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Publications 2010

Peer-reviewed scientific publications by GSC staff and students.

2010

  1. Farinha P, Kyle AH, Minchinton AI, Connors JM, Karsan A, Gascoyne RD. Vascularization predicts overall survival and risk of transformation in follicular lymphoma. Haematologica. 2010 Dec;95(12):2157-2160.
  2. Bretherick KL, Bu R, Gascoyne RD, Connors JM, Spinelli JJ and Brooks-Wilson AR. Elevated circulating (14;18) translocation levels prior to diagnosis of Follicular Lymphoma. Blood. 2010 Dec 23;116(26):6146-6147.
  3. McLarren KW, Severson T, du Souich C, Stockton DW, Kratz LE, Cunningham D, Hendson G, Morin RD, Wu D, Paul JE, An J, Nelson TN, Chou A, DeBarber AE, Merkens LS, Michaud JL, Waters PJ, Yin J, McGillivray B, Demos M, Rouleau GA, Grzeschik K-H, Smith R, Tarpey PS, Kini U, Schwartz CE, Gecz J, Stratton MR, Arbour L, Hurlburt J, Van Allen MI, Herman GE, Zhao YJ, Moore R, Kelley RI, Jones SJ, Steiner RD, Raymond L, Marra MA, Boerkoel CF. Hypomorphic temperature-sensitive alleles of NSDHL cause CK syndrome. Am J Hum Genet. 2010 Dec 10;87(6):905-914.
  4. Hirst M, Marra MA. Next Generation Sequencing Based Approaches to Epigenomics. Brief Funct Genomics. 2010 Dec;9(5-6):455-465.
  5. The modENCODE Consortium. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-1797.
  6. Yamada S, Richardson K, Tang M, Moadebi S, Halaschek-Wiener J, Fitzgerald JM, Elwood K, Marra F and Brooks-Wilson A. Genetic Variation in Carboxylesterase Genes and Susceptibility to Isoniazid-induced Hepatotoxicity. Pharmacogenomics J. 2010 Dec;10(6):524-536.
  7. Cheung KJ, Johnson NA, Affleck JG, Severson T, Steidl C, Ben-Neriah S, Schein J, Morin RD, Moore R, Shah SP, Qian H, Paul JE, Telenius A, Relander T, Lam W, Savage K, Connors JM, Brown C, Marra MA, Gascoyne RD, Horsman DE. Acquired TNFRSF14 Mutations in Follicular Lymphoma Are Associated with Worse Prognosis. Cancer Res. 2010 Nov 15;70(22):9166-9174.
  8. Cerchietti LC, Hatzi K, Caldas-Lopes E, Yang SN, Figueroa ME, Morin RD, Hirst M, Mendez L, Shaknovich R, Cole P, Bhalla K, Gascoyne RD, Marra M, Chiosis G, Melnick A. BCL6 repression of EP300 provides a basis for rational combinatorial therapy in diffuse large B cell lymphomas. J Clin Invest. 2010 Nov 1. pii: 42869. doi: 10.1172/JCI42869.
  9. Horspool DR, Coope RJ and Holt RA. Efficient assembly of very short oligonucleotides using T4 DNA Ligase. BMC Res Notes. 2010 Nov 9;3:291.
  10. Robertson G, Schein J, Chiu R, Field M, Jackman SD, Mungall K, Lee S, Okada SM, Corbett R, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield Y, Newsome R, Chan SK, Varhol R, Kamoh B, Prabhu A-L, Tam A, Zhao YJ, Moore R, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De Novo Assembly and Analysis of RNA Sequence Data. Nat Methods. 2010 Nov;7(11):909-912.
  11. Jinno H, Morozova O, Jones KL, Biernaskie JA, Paris M, Hosokawa R, Rudnicki M, Chai Y, Rossi F, Marra MA, Miller FD. Convergent genesis of an adult neural crest-like dermal stem cell from distinct developmental origins. Stem Cells. 2010 Nov;28(11):2027-2040.
  12. Lin D, Bayani J, Wang Y, Sadar MD, Yoshimoto M, Gout GW, Squire JA, Wang YZ. Development of metastatic and non-metastatic tumor lines from a patient’s prostate cancer specimen-Identification of a small subpopulation with metastatic potential in the primary tumor. Prostate. 2010 Nov 1;70(15):1636-1644.
  13. Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ. ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner.Cell. 2010 Oct 29;143(3):367-378.
  14. Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings LA, Morsberger LA, Latimer C, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal SA, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Griffin CA, Burton J, Swerdlow H, Quail MA, Stratton MR, Iacobuzio-Donahue C, Futreal PA. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature. 2010 Oct 28;467(7319):1109-1113.
  15. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct:28(10): 1045-1048.
  16. Harris RA, Wang T, Coarfa C, Zhou X, Xi Y, Nagarajan RP, Hong C, Downey S, Johnson BE, Delaney A, Zhao YJ, Olshen A, Ballinger T, Schillebeeckx M, Echipare L, O’Geen H, Lister R, Pelizzola M, Chung W-Y, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker J, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Sequence-based profiling of DNA methylation: comparisons of methods and catalogue of allelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1097-1105.
  17. 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. 2010 Oct 4:11(1):536.
  18. Bolton KL, Tyrer J, Song H, Ramus SJ, Notaridou M, Jones C, Sher T, Gentry-Maharaj A, Wozniak E, Tsai YY, Weidhaas J, Paik D, Van Den Berg DJ, Stram DO, Pearce CL, Wu AH, Brewster W, Anton-Culver H, Ziogas A, Narod SA, Levine DA, Kaye SB, Brown R, Paul J, Flanagan J, Sieh W, McGuire V, Whittemore AS, Campbell I, Gore ME, Lissowska J, Yang HP, Medrek K, Gronwald J, Lubinski J, Jakubowska A, Le ND, Cook LS, Kelemen LE, Brook-Wilson A, Massuger LF, Kiemeney LA, Aben KK, van Altena AM, Houlston R, Tomlinson I, Palmieri RT, Moorman PG, Schildkraut J, Iversen ES, Phelan C, Vierkant RA, Cunningham JM, Goode EL, Fridley BL, Kruger-Kjaer S, Blaeker J, Hogdall E, Hogdall C, Gross J, Karlan BY, Ness RB, Edwards RP, Odunsi K, Moyisch KB, Baker JA, Modugno F, Heikkinenen T, Butzow R, Nevanlinna H, Leminen A, Bogdanova N, Antonenkova N, Doerk T, Hillemanns P, Dürst M, Runnebaum I, Thompson PJ, Carney ME, Goodman MT, Lurie G, Wang-Gohrke S, Hein R, Chang-Claude J, Rossing MA, Cushing-Haugen KL, Doherty J, Chen C, Rafnar T, Besenbacher S, Sulem P, Stefansson K, Birrer MJ, Terry KL, Hernandez D, Cramer DW, Vergote I, Amant F, Lambrechts D, Despierre E, Fasching PA, Beckmann MW, Thiel FC, Ekici AB, Chen X; Australian Ovarian Cancer Study Group; Australian Cancer Study (Ovarian Cancer); Ovarian Cancer Association Consortium, Johnatty SE, Webb PM, Beesley J, Chanock S, Garcia-Closas M, Sellers T, Easton DF, Berchuck A, Chenevix-Trench G, Pharoah PD, Gayther SA. Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat Genet. 2010 Oct;42(10):880-884.
  19. Goode EL, Chenevix-Trench G, Song H, Ramus SJ, Notaridou M, Lawrenson K, Widschwendter M, Vierkant RA, Larson MC, Kjaer SK, Birrer MJ, Berchuck A, Schildkraut J, Tomlinson I, Kiemeney LA, Cook LS, Gronwald J, Garcia-Closas M, Gore ME, Campbell I, Whittemore AS, Sutphen R, Phelan C, Anton-Culver H, Pearce CL, Lambrechts D, Rossing MA, Chang-Claude J, Moysich KB, Goodman MT, Dörk T, Nevanlinna H, Ness RB, Rafnar T, Hogdall C, Hogdall E, Fridley BL, Cunningham JM, Sieh W, McGuire V, Godwin AK, Cramer DW, Hernandez D, Levine D, Lu K, Iversen ES, Palmieri RT, Houlston R, van Altena AM, Aben KK, Massuger LF, Brooks-Wilson A, Kelemen LE, Le ND, Jakubowska A, Lubinski J, Medrek K, Stafford A, Easton DF, Tyrer J, Bolton KL, Harrington P, Eccles D, Chen A, Molina AN, Davila BN, Arango H, Tsai YY, Chen Z, Risch HA, McLaughlin J, Narod SA, Ziogas A, Brewster W, Gentry-Maharaj A, Menon U, Wu AH, Stram DO, Pike MC; Wellcome Trust Case-Control Consortium, Beesley J, Webb PM; Australian Cancer Study (Ovarian Cancer); Australian Ovarian Cancer Study Group; Ovarian Cancer Association Consortium (OCAC), Chen X, Ekici AB, Thiel FC, Beckmann MW, Yang H, Wentzensen N, Lissowska J, Fasching PA, Despierre E, Amant F, Vergote I, Doherty J, Hein R, Wang-Gohrke S, Lurie G, Carney ME, Thompson PJ, Runnebaum I, Hillemanns P, Dürst M, Antonenkova N, Bogdanova N, Leminen A, Butzow R, Heikkinen T, Stefansson K, Sulem P, Besenbacher S, Sellers TA, Gayther SA, Pharoah PD; Ovarian Cancer Association Consortium (OCAC). A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat Genet. 2010 Oct;42(10):874-879.
  20. Griffith M, Griffith OL, Mwenifumbo J, Morin RD, Goya R, Tang MJ, Hou Y-C, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao YJ, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nat Methods. 2010 Oct;7(10):843-847.
  21. Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2010 Sep 30:11(9):403.
  22. Romanuik TL, Marra MA, Sadar MD. LNCaP Atlas: gene expression associated with in vivo progression to castration-recurrent prostate cancer. BMC Medical Genomics, 2010 Sep 24;3:43.
  23. 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. Proc Natl Acad Sci U S A. 2010 Sept 21:107(38): 16589-16594.
  24. Morozova O, Vojvodic M, Grinshtein N, Hansford L, Blakely K, Maslova A, Hirst M, Cezard T, Morin R, Moore R, Smith K, Miller F, Taylor P, Thiessen N, Varhol R, Zhao YJ, Jones S, Moffat J, Kislinger T, Moran M, Kaplan D, Marra M. Systems-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma. Clin Cancer Res. 2010 Sep 15;16(18):4572-4582.
  25. Law JH, Li Y, Wang M, Astanehe A, Lambie K, Dhillon J, Jones SJ, Gleave ME, Eaves CJ, DunnSE. Molecular decoy to the Y-box binding protein-1 suppresses the growth of breast and prostate cancer cells whilst sparing normal cell viability. PLoS One. 2010 Sept 10:5(9). Pii: e12661
  26. Smith KM, Datti A, Fujitani M, Grinshtein N, Zhang L, Morozova O, Blakely KM, Rotenberg SA, Hansford LM, Miller FD, Yeger H, Irwin MS, Moffat J, Marra MA, Baruchel S, Wrana JL, Kaplan DR. Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens. EMBO Mol Med. 2010 Sep;2(9):371-384.
  27. 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. J Mol Neurosci. 2010 Sep:42(1):127-133.
  28. Montgomery SB, Kasaian K, Jones SJ, Griffith OL. Annotating the regulatory genome. Methods Mol Biol. 2010;674:313-349.
  29. Morin RD, Zhao Y, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra M. Preparation and Analysis of MicroRNA Libraries Using the Illumina Massively Parallel Sequencing Technology. Methods Mol Biol. 2010;650:173-199.
  30. Petriv OI, Kuchenbauer F, Delaney AD, Lecault V, White A, Kent D, Marmolejo L, Heuser M, Berg T, Copley M, Ruschmann J, Sekulovic S, Antignano F, Kuroda E, Ho V, Benz C, Halim T, Giambra V, Krystal G, Takei CJF, Weng AP, Eaves C, Piret J, Marra MA, Humphries RK, Hansen CL. Comprehensive microRNA Expression Profiling of the Hematopoietic Hierarchy. Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15443-15448.
  31. Liang B, Luo M, Ball TB, Jones SJ, Plummer FA. QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approach. Biochem Cell Biol. 2010 Aug:88(4):671-681.
  32. Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao YJ, Hirst M, Verchere B, Helgason CD, Marra MA, Jones SJM, Hoodless PA. Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res. 2010 Aug;20(8):1037-1051.
  33. 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 Biol. 2010 Aug 9:11(8):R82.
  34. Cheung KJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE. High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer. 2010 Aug;49(8):669-681.
  35. Mandakova T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA. Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell. 2010 Jul;22(7)2277-2290.
  36. Conde L, Halperin E, Akers NK, Brown KM, Smedby KE, Rothman N, Nieters A, Slager SL, Brooks-Wilson A, Agana L, Riby J, Liu J, Adami HO, Darabi H, Hjalgrim H, Low HQ, Humphreys K, Melbye M, Chang ET, Glimelius B, Cozen W, Davis S, Hartge P, Morton LM, Schenk M, Wang SS, Armstrong B, Kricker A, Milliken S, Purdue MP, Vajdic CM, Boyle P, Lan Q, Zahm SH, Zhang Y, Zheng T, Becker N, Benavente Y, Boffetta P, Brennan P, Butterbach K, Cocco P, Foretova L, Maynadié M, de Sanjosé S, Staines A, Spinelli JJ, Achenbach SJ, Call TG, Camp NJ, Glenn M, Caporaso NE, Cerhan JR, Cunningham JM, Goldin LR, Hanson CA, Kay NE, Lanasa MC, Leis JF, Marti GE, Rabe KG, Rassenti LZ, Spector LG, Strom SS, Vachon CM, Weinberg JB, Holly EA, Chanock S, Smith MT, Bracci PM, Skibola CF. Genome-wide association study of follicular lymphoma identifies a risk locus at 6p21.32. Nat Genet. 2010 Aug;42(8):661-664.
  37. Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods. 2010 Aug;7(8):576-567.
  38. Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod. 2010 Jul;16(7):463-471.
  39. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse1 SD, Johnson BE, Hong C, Nielsen C, Zhao YJ, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters. Nature. 2010 Jul 8;466(7303):253-257.
  40. Wong RTF, Flibotte S, Corbett R, Saeedi P, Jones SJM, Marra MA, Schein JE, Birol I. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Transactions on Automation Science and Engineering. 2010 Jul; 7(3): 706-708.
  41. Vercauteren SM, Sung S, Starczynowski DT, Lam WL, Bruyere H, Horsman DE, Tsang P, Leitch H, Karsan A. Array comparative genomic hybridization of peripheral blood granulocytes of patients with myelodysplastic syndrome detects karyotypic abnormalities. Am J Clin Pathol. 2010 Jul;134(1):119-126.
  42. Chiu HHL, Yong TMK, Wang J, Wang Y, Vessella RL, Ueda T, Wang YZ, Sadar MD. Induction of Neuronal Apoptosis Inhibitory Protein Expression in Response to Androgen Deprivation in Prostate Cancer. Cancer Letters, 2010 Jun 28;292(2):176-185.
  43. Andersen RJ, Mawji NR, Wang J, Wang G, Haile S, Myung JK, Watt K, Tam T, Yang YC, Banuelos AC, Williams DE, McEwan IJ, Wang YZ, Sadar MD. Regression of castrate-recurrent prostate cancer by a small molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell. 2010 Jun 15;17(6)535-546.
  44. Flibotte S ,Edgley ML, Chaudhry I,Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfield Y, Jones SJ, Marra MA, Barstead RJ, Moerman DG. Whole-Genome profiling of mutagenesis in Caenorhabditis elegans. Genetics. 2010 Jun;185(2):431-441.
  45. Mead CL, Kuzyk MA, Moradian A, Wilson GM, Holt RA, Morin GB. Cytosolic Protein Interactions of the Schizophrenia Susceptibility Gene Dysbindin. J. Neurochemistry. 2010 Jun;113(6):1491-1503.
  46. Altanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 2010 Jun;20(6):791-803.
  47. Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics. 2010 May 15;26(10):1277-1283.
  48. Chan JH, Ho S, Tai IT. Secreted protein acidic and rich in cysteine-induced cellular senescence in colorectal cancers in response to irinotecan is mediated by p53. Carcinogenesis. 2010 May;31(5):812-819.
  49. Patenaude A, Parker J, Karsan A. Involvement of endothelial progenitor cells in tumor vascularization. Microvasc Res. 2010 May;79(3):217-223.
  50. Balasundaram M. Tsai M, Clarke A, Leung D, Munro S, Wagner S, Mayo 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. May 2010. 15:2.
  51. Chiu CG, Strugnell SS, Griffith OL, Jones SJ, Gown AM, Walker B, Nabi IR, Wiseman SM. Diagnostic utility of galectin-3 in thyroid cancer. Am J Pathol. 2010 May;176(5):2067-2081.
  52. Sleumer MC, Mah AK, Baillie DL, Jones SJ. Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res. 2010 May;38(9):2990-3004.
  53. Swanson TW, Chan SK, Jones SJ, Bugis S, Irvine R, Belzberg A, Levine D, Wiseman SM. Determinants of Tc-99m sestamibi SPECT scan sensitivity in primary hyperparathyroidism. Am J Surg. 2010 May;199(5):614-620.
  54. 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 sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics. 2010 Apr 30;11(1):279.
  55. International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010 Apr 15;464(7291): 993-998.
  56. Malhis N, Jones SJ. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics. 2010 Apr 15;26(8):1029-1035.
  57. Starczynowski DT, Karsan A. Innate immune signaling in the myelodysplastic syndromes. Hematol Oncol Clin North Am. 2010 Apr;24(2):343-359.
  58. Crispo JA, Piché M, Ansell DR, Eibl JK, Tai IT, Kumar A, Ross GM, Tai TC. Protective effects of methyl gallate on H(2)O(2)-induced apoptosis in PC12 cells. Biochem Biophys Res Commun. 2010 Mar 19:393(4):773-778.
  59. Warren RL and Holt RA. A census of predicted mutational epitopes suitable for immunologic cancer control. Hum Immunol. 2010 Mar 17;71(3):245-254.
  60. Goya R, Sun MGF, Morin RD, Leung G, Ha G, Wiegand K, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting single nucleotide variants from next generation sequencing of tumors. Bioinformatics. 2010 Mar 15;26(6):730-7362.
  61. Khan MA, Steiner Ts, Sham HP, Bergstrom KS, Huang JT, Assi K, Salh B, Tai IT, Li X, Vallance BA. The single IgG IL-1-related receptor controls TLR responses in differentiated human intestinal epithelial cells. J Immunol. 2010 Mar 1;184(5):2305-2313.
  62. Starczynowski DT, Karsan A. Deregulation of innate immune signaling in myelodysplastic syndromes is associated with deletion of chromosome arm 5q. Cell Cycle. 2010 Mar 1;9(5):855-856.
  63. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods. 2010 Mar;7(3 Suppl):S5-S15.
  64. O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B. Visualizing biological data-now and in the future. Nat Methods. 2010 Mar;7(3 Suppl):S2-4.
  65. Skibola CF, Bracci PM, Nieters A, Brooks-Wilson A, de Sanjose S, Hughes AM, Cerhan JR, Skibola DR, Purdue M, Willett E, Lan Q, Foretova L, Schenk M, Spinelli JJ, Slager SL, DeRoos A, Smith MT, Roman E, Cozen W, Boffetta P, Kricker A, Zheng T, Lightfoot T, Cocco P, Benavente Y, Zhang Y, Hartge T, Linet M, Becker N, Brennan P, Zhang L, Armstrong B, Smith A, Shiao R, Novak AJ, Maynadie M, Chanock S, Staines A, Holford TR, Holly EA, Rothman R, and S Wang. Tumor necrosis factor (TNF) and lymphotoxin-alpha (LTA) polymorphisms and risk of non-Hodgkin lymphoma in the InterLymph Consortium. Am J Epidemiol. 2010 Feb 1;171(3):267-276.
  66. Rose AM, O’Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Feb 23;11(1):131.
  67. 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. Nat Genet. 2010 Feb;42(2):181-185.
  68. Vrljicak P, Chang A, Morozova O, Wederell E, Niessen K, Marra M, Karsan A, Hoodless P. Genomic Analysis Distinguishes Phases of Early Development of the Mouse Atrio-Ventricular Canal. Physiol Genomics. 2010 Feb 4;40(3):150-157.
  69. Jackman SD, Birol I. Assembling genomes using short-read sequencing technology. Genome Biol. 2010 Jan 28;11(1):202.
  70. Murphy D, Parker J, Zhou M, Fadlelmola FM, Steidl C, Karsan A, Gascoyne RD, Chen H, Banerjee D. Constitutively overexpressed 21 kDa protein in Hodgkin lymphoma and aggressive non-Hodgkin lymphomas identified as cytochrome B5b (CYB5B). Mol Cancer. 2010 Jan 26;9:14.
  71. Starczynowski DT, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, Hirst M, Hogge D, Marra M, Wells RA, Buckstein R, Lam W, Humphries RK, Karsan A. Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype. Nat Med. 2010 Jan;16(1):49-58.
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