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Publications

Michael Smith Genome Sciences Centre Publications in peer-reviewed journals for 2011 and 2012 (to date). GSC staff and students are in bold text.

2012

  1. Sohrab P. Shah, Andrew Roth, Rodrigo Goya, Arusha Oloumi, Gavin Ha, Yongjun Zhao, Gulisa Turashvili, Jiarui Ding, Kane Tse, Gholamreza Haffari, Ali Bashashati, Leah M. Prentice, Jaswinder Khattra, Angela Burleigh, Damian Yap, Virginie Bernard, Andrew McPherson, Karey Shumansky, Anamaria Crisan, Ryan Giuliany, Alireza Heravi-Moussavi, Jamie Rosner, Daniel Lai, Inanc Birol, Richard Varhol, Angela Tam, Noreen Dhalla, Thomas Zeng, Kevin Ma, Simon K. Chan, Malachi Griffith, Annie Moradian, S.-W. Grace Cheng, Gregg B. Morin, Peter Watson, Karen Gelmon, Stephen Chia, Suet-Feung Chin, Christina Curtis, Oscar M. Rueda, Paul D. Pharoah, Sambasivarao Damaraju, John Mackey, Kelly Hoon, Timothy Harkins, Vasisht Tadigotla, Mahvash Sigaroudinia, Philippe Gascard, Thea Tlsty, Joseph F. Costello, Irmtraud M. Meyer, Connie J. Eaves, Wyeth W. Wasserman, Steven Jones, David Huntsman, Martin Hirst, Carlos Caldas, Marco A. Marra & Samuel Aparicio The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012 (doi:10.1038/nature10933) Published online 04 April 2012.
  2. Astanehe A, Finkbeiner MR, Krzywinski M, Fotovati A, Dhillon J, Berquin IM, Mills GB, Marra MA, Dunn SE. MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition. Oncogene. 2012 Jan 16.
  3. Baradaran-Heravi A, Cho KS, Tolhuis B, Sanyal M, Morozova O, Morimoto M, Elizondo LI, Bridgewater D, Lubieniecka J, Beirnes K, Myung C, Leung D, Fam HK, Choi K, Huang Y, Dionis KY, Zonana J, Keller K, Stenzel P, Mayfield C, Lücke T, Bokenkamp A, Marra MA, van Lohuizen M, Lewis DB, Shaw C, Boerkoel CF. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. Hum Mol Genet. 2012 Mar 13.
  4. Chu JS-C, Johnsen RC, Chua S-Y, Tu D, Dennison M, Marra M, Jones SJM, Baillie DL, Rose AM. Allelic Ratios and the Mutational Landscape Reveal Biologically Significant Heterozygous SNVs. Genetics. 2012 Apr;190(4):1225-33. Epub 2012 Jan 20.
  5. Collins CC, Volik SV, Lapuk A, Wang Y, Gout PW, Wu C, Xue H, Cheng H, Haegert A, Bell RH, Brahmbhatt S, Anderson S, Fazli L, Hurtado-Coll A, Rubin MA, Demichelis F, Beltran H, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Gleave ME, Bertino JR, Lubin M, Wang Y. Next Generation Sequencing of Prostate Cancer from a Patient Identifies a Deficiency of Methylthioadenine Phosphorylase (MTAP), an Exploitable Tumor Target. Molecular cancer therapeutics. 2012 Mar;11(3):775-83. Epub 2012 Jan 17.
  6. Dubuc AM, Morrissy AS, Kloosterhof NK, Northcott PA, Yu EPY, Shih D, Peacock J, Grajkowska W, van Meter T, Eberhart CG, Pfister S, Marra MA, Weiss WA, Scherer SW, Rutka JT, French PJ, Taylor MD. Subgroup-specific alternative splicing in medulloblastoma. Acta Neuropathol. 2012 Apr 1;123(4):485-99.
  7. Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ, Eydoux P, Babul-Hirji R, An J, Marra MA, Consortium FC, Chitayat D, Boycott KM, Weaver DD, Jones SJM. Mutations in EZH2 Cause Weaver Syndrome. Am J Hum Genet. 2012 Jan 13;90(1):110-8.
  8. Greenman CD, Pleasance ED, Newman S, Yang F, Fu B, Nik-Zainal S, Jones D, Lau KW, Carter N, Edwards PAW, Futreal PA, Stratton MR, Campbell PJ. Estimation of rearrangement phylogeny for cancer genomes. Genome Res. 2012 Feb 1;22(2):346-61.
  9. Griffith M, Mwenifumbo JC, Cheung PY, Paul JE, Pugh TJ, Tang MJ, Chittaranjan S, Morin RD, Asano JK, Ally AA, Miao L, Lee A, Chan SY, Taylor G, Severson T, Hou Y-C, Griffith OL, Cheng GSW, Novik K, Moore R, Luk M, Owen D, Brown CJ, Morin GB, Gill S, Tai IT, Marra MA. Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer. The Pharmacogenomics journal. 2012 Jan 17.
  10. Heravi-Moussavi A, Anglesio MS, Cheng S-WG, Senz J, Yang W, Prentice L, Fejes AP, Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan ANC, Maines-Bandiera S, Salamanca C, Pasini B, Clarke BA, Lee AF, Lee C-H, Zhao C, Young RH, Aparicio SA, Sorensen PHB, Woo MMM, Boyd N, Jones SJM, Hirst M, Marra MA, Gilks B, Shah SP, Foulkes WD, Morin GB, Huntsman DG. Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med. 2012 Jan 19;366(3):234-42.
  11. Kridel R, Meissner B, Rogic S, Boyle M, Telenius A, Woolcock B, Gunawardana J, Jenkins C, Cochrane C, Ben-Neriah S, Tan K, Morin RD, Opat S, Sehn LH, Connors JM, Marra MA, Weng AP, Steidl C, Gascoyne RD. Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma. Blood. 2012 Jan 18.
  12. Lebovitz CB, Bortnik SB, Gorski SM. Here, There Be Dragons: Charting Autophagy-Related Alterations in Human Tumors. Clinical Cancer Research. 2012 Mar 1;18(5):1214-26.
  13. Lee C-H, Ou W-B, Mariño-Enriquez A, Zhu M, Mayeda M, Wang Y, Guo X, Brunner AL, Amant F, French CA, West RB, McAlpine JN, Gilks CB, Yaffe MB, Prentice LM, McPherson A, Jones SJM, Marra MA, Shah SP, van de Rijn M, Huntsman DG, Dal Cin P, Debiec-Rychter M, Nucci MR, Fletcher JA. 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc Natl Acad Sci USA. 2012 Jan 5.
  14. Najafzadeh M, Lynd LD, Davis JC, Bryan S, Anis A, Marra M, Marra CA. Barriers to integrating personalized medicine into clinical practice: a best-worst scaling choice experiment. Genetics in medicine : official journal of the American College of Medical Genetics. 2012 Jan 19.
  15. Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics (Oxford, England). 2012 Apr 1;28(7):907-13.
  16. Schmouth J-F, 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. Mol Cell Biol. 2012 Apr 1;32(7):1296-311.
  17. Schuetz JM, Daley D, Graham J, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Spinelli JJ, Brooks-Wilson AR. Genetic variation in cell death genes and risk of non-Hodgkin lymphoma. PLoS ONE. 2012 Jan 1;7(2):e31560.
  18. Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012 May 1;227(1):53-61.
  19. Blough MD, Al-Najjar M, Chesnelong C, Binding CE, Rogers AD, Luchman HA, Kelly JJ, Fliegel L, Morozova O, Yip S, Marra M, Weiss S, Chan JA, Cairncross JG. DNA hypermethylation and 1p Loss silence NHE-1 in oligodendroglioma. Ann Neurol. 2012 July 0;71(6):845-9.
  20. 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 March 0;22(2):299-306.
  21. Chang L, Noseda M, Higginson M, Ly M, Patenaude A, Fuller M, Kyle AH, Minchinton AI, Puri MC, Dumont DJ, Karsan A. Differentiation of vascular smooth muscle cells from local precursors during embryonic and adult arteriogenesis requires Notch signaling. Proc Natl Acad Sci U S A. 2012 June 1;109(18):6993-8.
  22. Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics (Oxford, England). 2012 August 15;28(14):1923-4.
  23. Chiu CG, Chan SK, Fang ZA, Masoudi H, Wood-Baker R, Jones SJ, Gilks B, Laskin J, Wiseman SM. Beta-catenin expression is prognostic of improved non-small cell lung cancer survival. American journal of surgery. 2012 June 0;203(5):654-9.
  24. Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics (Oxford, England). 2012 February 15;28(2):167-75.
  25. Doherty D, Chudley AE, Coghlan G, Ishak GE, Innes AM, Lemire EG, Rogers RC, Mhanni AA, Phelps IG, Jones SJ, Zhan SH, Fejes AP, Shahin H, Kanaan M, Akay H, Tekin M, FORGE Canada Consortium, Triggs-Raine B, Zelinski T. GPSM2 Mutations Cause the Brain Malformations and Hearing Loss in Chudley-McCullough Syndrome. American journal of human genetics. 2012 July 8;90(6):1088-93.
  26. Dubuc AM, Morrissy AS, Kloosterhof NK, Northcott PA, Yu EP, Shih D, Peacock J, Grajkowska W, Meter T, Eberhart CG, Pfister S, Marra MA, Weiss WA, Scherer SW, Rutka JT, French PJ, Taylor MD. Subgroup-specific alternative splicing in medulloblastoma. Acta Neuropathol. 2012 May 0;123(4):485-99.
  27. Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K, Chin S, Turashvili G, Hirst M, Caldas C, Marra MA, Aparicio S, Shah SP. Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Res. 2012 June 25.
  28. Huang Y, Sitwala K, Bronstein J, Sanders D, Dandekar M, Collins C, Robertson G, MacDonald J, Cezard T, Bilenky M, Thiessen N, Zhao Y, Zeng T, Hirst M, Hero A, Jones S, Hess JL. Identification and characterization of Hoxa9 binding sites in hematopoietic cells. Blood. 2012 February 12;119(2):1-12.
  29. Keeling CI, Henderson H, Li M, Yuen M, Clark EL, Fraser JD, Huber DP, Liao NY, Roderick Docking T, Birol I, Chan SK, Taylor GA, Palmquist D, Jones SJ, Bohlmann J. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect biochemistry and molecular biology. 2012 May 7.
  30. Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajiresouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol. 2012 June 3.
  31. Lee J, Sandford AJ, Connett JE, Yan J, Mui T, Li Y, Daley D, Anthonisen NR, Brooks-Wilson A, Man SF, Sin DD. The Relationship between Telomere Length and Mortality in Chronic Obstructive Pulmonary Disease (COPD). PloS one. 2012 January 0;7(4):e35567.
  32. Liu X, Chen M, Lobo P, An J, Grace Cheng SW, Moradian A, Morin GB, Petegem F, Jiang X. Molecular and structural characterization of the SH3 domain of AHI-1 in regulation of cellular resistance of BCR-ABL(+) chronic myeloid leukemia cells To tyrosine kinase inhibitors. Proteomics. 2012 June 24.
  33. Lu Y, Chen X, Beesley J, Johnatty SE, Defazio A, Lambrechts S, Lambrechts D, Despierre E, Vergotes I, Chang-Claude J, Hein R, Nickels S, Wang-Gohrke S, Dörk T, Dürst M, Antonenkova N, Bogdanova N, Goodman MT, Lurie G, Wilkens LR, Carney ME, Butzow R, Nevanlinna H, Heikkinen T, Leminen A, Kiemeney LA, Massuger LF, Altena AM, Aben KK, Kjaer SK, Høgdall E, Jensen A, Brooks-Wilson A, Nhu, Cook L, Earp M, Kelemen L, Easton D, Pharoah P, Song H, Tyrer J, Ramus S, Menon U, Gentry-Maharaj A, Gayther SA, Bandera EV, Olson SH, Orlow I, Rodriguez-Rodriguez L, Macgregor S, Chenevix-Trench G. Genome-Wide Association Study for Ovarian Cancer Susceptibility Using Pooled DNA. Twin research and human genetics : the official journal of the International Society for Twin Studies. 2012 August 13:1-9.
  34. McConechy MK, Ding J, Cheang MC, Wiegand KC, Senz J, Tone AA, Yang W, Prentice LM, Tse K, Zeng T, McDonald H, Schmidt AP, Mutch DG, McAlpine JN, Hirst M, Shah SP, Lee C, Goodfellow PJ, Gilks CB, Huntsman DG. Use of mutation profiles to refine the classification of endometrial carcinomas. The Journal of pathology. 2012 October 1;228(1):1-11.
  35. Meimetis LG, Williams DE, Mawji NR, Banuelos CA, Lal AA, Park JJ, Tien AH, Fernandez JG, Voogd NJ, Sadar MD, Andersen RJ. Niphatenones, glycerol ethers from the sponge Niphates digitalis block androgen receptor transcriptional activity in prostate cancer cells: structure elucidation, synthesis, and biological activity. Journal of medicinal chemistry. 2012 February 12;55(1):503-14.
  36. Mo F, Wyatt AW, Wu C, Lapuk AV, Marra MA, Gleave ME, Volik SV, Collins CC. Next-generation sequencing of prostate tumors provides independent evidence of xenotropic murine leukemia virus-related gammaretrovirus contamination. J Clin Microbiol. 2012 March 0;50(2):536-7.
  37. Myung J, Sadar MD. Large scale phosphoproteome analysis of LNCaP human prostate cancer cells. Molecular bioSystems. 2012 July 14.
  38. 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 B, Kim S, Wang K, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, 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, Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, 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 Y, 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 September 2;488(7409):1-8.
  39. Northcott PA, Shih DJ, Remke M, Cho Y, Kool M, Hawkins C, Eberhart CG, Dubuc A, Guettouche T, Cardentey Y, Bouffet E, Pomeroy SL, Marra M, Malkin D, Rutka JT, Korshunov A, Pfister S, Taylor MD. Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples. Acta Neuropathol. 2012 May 0;123(4):615-26.
  40. Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen S, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson MN, Hu Y, Buetow KE, Chen I, Carroll WL, Wei L, Ma J, Kleppe M, Levine RL, Garcia-Manero G, Larsen E, Shah NP, Devidas M, Reaman G, Smith M, Paugh SW, Evans WE, Grupp SA, Jeha S, Pui C, Gerhard DS, Downing JR, Willman CL, Loh M, Hunger SP, Marra MA, Mullighan CG. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer cell. 2012 September 14;22(2):1-14.
  41. Sadar MD. Advances in small molecule inhibitors of androgen receptor for the treatment of advanced prostate cancer. World journal of urology. 2012 July 0;30(3):311-8.
  42. Scott DW, Mungall KL, Ben-Neriah S, Rogic S, Morin RD, Slack GW, Tan KL, Chan FC, Lim RS, Connors JM, Marra MA, Mungall AJ, Steidl C, Gascoyne RD. TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma. Blood. 2012 May 11.
  43. Shankar J, Wiseman SM, Meng F, Kasaian K, Strugnell S, Mofid A, Gown A, Jones SJ, Nabi IR. Coordinate Expression of Galectin-3 and Caveolin-1 in Thyroid Cancer. The Journal of pathology. 2012 May 18.
  44. Tognon CE, Martin MJ, Moradian A, Trigo G, Rotblat B, Cheng SG, Pollard M, Uy E, Chow C, Carboni JM, Gottardis MM, Pollak M, Morin GB, Sorensen PH. A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation. Oncogene. 2012 April 8;31(10):1334-40.
  45. Vrljicak P, Cullum R, Xu E, Chang AC, Wederell ED, Bilenky M, Jones SJ, Marra MA, Karsan A, Hoodless PA. Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse. PloS one. 2012 February 1;7(7):1-14.
  46. Yakovenko OY, Li YY, Oliferenko AA, Vashchenko GM, Bdzhola VG, Jones SJ. Ab initio parameterization of YFF1, a universal force field for drug-design applications. Journal of molecular modeling. 2012 March 10;18(2):663-73.
  47. Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, Perizzolo M, Qian J, Roldan G, Smith EE, Tamura-Wells J, Thiessen N, Varhol R, Weiss S, Wu W, Young S, Zhao Y, Mungall AJ, Jones SJ, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. The Journal of pathology. 2012 February 1;226(1):7-16.
  48. Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC. Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinformatics (Oxford, England). 2012 July 15;28(12):179-87.
  49. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 August 19;487(7407):1-8.

2011

  1. Yip S, Butterfield Y, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, Perizzolo M, Qian J, Roldan G, Smith EE, Tamura-Wells J, Thiessen N, Varhol R, Weiss S, Wu W, Young S, Zhao Y, Mungall AJ, Jones SJ, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC Mutations, IDH Mutations and 1P/19Q Loss Distinguish Oligodendrogliomas from Other Cancers J Pathol. 2011 Sep 7. [Epub ahead of print]
  2. 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 Res. 2011 Oct 18. [Epub ahead of print] *Authors contributed equally to this work. Castellarin M*, Warren RL*
  3. Brooks-Wilson A and Marra F. Response to Leiro-Fernandez et al. Pharmacogenomics. Brooks-Wilson A et al. In press.
  4. Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC, Mager DL.  Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genetics. 2011 Sep;7(9):e1002301. Epub 2011 Sep 29.
  5. Rahman M, Chan APK, Tai IT. A peptide of SPARC interferes with the interaction between caspase8 and Bcl2 to resensitize chemoresistant tumors and enhance their regression in vivo. PLoS One. 2011;6(11):e26390. Epub 2011 Nov 1.
  6. Chiu CG, Yao R, Chan SK, Strugnell SS, Bugis S, Irvine R, Anderson D, Walker B, Jones SJ, and Wiseman SM. Hemithyroidectomy is the preferred initial operative approach for an indeterminant fine needle aspiration biopsy diagnosis. Can J Surg. In press.
  7. Johner A, Griffith OL, Walker B, Wood L, Piper H, Wilkins G, Baliski C, Jones SJ, Wiseman SM. Detection and management of hypothyroidism following thyroid lobectomy: evaluation of a clinical algorithm. Ann Surg Oncol. 2011 Sep;18(9):2548-2554.
  8. Earl DA, Bradnam K, St. John J, Darling A, Lin D, Faas J, Yu HOK, Vince B, Zerbino DR, Diekhans M, Nguyen N, Nuwantha P, Wing-Kin Sung A, Ning Z, Haimel M, Simpson JT, Fronseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelly DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Zhenyu L, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green R, Haussler D, Korf I, Paten B. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Res. 2011 Sep 16.
  9. Linger BR, Morin GB, and Price CM. The Pot1a-Associated Proteins Tpt1 And Pat1 Coordinate Telomere Protection And Length Regulation In Tetrahymena. Mol Biol Cell. Nov;22(21):4161-70. Epub 2011 Sep 7.
  10. Starczynowski DT, Lockwood WW, Delehouzee S, Chari R, Wegrzyn J, Tsao M-S, Lam S, Gazdar AF, Lam WL, Karsan A. TRAF6 is an amplified oncogene bridging the Ras and nuclear factor-?B cascade in human lung cancer. J Clin Invest. 2011 Sep 12. pii: 58818. doi: 10.1172/JCI58818
  11. Haile S, Lal A, Myung J-K. Sadar MD. FUS/TLS is a co-activator of the androgen receptor in prostate cancer cells. PLoS One. 2011;6(9):324197.
  12. Tognon CE, Martin MJ, Moradian A, Trigo G, Rotblat B, Cheng SW, Pollard M, Uy E, Chow C, Carboni JM, Gottardis MM, Pollak M, Morin GB, Sorensen PH. A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation. Oncogene. 2011 Aug 1. doi: 10.1038/onc.2011.323.
  13. Chan QWT, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJM, de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC Genomics. 2011, 12:450doi:10.1186/1471-2164-12-450.
  14. Sadar MD. Advances in Small Molecule Inhibitors of Androgen Receptor for the Treatment of Advanced Prostate Cancer. World J Urol. 2011 Aug 11.
  15. Haile S, Sadar MD. Androgen receptor and its splice variants in prostate cancer. Cell Mol Life Sci. 2011 Dec;68(24):3971-81. Epub 2011 Jul 12.
  16. Li YY, An J, Jones SJM. A Computational Approach to Finding Novel Targets for Existing Drugs. PLoS Comput Biol 7(9): e1002139. doi:10.1371/journal.pcbi.1002139.
  17. Kasaian K, Jones SJ. A new frontier in personalized cancer therapy: mapping molecular changes. Future Oncol. 2011 Jul;7(7):873-894.
  18. Qu C, Schuetz JM, Min JE, Leach S, Daley D, Spinelli JJ, Brooks-Wilson A and J Graham. Cost-effective prediction of gender-labeling errors and estimation of gender-labeling error rates in candidate-gene association studies. Front. Gene. 2011 June 15. doi: 10.3389/fgene.2011.00031.
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2010 Publications

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