Robert Holt Publications

Robert Holt Complete Bibliography
  1. Korecki AJ, Hickmott JW, Lam SL, Dreolini L, Mathelier A, Baker O, Kuehne C, Bonaguro RJ, Smith J, Tan CV, Zhou M, Goldowitz D, Deussing JM, Stewart AF, Wasserman WW, Holt RA, Simpson EM. Twenty-seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain; Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. Genetics. 2019 Feb 14. 
  2. Haile S, Corbett RD, Bilobram S, Bye MH, Kirk H, Pandoh P, Trinh E, MacLeod T, McDonald H, Bala M, Miller D, Novik K, Coope RJ, Moore RA, Zhao Y, Mungall AJ, Ma Y, Holt RA, Jones SJ, Marra MA. Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples. Nucleic Acids Res. 2019 Jan 25;47(2):e12.
  3. The Cancer Genome Atlas Research Network. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Syst. 2018 Oct 24;7(4):422-437.e7.
  4. The Cancer Genome Atlas Research Network. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell. 2018 Aug 13;34(2):211-224.e6. 
  5. The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19;23(12):3698. 
  6. Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, Kulis T, Cárcano FM, Leraas KM, Lichtenberg TM, Brooks D, Cherniack AD, Cho J, Heiman DI, Kasaian K, Liu M, Noble MS, Xi L, Zhang H, Zhou W, ZenKlusen JC, Hutter CM, Felau I, Zhang J, Schultz N, Getz G, Meyerson M, Stuart JM; Cancer Genome Atlas Research Network, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA. Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep. 2018 Jun 12;23(11):3392-3406. 
  7. The Cancer Genome Atlas Research Network. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst. 2018 Mar 28;6(3):282-300.e2.
  8. The Cancer Genome Atlas Research Network. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 Mar 28;6(3):271-281.e7.
  9. The Cancer Genome Atlas Research Network. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell. 2018 Apr 9;33(4):706-720.e9.
  10. The Cancer Genome Atlas Research Network. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 Apr 9;33(4):676-689.e3. 
  11. The Cancer Genome Atlas Research Network. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 9;33(4):690-705.e9.
  12. The Cancer Genome Atlas Research Network. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell. 2018 Apr 9;33(4):721-735.e8. 
  13. The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Apr 3;23(1):313-326.e5. 
  14. The Cancer Genome Atlas Research Network. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep. 2018 Apr 3;23(1):297-312.e12. 
  15. The Cancer Genome Atlas Research Network. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep. 2018 Apr 3;23(1):282-296.e4. 
  16. The Cancer Genome Atlas Research Network. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep. 2018 Apr 3;23(1):270-281.e3.
  17. The Cancer Genome Atlas Research Network. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep. 2018 Apr 3;23(1):255-269.e4.
  18. The Cancer Genome Atlas Research Network. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6.
  19. The Cancer Genome Atlas Research Network. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. 
  20. The Cancer Genome Atlas Research Network. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep. 2018 Apr 3;23(1):213-226.e3.
  21. The Cancer Genome Atlas Research Network.  Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. 
  22. The Cancer Genome Atlas Research Network. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr 5;173(2):400-416.e11.
  23. The Cancer Genome Atlas Research Network. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 Apr 5;173(2):386-399.e12. 
  24. The Cancer Genome Atlas Research Network. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5;173(2):371-385.e18.
  25. The Cancer Genome Atlas Research Network. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. 
  26. The Cancer Genome Atlas Research Network. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15.
  27. The Cancer Genome Atlas Research Network. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.e10. 
  28. The Cancer Genome Atlas Research Network. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. 
  29. The Cancer Genome Atlas Research Network. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6.
  30. Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang YK, Bashashati A, Grewal DS, Brown SD, Lai D, Wan ANC, Nielsen CB, Huebner C, Tessier-Cloutier B, Anglesio MS, Bouchard-Côté A, Yuan Y, Wasserman WW, Gilks CB, Karnezis AN, Aparicio S, McAlpine JN, Huntsman DG, Holt RA, Nelson BH, Shah SP. Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell. 2018 Jun 14;173(7):1755-1769.e22. 
  31. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The immune landscape of cancer. Immunity. 2018 Apr 17;48(4):812-830.e14.
  32. The Cancer Genome Atlas Research Network. The integrated genomic landscape of thymic epithelial tumors. Cancer Cell. 2018 Feb 12;33(2):244-258.e10.
  33. Sneddon S, Dick I, LEE YCG, Musk AW, Patch AM, Pearson JV, Waddell N, Allcock RJN, Holt RA, Robinson BWS, Creaney J. Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations. Lung Cancer. May 2018; 119:64-70. 
  34. Grigor E, Fergusson D, Haggar F, Kekre N, Atkins H, Shorr R, Holt R, Hutton B, Ramsay T, Seftel M, Jonker D, Daugaard M, Thavorn K, Presseau J, Lalu MM. Efficacy and safety of Chimeric Antigen Receptor T-cell  (CAR-T) therapy in patients with hematologic and solid malignancies: protocol for a systematic review and meta-analysis. BMJ Open. 2017 Dec 29;7(12):e019321. 
  35. Woodsworth DJ, Dreolini L, Abraham L, Holt RA. Targeted Cell-to-Cell Delivery of Protein Payloads via the Granzyme-Perforin Pathway. Molecular Therapy – Methods & Clinical Development. 2017 Oct 10;7:132-145.
  36. Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. Nature Communications. 2017 Nov 10;8(1):1433.
  37. Cancer Genome Atlas Research Network. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017 Nov 2;171(4);950-965.e28.
  38. Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19;171(3):540-556.e25.
  39. Martin SD, Wick DA, Nielsen JS, Little N, Holt RA, Nelson BH. A library-based screening method identifies neoantigen-reactive T cells in peripheral blood prior to relapse of ovarian cancer. OncoImmunology. 2017 Sep 21;7(1):e1371895. 
  40. Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13.
  41. Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 Aug 14;32(2):204-220.e15. 
  42. Haile S, Corbett RD, MacLeod T, Bilobram S, Smailus D, Tsao P, Kirk H, McDonald H, Pandoh P, Bala M, Hirst M, Miller D, Moore RA, Mungall AJ, Schein J, Coope RJ, Ma Y, Zhao Y, Holt RA, Jones SJ, Marra MA. Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing. BMC Genomics. 2017 Jul 5;18(1):515.
  43. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.Cell Reports. 2017 Mar 14;18(11):2780-2794.
  44. Cancer Genome Atlas Research Network. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell. 2017 Jun 15;169(7):1327-1341.e23. 
  45. Sneddon S, Patch AM, Dick IM, Kazakoff S, Pearson JV, Waddell N, Allcock RJN, Holt RA, Robinson BWS, Creaney J. Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma. BMC Cancer. 2017 Jun 2;17(1):396. 
  46. Haile S, Pandoh P, McDonald H, Corbett RD, Tsao P, Kirk H, MacLeod T, Jones M, Bilobram S, Brooks D, Smailus D, Steidl C, Scott DW, Bala M, Hirst M, Miller D, Moore RA, Mungall AJ, Coope RJ, Ma Y, Zhao Y, Holt RA, Jones SJ, Marra MA. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis. PLoS One. 2017 Jun 1;12(6):e0178706.
  47. Chee J, Robinson BW, Holt RA, Creaney J. Immunotherapy for Lung Malignancies: From Gene Sequencing to Novel Therapies. Chest. 2017 Apr;151(4):891-897.
  48.  Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384. 
  49. Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB; Cancer Genome Atlas Research Network, Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell. 2017 Mar 13;31(3):411-423. 
  50. Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu C, Patrick DM, Complex Chronic Disease Study Group. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-cell/ T-cell Receptor Signatures in Complex Chronic Disease. Clinical Infectious Diseases. 2017 Feb 15; 64(4):476-481. 
  51. Fishbein L, Leshchiner I, Walter V, Danilova L, Robertson AG, Johnson AR, Lichtenberg TM, Murray BA, Ghayee HK, Else T, Ling S, Jefferys SR, de Cubas AA, Wenz B, Korpershoek E, Amelio AL, Makowski L, Rathmell WK, Gimenez-Roqueplo AP, Giordano TJ, Asa SL, Tischler AS; Cancer Genome Atlas Research Network, Pacak K, Nathanson KL, Wilkerson MD. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell. 2017 Feb 13;31(2):181-193. 
  52. Woodsworth DJ, Holt RA. Cell-Based Therapeutics: Making a Faustian Pact with Biology. Trends in Molecular Medicine. 2017 Feb;23(2):104-115.
  53. Cancer Genome Atlas Research Network. Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175.
  54. Brown SD, Hapgood G, Steidl C, Weng AP, Savage KJ, Holt RA. Defining the clonality of peripheral T cell lymphomas using RNA-seq. Bioinformatics. 2016 Dec 21;33(8):1111-1115.
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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. 
  61. 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
  62. 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. 
  63. 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
  64. 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
  65. 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
  66. The Cancer Genome Atlas Research Network. Comprehensive, Integrative Genomic Analysis of Diffuse Lower Grade Gliomas.  The New England Journal of Medicine. 2015 Jun 25;372(26):2481-98. PMID: 26061751.
  67. The Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. PMID: 26091043. 
  68. Gibb EA, Warren RL, Wilson GE, Brown SD, Robertson G, Morin GB and Holt RA.  Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.  Genome Medicine.  2015 Mar 5;7(1):22. PMID:25821520. 
  69. 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.
  70. 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. 
  71. The Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell. 2014 Oct 23;159(3):676-90. PMID: 25417114.
  72. 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. 
  73. 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. 
  74. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. PMID: 25079317. 
  75. 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. 
  76. The Cancer Genome Atlas Research Network.  Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 July 31; 511(7511):543-50. PMID: 25079552
  77. Sharma G and Holt RA. T-cell epitope discovery technologies. Human Immunology. 2014 Jun;75(6):514-519. PMID: 24755351.
  78. 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. 
  79. 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 
  80. 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.
  81. 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. 
  82. 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. 
  83. Woodsworth DJ, Castellarin M, Holt RA.  Sequence analysis of T-cell repertoires in health and disease.  Genome Medicine. 2013 Oct 30;5(10):98. PMID: 24172704. 
  84. 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 mice.  BMC Biology.  2013 Oct 14;11(1):106. PMID: 24124870
  85. 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.
  86. 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 sequencing.  Blood. 2013 Aug 15;122(7):1256-65. PMID: 23699601. 
  87. The Cancer Genome Atlas Research Network.  Comprehensive molecular characterization of clear cell renal cell carcinoma.  Nature.  2013 Jul 4;499(7456):43-9. PMID: 23792563. PMCID: PMC3771322. Citations: 40
  88. Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, Allen-Vercoe E, Holt RA.  Co-occurrence of anaerobic bacteria in colorectal carcinomas.   Microbiome. 2013 May 15;1(1):16. PMID: 24450771. 
  89. 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.
  90. The Cancer Genome Atlas Research Network.  The Genomic and Epigenomic Landscape of Adult de novo Acute Myeloid Leukemia.  New England Journal of Medicine  2013 May 30;368(22):2059-74. PMID: 23634996.
  91. 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. 
  92. Castellarin M, Milne K, Zeng T, Tse K, Mayo M, Zhao YJ, Webb JR, Watson PH, Nelson BH, Holt RA.  Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease.  Journal of Pathology. 2013 Mar;229(4):515-24. PMID: 22996961.
  93. 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. 
  94. 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. 
  95. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA.  Derivation of HLA types from shotgun sequence datasets.  Genome Medicine. 2012 Dec 10;4(12):95. PMID: 23228053. 
  96. The Cancer Genome Atlas Research Network.  Comprehensive molecular portraits of human breast tumours.  Nature. 2012 Oct 4;490(7418):61-70. PMID: 23000897.
  97. The Cancer Genome Atlas Research Network.  Comprehensive genomic characterization of squamous cell lung cancers.  Nature.  2012 Sep 27;489(7417):519-25. PMID: 22960745.
  98. 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.
  99. 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.
  100. 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. 
  101. 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. 
  102. 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 lymphoma.  Nature. 2011 Jul 27 ;476(7360):298-303. PMID: 21796119. 
  103. 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 tissues.  PLoS One. 2011;6(5):e19838. PMID: 21603639. 
  104. Warren RL, Holt RA.  Targeted assembly of short sequence reads.  PLoS One. 6(5):e19816.11 May 2011. PMID: 21589938.
  105. 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.
  106. 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. 
  107. 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 pathogen.  Genome.  108(6):2504-9. 2011 February 8. PMID: 21262841.
  108. 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. 
  109. 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. 
  110. 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.
  111. 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.
  112. 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. 
  113. 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. 
  114. 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. 
  115. 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.
  116. 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. 
  117. 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.
  118. 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
  119. 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
  120. 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. 
  121. 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. 
  122. 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.
  123. 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. 
  124. 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. 
  125. 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. 
  126. 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. 
  127. 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. 
  128. 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
  129. 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. 
  130. Warren RL, Nelson BH, Holt RA.  Profiling model T-cell metagenomes with short reads. Bioinformatics. 25(4):458-464. 2009 Feb 15. PMID: 19136549. 
  131. 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. 
  132. 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.
  133. 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.
  134. 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. 
  135. 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.
  136. Holt RA and Jones SJM.  The new paradigm of flow cell sequencing. Invited review article. Genome Research. 18(6):839-846. 2008. PMID: 18519653. 
  137. Cai F, Chen B, Zhou W, Zis O, Liu S, Holt RA, Honer GW, Song W.  SP1 regulates the human SNAP-25 gene expression.  Journal of Neurochemistry. 105(2);512-523. 2008. PMID: 18194215. Citations: 12
  138. Ralph S, Chun H, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan G, Douglas C, Holt R, Jones S, Marra M, Bohlmann J.  Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.  BMC Genomics. 2008 Jan 29; 9:57. PMID: 18230180. 
  139. von Schalburg KR, Leong J, Cooper GA, Robb A, Beetz-Sargent MR, Lieph R, Holt RA, Moore R, Ewart KV, Driedzic WR, Ten Hallers BF, Zhu B, de Jong PJ, Davidson WS, Koop BF.  Rainbow Smelt (Osmerus mordax) Genomic Library and EST Resources.  Marine Biotechnology. 10(5): 487-491. 2008. PMID: 18386095.
  140. Peng FY, Reid KE, Liao N, Schlosser J, Holt RA, Martínez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation and Analysis of Expressed Sequence Tags in Vitis vinifera Wine Grape (Cabernet Sauvignon) and Table Grape (Muscat Hamburg) Cultivars. Enhancing the Functional Genomics Platform for Grapevine. Gene. 2007 Nov 1; 402(1-2):40-50. PMID: 17761391. Citations: 25
  141. Etchberger JF, Lorch  A, Sleumer  M, Zapf  R, Jones  SJ, Marra  MA, Holt RA, Moerman  DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes and Development. 2007 Jul 1;21(13):1653-1674. PMID: 17606643. 
  142. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt RA, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biology. 2007;8(8):R165. PMID: 17697342.
  143. Holt RA, Warren R, Flibotte S, Missirlis PI and Smailus DE. Rebuilding microbial genomes. Bioessays. 2007 Jun;29(6): 580-590. PMID: 17508395. 
  144. Kelleher CT, Chiu R. Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Pradhu A-L, Smailus DE, Stott JM,  Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ and Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. The Plant Journal. 2007 Jun;50(6):1063-1078. PMID: 17488239. 
  145. Butland SL, Devon RS, Huang Y, Mead CL, Meynert AM, Neal SJ, Lee SS, Wilkinson A, Yang GS, Yuen MMS, Hayden MR, Holt RA, Leavitt BR and Ouellette BFF. CAG-encoded polyglutamine length polymorphism in the human genome. BMC Genomics.  2007 May 22;8:126. PMID: 17519034. 
  146. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007 Feb 15;23(4): 500-501. PMID: 17158514
  147. DiGustini S, Ralph S, Lim Y, Holt RA, Jones S, Bohlmann J and Breuil C.  Generation and annotation of lodgepole pine and oleoresin induced expressed sequences from the blue-stain fungus Ophiostoma cavigerum, a Mountain Pine Beetle associated pathogen.  FEMS Microbiology Letters.  2007 Feb;267(2); 151-158. PMID: 17328114. 
  148. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG and Robertson AG. The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. elegans Intestine. Developmental Biology. 2007 Feb 15;302(2): 627-645. PMID: 17113066. 
  149. Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O’Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu A-L, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt RA, Jones S, Gerhard DS, Thomson JA, Eaves CJ and Marra MA. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biology. 8(6):R113. 2007. PMID: 17570852.
  150. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Hirst M, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu A, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Jones S, Holt RA, Hoodless P and  Marra MA. Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells and cell lines. Genome Research. 2007 Jan;17(1):108-116. PMID: 17135571. 
  151. McLeod MP, Warren RL, Araki N, Hsiao WWL, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt RA, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD.  The complete genome of Rhodoccocus sp. RHA1: insights into a catabolic powerhouse.  Proceedings of the National Academy of Sciences.  103(42):15582-15587. 2006 Oct. 17. PMID: 17030794. 
  152. Tuskan G, DiFazio S, Bohlmann J, Griogoriev I, Hellsten U, Jansson S, Putnam N, Ralph S, Rombauts S, Salanov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho P, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Dupleissis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henirssat B, Holligan D, Holt RA, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A,, Kalluri U, Larimer F, Leebens-Mack J, Leplé J, Locascio P, Luo Y, Lucas S, Martin F, Montanini B, Napoli C, Pilate DR, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Siddiqui A, Sterky F, Terry A, Tsai C, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Sandberg G, Van de Peer Y, Rokhsar D.  The Genome of Black Cottonwood  Populus trichocarpa. Science. 313:1596-1604. 2006 Sep. 15. PMID: 16973872. 
  153. Scheinman JE, Holt RA, Auerbach MR, Stewart CB.  Duplication and Divergence of Two Distinct Pancreatic Ribonuclease Genes in Leaf-Eating African and Asian Colobine Monkeys.  Molecular Biology and Evolution. 23(8):1465-1479. 2006 Aug. PMID: 16751256. 
  154. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley III CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SK, Blakesley RW, Prange C, Myers RM, Green ED, Wagner K, Gerhard DS, Marra MA, Jones SJM and  Holt RA.  Sequencing and analysis of 10967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.  Genome Research. 16(6):796-803. 2006 Jun. PMID: 16672307.
  155. Missirlis PI, Smailus DE and Holt RA.  A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination.  BMC Genomics. 7:73. 2006 April 4. PMID: 16595017. 
  156. Wilson GM, Flibotte S, Chopra V, Melnyk BL, Honer WG and Holt RA.  DNA copy number analysis in bipolar disorder and schizophrenia reveals aberrations in genes involved in glutamate signing.  Human Molecular Genetics.  2006 Mar 1;15(5): 743-749. PMID: 16434481. 
  157. Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG and Holt RA.  Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.  Genome Research. 16(2):173-181. 2006 Feb. PMID: 16365383. 
  158. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA.  Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation. American Journal of Human Genetics.  79:500-513. 2006. PMID: 16909388. 
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