Platforms

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.
19. Pharoah PDP, Palmieri RT, Ramus SJ, Gayther SA, Andrulis IL, Anton-Culver HA, Antonenkova N, Antoniou AC, Study Group of BCFR Investigators, Beattie MS, Beckman M, Birrer MJ, Bogdanova N, Bolton KL, Brewster W, Brooks-Wilson A, Brown R, Butzow R, Caldes T, Caligo MA, Campbell IG, Chang-Claude J, Chen A, Chenevix-Trench G, Cook LS, Couch FJ, Cramer DW, Cunningham JM, Despierre E, Doherty JA, Dörk T, Dürst M, Eccles D, Ekici AB, Study Group of EMBRACE Investigators, Fasching PA, de Fazio A, Fenstermacher DA, Flanagan JM, Fridley BL, Friedman E, Gao B, Study Group of GEMO Study Collaborators, Gentry-Maharaj A, Godwin AK, Goode E, Goodman MT, Gross J, Hansen TVO, Harnett PR, Study Group of HEBON Investigators, Heikkinen T, Hein R, Høgdall CK, Høgdall EV, Iversen E, Jakubowska A, Johnatty SE, Karlan BY, Kauff ND, Kaye SB, Study Group of kConFab Investigators, Kelemen LE, Kiemeney LA, Kjaer SK, Lambrechts D, LaPolla JP, Lázaro C, Le ND, Leminen A, Leunen K, Levine DA, Lu Y, Lundvall L, Macgregor S, Marees T, Massuger L, McLaughlin JR, Menon U, Montagna M, Moysich KB, Narod S, Nathanson KL, Nedergaard L, Ness RB, Nevanlinna HA, Nickels S, Osorio A, Paul J, Pearce CL, Phelan CM, Pike MC, Radice P, Rossing MA, Schildkraut J, Sellers TA, Singer CF, Song H, Stram DO, Sutphen R, Study Group of SWE-BRCA Investigators, Terry KL, Tsai Y-Y, van Altena AM, Vergote I, Vierkant RA, Vitonis AF, Walsh C, Wang-Gohrke S, Wappenschmidt B, Wu AH, Ziogas A, Berchuck A and HA Risch. The role of KRAS rs61764370 in invasive epithelial ovarian cancer: implications for clinical testing. Clin Cancer Res. 2011 Jun 1;17(11):3742-3750.
20. Wong JCT*, Chan SK*, Schaeffer DF, Sagaert X, Lim H, Kennecke H, Owen D, Suh KW, Kim YB, Tai IT. Absence of MMP2 expression correlates with poor clinical outcomes in rectal cancer, and is distinct from MMP1-related outcomes in colon cancer. Clin Cancer Res. 2011 Jun 15;17(12):4167-4176.
21. Hasan MR, Ho SHY, Owen D, Tai IT. Inhibition of VEGF induces cellular senescence in colorectal cancer cells. Int J Cancer. 2011 May 26:10.1002/ijc.26179.
22. Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young TL, Jones SJ, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. J Pathol. 2011 Sep;225(1):12-8. doi: 10.1002/path.2941.
23. Chang ACY, Fu Y, Garside VC, Niessen K, Chang L, Fuller M, Setiadi A, Smrz J, Kyle A, Minchinton A, Marra M, Hoodless PA, Karsan A. Notch initiates endothelial-to-mesenchymal transition in the atrioventricular canal through autocrine activation of soluble guanylyl cyclase. Dev Cell. 2011 Aug 16;21(2):288-300.
24. Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res. 2011 Aug;21(8):1203-1212.
25. O'Connor MD, Wederell E, Robertson G, Delaney A, Morozova O, Poon SS, Yap D, Fee J, Zhao Y, McDonald H, Zeng T, Hirst M, Marra MA, Aparicio SA, Eaves CJ. Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance. Exp Hematol. 2011 Aug;39(8):866-879.e1
26. White AK, Vaninsberghe M, Petriv OI, Hamidi M, Sikorski D, Marra MA, Piret J, Aparicio S, Hansen CL. High-Throughput Microfluidic RT-qPCR of Single Cells. Proc Natl Acad Sci U SA. 2011 Aug 1.
27. 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 R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone- modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27. doi: 10.1038/nature10351.
28. Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK. Cell of Origin in AML: Susceptibility to MN1-Induced Transformation Is Regulated by the MEIS1/AbdB-like HOX Protein Complex. Cancer Cell. 2011 Jul 12;20(1):39-52.
29. Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC. DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell. 2011 Jun 3;8(6):676-87.
30. McPherson AW, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah S. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. PLoS Comput Biol. 2011 May;7(5):e1001138.
31. Kuchenbauer F, Mah SM, Heuser M, McPherson A, Ruschmann J, Rouhi A, Berg T, Bullinger L, Argiropoulos B, Morin RD, Lai D, Starczynowski DT, Karsan A, Eaves CJ, Watahiki A, Wang Y, Aparicio SA, Ganser A, Krauter J, Döhner H, Döhner K, Marra MA, Camargo FD, Palmqvist L, Buske C, Humphries RK. Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells. Blood. 2011 May 31.
32. Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS One. 2011;6(5):e19838. Epub 2011 May 13.
33. Warren RL, Holt RA. Targeted assembly of short sequence reads. PLoS One. 2011 May 11;6(5):e19816.
34. Bashash M, Hislop TG, Shah AM, Le N, Brooks-Wilson A, Bajdik CD. The prognostic effect of ethnicity for gastric and esophageal cancer: the population-based experience in British Columbia, Canada. BMC Cancer. 2011 May 9;11(1):164.
35. 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 Res. 2011 May;21(5):790-797.
36. Wiseman SM, Griffith OL, Gown A, Walker B, Jones SJ. Immunophenotyping of thyroid tumors identifies molecular markers altered during transformation of differentiated into anaplastic carcinoma. Am J Surg. 2011 May;201(5):578-584.
37. Fejes AP, Khodabakhshi AH, Birol I, Jones SJ. Human variation database: an open-source database template for genomic discovery. Bioinformatics. 2011 Apr 15;27(8):1155-1156.
38. Wong JC, Chan SK, Schaeffer DF, Sagaert X, Lim H, Kennecke H, Owen D, Suh KW, Kim YB, Tai IT. Absence of MMP2 expression correlates with poor clinical outcomes in rectal cancer, and is distinct from MMP1-related outcomes in colon cancer. Clin Cancer Res. 2011 Apr 29. (Epub ahead of print)
39. Wegrzyn J, Lam JC, Karsan A. Mouse models of myelodysplastic syndromes. Leuk Res. 2011 Jul;35(7):853-62. Epub 2011 Apr 3
40. Bhat RK, Ellestad KK, Wheatley BM, Warren R, Holt RA, Power C. Age- and Disease-Dependent HERV-W Envelope Allelic Variation in Brain: Association with Neuroimmune Gene Expression. PLoS One. 2011 Apr 29;6(4):e19176.
41. Smedby KE, Foo JN, Skibola CF, Darabi H, Conde L, Hjalgrim H, Kumar V, Chang ET, Rothman N, Cerhan JR, Brooks-Wilson AR, Rehnberg E, Irwan ID, Ryder LP, Brown PN, Bracci PM, Agana L, Riby J, Cozen W, Davis S, Hartge P, Morton LM, Severson RK, Wang SS, Slager SL, Fredericksen ZS, Novak AJ, Kay NE, Habermann TM, Armstrong B, Kricker A, Milliken S, Purdue MP, Vajdic CM, Boyle P, Lan Q, Zahm SH, Zhang Y, Zheng T, Leach S, Spinelli JJ, Smith MT, Chanock SJ, Padyukov L, Alfredsson L, Klareskog L, Glimelius B, Melbye M, Liu ET, Adami HO, Humphreys K, Liu J. GWAS of Follicular Lymphoma Reveals Allelic Heterogeneity at 6p21.32 and Suggests Shared Genetic Susceptibility with Diffuse Large B-cell Lymphoma. PLoS Genet. 2011 Apr;7(4):e1001378.
42. Starczynowski DT, Vercauteren S, Sung S, Brooks-Wilson A, Lam WL, Karsan A. Copy number alterations at polymorphic loci may be acquired somatically in patients with myelodysplastic syndromes. Leuk Res. 2011 Apr;35(4):444-447.
43. Fu Y, Chang AC, Fournier M, Chang L, Niessen K, Karsan A. RUNX3 maintains the mesenchymal phenotype after termination of the notch signal. J Biol Chem. 2011 Apr 1;286(13):11803-11813.
44. McConechy MK, Anglesio MS, Kalloger SE, Yang W, Senz J, Chow C, Heravi-Moussavi A, Morin GB, Mes-Masson AM; Australian Ovarian Cancer Study Group, Carey MS, McAlpine JN, Kwon JS, Prentice LM, Boyd N, Shah SP, Gilks CB, Huntsman DG. Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas. J Pathol. 2011 Apr;223(5):567-73. doi: 10.1002/path.2848.
45. Bashash M, Yavari P, Hislop TG, Shah A, Sadjadi A, Babaei M, Le N, Brooks-Wilson A, Malekzadeh R, Bajdik C. Comparison of two diverse populations, British Columbia, Canada, and Ardabil, Iran, indicates several variables associated with gastric and esophageal cancer survival. J Gastrointest Cancer. 2011 Mar;42(1):40-45.
46. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R. PICS: Probabilistic Inference for ChIP-seq . Biometrics. 2011 Mar;67(1):151-63. doi: 10.1111/j.1541-0420.2010.01441.x.
47. Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics. 2011 Mar 25;4(1):25.
48. Slobodan J, Corbett R, Wye N, Schein JE, Marra MA, Coope RJN. High performance gel imaging with a commercial single lens reflex camera. Rev Sci Instrum. 2011 Mar;82(3):034301.
49. Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P, Johnson NA, Zhao Y, Telenius A, Ben-Neriah S, McPherson A, Meissner B, Okoye UC, Diepstra A, van den Berg A, Sun M, Leung G, Jones SJ, Connors JM, Huntsman DG, Savage KJ, Rimsza LM, Horsman DE, Staudt LM, Steidl U, Marra MA, Gascoyne RD. MHC Class II Transactivator CIITA is a Recurrent Gene Fusion Partner in Lymphoid Cancers. Nature. 2011 Mar 17;471(7338):377-381
50. Yap DB, Chu J, Berg T, Schapira M, Cheng SW, Moradian A, Morin RD, Mungall AJ, Meissner B, Boyle M, Marquez VE, Marra MA, Gascoyne RD, Humphries RK, Arrowsmith CH, Morin GB, Aparicio SA. Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood. 2011 Feb 24;117(8):2451-2459.
51. 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. N Engl J Med. 2011 Feb 24;364(8):730-739.
52. Sadar MD. Small molecule inhibitors targeting the "achilles' heel" of androgen receptor activity. Cancer Res. 2011 Feb 15;71(4):1208-1213.
53. Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao YJ, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.PLoS One. 2011 Feb 15;6(2):e17121.
54. D'Souza C, Kronstad J, Taylor G, Warren R, 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, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren B, Galagan J, Cuomo C. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio. 2011 Feb 8;2(1). pii: e00342-10. doi: 10.1128/mBio.00342-10.
55. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking R, Levasseur A, Haridas S, Robertson G, Birol I, Holt R, Marra M, 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. Proc Natl Acad Sci U SA. 2011 Feb 8;108(6):2504-2509.
56. Shin H, Lee H, Fejes AP, Baillie DL, Koo HS, Jones SJ. Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing. BMC Res Notes. 2011 Feb 8;4:34.
57. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao YJ, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. 2011 Feb;21(2):203-215.
58. Jädersten M, Karsan A. Clonal evolution in myelodysplastic syndromes with isolated del(5q): the importance of genetic monitoring. Haematologica. 2011 Feb;96(2):177-180.
59. Starczynowski DT, Kuchenbauer F, Wegrzyn J, Rouhi A, Petriv O, Hansen CL, Humphries RK, Karsan A. MicroRNA-146a disrupts hematopoietic differentiation and survival. Exp Hematol. 2011 Feb;39(2):167-178.e4.
60. Starczynowski D, Morin RD, McPherson A, Kuchenbauer F, Tohyama K, Hirst M, Humphries K, Marra M, Lam W, Karsan A. Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations. Blood. 2011 Jan 13;117(2):595-607.
61. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011 Jan 7;144(1):27-40.
62. Schrader K, Masciari S, Boyd N, Salamanca C, Senz J, Saunders DN, Yorida E, Maines-Bandiera S, Kaurah P, Tung N, Robson M, Ryan PD, Olopade OI, Domchek SM, Ford J, Isaacs C, Brown P, Balmana J, Miron P, Coffey K, Terry MB, John EM, Andrulis IL, Knight JA, O’Malley FP, Daly M, Bender P, ConFab K, Moore R, Southey MC, Hopper JL, Garber J, Huntsman D. Germline mutations in CDH1 are infrequent in in women with early-onset or familial lobular breast cancers. Journal of Medical Genetics. 2011 Jan;48(1):64-8. Epub 2010 Oct 4.
63. Yakovenko OY, Li YY, Oliferenko AA, Vashchenko GM, Bdzhola VG, Jones SJM. Ab initio parameterization of YFF1, a universal force field for drug-design applications. Journal of molecular modeling. 2011 May 12.
64. Laing R, Hunt M, Protasio AV, Saunders G, Mungall K, Laing S, Jackson F, Quail M, Beech R, Berriman M, Gilleard JS. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS ONE. 2011 Jan 1;6(8):e23216.
65. Earp MA, Rahmani M, Chew K, Brooks-Wilson A. Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies. BMC medical genomics. 2011 Nov 28;4(1):81.
66. 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). 2011 Nov 13.
67. Beesley J, Pickett HA, Johnatty SE, Dunning AM, Chen X, Li J, Michailidou K, Lu Y, Rider DN, Palmieri RT, Stutz MD, Lambrechts D, Despierre E, Lambrechts S, Vergote I, Chang-Claude J, Nickels S, Vrieling A, Flesch-Janys D, Wang-Gohrke S, Eilber U, Bogdanova N, Antonenkova N, Runnebaum IB, Dörk T, Goodman MT, Lurie G, Wilkens LR, Matsuno RK, Kiemeney LA, Aben KKH, Marees T, Massuger LFAG, Fridley BL, Vierkant RA, Bandera EV, Olson SH, Orlow I, Rodriguez-Rodriguez L, Cook LS, Le ND, Brooks-Wilson A, Kelemen LE, Campbell I, Gayther SA, Ramus SJ, Gentry-Maharaj A, Menon U, Ahmed S, Baynes C, Pharoah PD, Investigators K, Group AOCS, Investigators A, Muir K, Lophatananon A, Chaiwerawattana A, Wiangnon S, Macgregor S, Easton DF, Reddel RR, Goode EL, Chenevix-Trench G, Consortium obotOCA. Functional Polymorphisms in the TERT Promoter Are Associated with Risk of Serous Epithelial Ovarian and Breast Cancers. PLoS ONE. 2011 Jan 1;6(9):e24987.
68. Chu Y, Gao P, Zhao P, He Y, Liao N, Jackman S, Zhao Y, Birol I, Duan X, Lu Z. Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601. J Bacteriol. 2011 Nov 1;193(21):6098-9.
69. Dauphinee SM, Voelcker V, Tebaykina Z, Wong F, Karsan A. Heterotrimeric Gi/Go proteins modulate endothelial TLR signaling independent of the MyD88-dependent pathway. Am J Physiol Heart Circ Physiol. 2011 Sep 23.
70. Krzywinski M, Birol I, Jones SJ, Marra MA. Hive plots--rational approach to visualizing networks. Briefings in bioinformatics. 2011 Dec 9.
71. Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PAF, Costello JF, Wang T. The human epigenome browser at washington university. Nat Methods. 2011 Jan 1;8(12):989-90.
72. 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. 2011 Nov 9.
73. Mo F, Wyatt AW, Wu C, Lapuk AV, Marra MA, Gleave ME, Volik SV, Collins CC. Next generation sequencing of prostate tumours provides independent evidence of XMRV contamination. Journal of clinical microbiology. 2011 Dec 7.
74. Andersen R, Sadar M, Williams D, Meimetis L, Mawji N, Banuelos C, Lal A, Park J, de Voogd NJ, Tien A, Fernandez J. 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. 2011 Dec 8.
75. Amankwah EK, Wang Q, Schildkraut JM, Tsai Y-Y, Ramus SJ, Fridley BL, Beesley J, Johnatty SE, Webb PM, Chenevix-Trench G, Group AOCS, Dale LC, Lambrechts D, Amant F, Despierre E, Vergote I, Gayther SA, Gentry-Maharaj A, Menon U, Chang-Claude J, Wang-Gohrke S, Anton-Culver H, Ziogas A, Dörk T, Dürst M, Antonenkova N, Bogdanova N, Brown R, Flanagan JM, Kaye SB, Paul J, Bützow R, Nevanlinna H, Campbell I, Eccles DM, Karlan BY, Gross J, Walsh C, Pharoah PDP, Song H, Krüger Kjær S, Høgdall E, Høgdall C, Lundvall L, Nedergaard L, Kiemeney LALM, Massuger LFAG, van Altena AM, Vermeulen SHHM, Le ND, Brooks-Wilson A, Cook LS, Phelan CM, Cunningham JM, Vachon CM, Vierkant RA, Iversen ES, Berchuck A, Goode EL, Sellers TA, Kelemen LE. Polymorphisms in stromal genes and susceptibility to serous epithelial ovarian cancer: a report from the Ovarian Cancer Association Consortium. PLoS ONE. 2011 Jan 1;6(5):e19642.
76. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour. 2011 Mar 1;11 Suppl 1:81-92.

2010 Publications

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.
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