20807748. 
  59. Zhou W, Cai F, Li Y, Yang GS, O'Connor KD, Holt RA, Song W.  BACE1 Gene Promoter Single-Nucleotide Polymorphisms in Alzheimer's Disease.  Journal of Molecular Neuroscience. 42(1):127-133. 2010 Sep. PMID: 20455082. 
  60. Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A,  Griffith M, Yee J, Montgomery M, Mayo M, Melnyk N, Morin RD,  Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao YJ, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 2010 Aug. 9;11(8):R82. PMID: 20696054. 
  61. Balasundaram M, Tsai M, Clarke A, Leung D, Munro S, Wagner S, Michael M, Moore R, Holt RA. A quality management system application to investigate and troubleshoot process failures: A case Study of the BC Cancer Agency. Clinical Governance. 15:2. 2010.
  62. Mead CL, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. Journal of Neurochemistry. 113(6):1491-1503. 2010 Jun. PMID: 20236384. 
  63. Leong JS, Jantzen SG, von Schalburg KR, Cooper GA, Messmer Am,  Liao NY, Munro S, Moore R, Holt RA, Jones SJM, Davidson WS, Koop BF.  Salmo salar and Esox lucius full-length cDNA clones reveal changes in evolutionary pressures on a post-tetraploidization genome.  BMC Genomics. 11(1):279. 2010 Apr 30. PMID: 20433749.
  64. Warren RL and Holt RA.  A census of predicted mutational epitopes suitable for immunologic cancer control.  Human Immunology.  71(3):245-254. 2010 Mar. PMID: 20035814. Citations: 10
  65. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genetics. 42(2):181-185. 2010 Feb. PMID: 20081860
  66. Romanuik TL, Wang G, Holt RA, Jones SJM, Marra MA, Sadar M.  Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries.  BMC Genomics. 2009 Oct 15; 10:476. PMID: 19832994. 
  67. Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao Y, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution and RNA editing in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-813. PMID: 19812674. 
  68. The MGC Project Teams (incl Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA). The Completion of the Mammalian Gene Collection (MGC). Genome Research. 19(12): 2324-2333. 2009 Dec. PMID: 19767417.
  69. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research. 19(10):1817-1824. 2009 Oct. PMID: 19541912. 
  70. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology.  10(9):R94. 2009 Sep 11. PMID: 19747388. 
  71. Pel J, Broemeling D, Mai L, Poon HL, Tropini G, Warren RL, Holt RA, Marziali A. Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules. Proceedings of the National Academy of Sciences. 2009 Sep  1;106(35):14796-14801. PMID: 19706437. 
  72. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM 3rd, Baillie DL, Holt RA, Jones SJ, Marra MA, Moerman DG. An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans. Public Library of Science Genetics. 5(6):e1000537. 2009 Jun. PMID: 19557190. 
  73. Wang X, Zhao Y, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics. 2009 May 9;10:213. PMID: 19426519. 
  74. The Bovine Genome Sequencing and Analysis Consortium (incl  Chiu R, Jones S, Marra M, Holt RA, Moore R, & Schein J). The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 2009 Apr 24;324(5926):522-528. PMID: 19390049. PMCID: PMC2943200. Citations: 473
  75. Yang GS, Banks KG, Bonaguro RJ, Wilson G, Dreolini L, de Leeuw CN, Liu L, Swanson DJ, Goldowitz D, Holt RA, Simpson EM. Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus. Genomics. 93(3):196-204. 2009 Mar. PMID:18950699. 
  76. Warren RL, Nelson BH, Holt RA.  Profiling model T-cell metagenomes with short reads. Bioinformatics. 25(4):458-464. 2009 Feb 15. PMID: 19136549. 
  77. Smailus DE, Warren R L and Holt RA. Constructing large DNA segments by iterative clone recombination.  Systems and Synthetic Biology. 2007 Aug;1(3):139-144. PMID: 19003448. 
  78. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad III CE, McGowan CR and Davidson WS.  A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.  BMC Genomics. 2008 Nov 17; 9:545. PMID: 19014685.
  79. Ralph SG1, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics. 2008 Oct 14;9:484. PMID: 18854048.
  80. D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ.  Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neuroscience. 2008 Jul 14;9:66. PMID: 18625066. 
  81. Warren RL, Freeman JD, Levesque RC, Smailus DE, Flibotte S, Holt RA. Transcription of foreign DNA in Escherichia coli. Genome Research. 18(11):1798-1805. 2008. PMID: 18701636.
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