Professor and Head, Department of Medical Genetics, University of British Columbia
Director, Genome Sciences Centre, BC Cancer Agency
Canada Research Chair in Genome Science
phone: 6048758168

I am Professor and Head of Medical Genetics at UBC; UBC Canada Research Chair in Genome Science; and Director of the BC Cancer Agency Genome Sciences Centre (GSC). I was trained as a geneticist, and have been involved in the development and application of high-throughput genomics strategies, with special emphasis on large-scale DNA sequencing and bioinformatics. I have spent much of my career working within, and leading, teams to conduct large-scale high throughput genomics projects.

A current focus of my research activities involves the development and application of “next generation” sequencing approaches to characterize cancer genomes, transcriptomes and epigenomes, with the aim of comprehensive identification of the genetic and epigenetic changes that drive cancer progression. With such data, and as co-Leader of the BC Cancer Agency Personalized Oncogenomics Project, my objective is the development of a new generation of diagnostic, prognostic and treatment strategies to benefit cancer patients.

A second focus of my research revolves around the functional interplay between cancer genomes and epigenomes. My team has described the strikingly high frequency of mutations in transcriptional regulators, including chromatin modifiers, implying they are “cancer genes,” and that mutations in them drive cancers. The interplay between the genome and the epigenome is thus exploited by cancer cells, but exactly how, the extent to which common mechanisms exist across cancers and whether answers to such questions might reveal therapeutic opportunities, all require investigation. My team is analyzing the cancer regulatory networks impacted by epigenome dysregulation, using cell biology, genetics, genomics, bioinformatics, and functional genomics tools, and we aim to understand the selective advantages conferred to cancer cells as a consequence of such dysregulation. My objectives are: (1) to identify and characterize regulatory networks disrupted by epigenome dysregulation in cancer; (2) to assess the extent to which epigenome dysregulation converges on common pathways/networks in different malignancies; and, (3) to identify candidate therapeutic vulnerabilities resulting from epigenome dysregulation.

Publications in the last 10 years:

Waszak SM, Northcott PA, Buchhalter I,  Robinson GW, Sutter C, Groebner S, Grund KB, Brugieres L,  Jones DTW, Pajtler KW, Morissy S, Kool M, Sturm D, Chavez K, Ernst A, Brabetz S, Hain M, Zichner T, Wang MS, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan J, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra Y-S, Zitterbart K, Shringarpure SS, De La Vega FM,  Bustamante CD, Ng H-K, Perry A, MacDonald TJ, Hernaiz-Driever P, Bendel AE, Bowers D, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff  K, Rutkowski S, Ramaswamy V, Korshunov A, Malkin D, Lichter P, Taylor MD,  Gajjar A, Korbel JO,  Pfister SM. Spectrum and Prevalence of Hereditary Predisposition in Medulloblastoma. Lancet Oncol. 2018 May 9. pii: S1470-2045(18)30242-0.  doi: 10.1016/S1470-2045(18)30242-0.

Newton Y, Rassekh R, Deyell R, Shen Y, Jones M, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Wat S,  Salama S, Ng T, Hendson G, Lee AF, Ma Y, Moore R, Mungall A, Haussler D, Stuart J, Jantzen C, Laskin J, Jones S, Marra M, Morozova O. Comparative RNA-Seq analysis benefits a relapsed pediatric cancer patient. JCO PO. http://ascopubs.org/doi/pdf/10.1200/PO.17.00198.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023.

Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R; Cancer Genome Atlas Research Network, Thorsson V, Bass AJ, Laird PW. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell. 2018 Apr 9;33(4):721-735.e8. doi: 10.1016/j.ccell.2018.03.010.

Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S; Cancer Genome Atlas Research Network, Xie W, Yang D. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell. 2018 Apr 9;33(4):706-720.e9. doi: 10.1016/j.ccell.2018.03.006.

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014.

Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ; Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R, Meyerson M. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 Apr 9;33(4):676-689.e3. doi: 10.1016/j.ccell.2018.03.007.

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V; Cancer Genome Atlas Research Network, Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr 5;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052.

Chen H, Li C, Peng X, Zhou Z, Weinstein JN; Cancer Genome Atlas Research Network, Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 Apr 5;173(2):386-399.e12. doi: 10.1016/j.cell.2018.03.027.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033.

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwaitkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WT, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075.

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064.

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG; Cancer Genome Atlas Research Network, Buonamici S, Yu L. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep. 2018 Apr 3;23(1):282-296.e4. doi: 10.1016/j.celrep.2018.01.088

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN; Cancer Genome Atlas Research Network, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep. 2018 Apr 3;23(1):255-269.e4. doi: 10.1016/j.celrep.2018.03.077.

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I; Cancer Genome Atlas Research Network, Monnat RJ Jr., Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050.

Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H; Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep. 2018 Apr 3;23(1):213-226.e3. doi: 10.1016/j.celrep.2018.03.047.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J; Cancer Genome Atlas Research Network, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086.

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.

Chahal M, Pleasance E, Grewal J, Zhao E, Ng T, Chapman E, Jones MR, Shen Y, Mungall KL, Bonakdar M, Taylor GA, Ma Y, Mungall AJ, Moore RA, Lim H, Renouf D, Yip S, Jones SJM, Marra MA, Laskin J. Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002626.

Ronsley R, Rassekh R, Shen Y,  Lee A,  Jantzen C, Halparin J, Albert C,  Hawkins D, Amed S, Rothstein R,  Mungall AJ,  Dix D, Blair G, Jones SJM,  Laskin J, Marra MA, Deyell R. Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002568.

Owen DR, Wong HL, Bonakdar M, Jones M, Hughes CS, Morin GB, Jones SJM, Renouf DJ, Lim H, Laskin J, Marra M, Yip S, Schaeffer DF. Molecular characterization of ERBB2-amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: A report of two instructive cases. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002535. doi: 10.1101/mcs.a002535.

Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C; Cancer Genome Atlas Network. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst. 2018 Mar 28;6(3):282-300.e2. doi: 10.1016/j.cels.2018.03.003.

Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L; MC3 Working Group; Cancer Genome Atlas Research Network. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.Cell Syst. 2018 Mar 28;6(3):271-281.e7. doi: 10.1016/j.cels.2018.03.002.

Merk DJ, Ohli J, Merk ND, Thatikonda V, Morrissy S, Schoof M, Schmid SN, Harrison L, Filser S, Ahlfeld J, Erkek S, Raithatha K, Andreska T, Weißhaar M, Launspach M, Neumann JE, Shakarami M, Plenker D, Marra MA, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJM, Lutz B, Ertl-Wagner B, Rossi A, Wagener R, Siebert R, Jung A, Eberhart CG, Lach B, Sendtner M, Pfister SM, Taylor MD, Chavez L, Kool M, Schüller U. Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma. Dev Cell. 2018 Mar 26;44(6):709-724.e6.

Hung SS, Meissner B, Chavez EA, Ben-Neriah S, Ennishi D, Jones MR, Shulha HP, Chan FC, Boyle M,  Kridel R, Gascoyne RD, Mungall AJ,  Marra MA, Scott DW,  Connors JM,  Steidl C. Assessment of Capture and Amplicon-based Approaches for the Development of a Targeted Next-generation Sequencing Pipeline to Personalize Lymphoma Management. J Mol Diagn. 2018 Mar;20(2):203-214. doi: 10.1016/j.jmoldx.2017.11.010.

Thibodeau ML, Bonakdar M, Mungall KL, Thiessen N, Mungall AJ, Ma YP, Jones M, Renouf D, Lim H, Yip S, Ng T, Ho C, Laskin J, Marra M, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of metastatic eccrine porocarcinoma. Precis Oncol. 2018 Mar 19. doi:10.1038/s41698-018-0050-5.

Garzia L, Kijima N, Morrissy AS, Wu X, Wang X, Donovan LK, De Antonellis P, Liu K-W, Luu B, Alamsahebpour A, Thompson YY, Holgado BL, Ramaswamy V, Farooq H, Skowron P, Shih DJH, Li A, Ensan S, Robbins CS, Manno A, Liu J, Qin L, Cybulsky M, Mitra S, Cho Y-J, Weiss WA, Chan JA, Hawkins CE, Massimino M, Jabado N, Bouffet E, Sorensen PHB, Aldape K, Marra MA, Wechsler-Reya RJ, Fults DW, Taylor MD. A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases. Cell. 2018 Feb 22;172(5):1050-1062.e14.

Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC; Cancer Genome Atlas Network, Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 2018 Feb 12;33(2):244-258.e10. doi: 10.1016/j.ccell.2018.01.003.

Wong HL, Yang KC, Shen Y, Zhao EY, Loree JM, Kennecke HF, Kalloger SE, Karasinska JM, Lim HJ, Mungall A, Feng X, Davies JM, Schrader K, Zhou C, Karsan A, Laskin J, Marra MA, Schaeffer DF, Gorski SM, Renouf DJ. Molecular characterisation of metastatic pancreatic neuroendocrine tumours (PNETs) using whole genome and transcriptome sequencing. Cold Spring Harb Mol Case Stud. 2018 Feb 1;4(1). pii: a002329. doi: 10.1101/mcs.a002329.

Bolouri H, Farrar JE, Triche T Jr, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2018 Jan;24(1):103-112.

Zhao E, Shen Y, Pleasance ED, Kasaian K, Leelakumari S, Jones M, Bose P, Ch’ng C, Reisle C, Eirew P, Corbett R, Mungall KL, Thiessen N, Ma Y, Schein JE, Mungall AJ, Zhao YJ, Moore R, Den Brok W, Wilson S, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Renouf D, Sun S, Schrader KA, Young S, Bosdet I, Karsan A, Laskin J, Marra MA,  Jones SJM.  Homologous Recombination Deficiency and Platinum-based Therapy Outcomes in Advanced Breast Cancer. Clin Cancer Res. 2017 Dec 15;23(24):7521-7530.

Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. The genome of the northern sea otter (Enhydra lutris kenyoni). Genes (Basel). 2017 Dec 11;8(12). pii: E379. doi: 10.3390/genes8120379.

Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. The genome of the beluga whale (Delphinapterus leucas). Genes (Basel). 2017 Dec 11;8(12). pii: E378. doi: 10.3390/genes8120378.

Lim EL, Trinh DL, Ries RE, Wang J, Gerbing RB, Ma Y, Topham J, Hughes M, Pleasance E, Mungall AJ, Moore R, Zhao Y, Aplenc R, Sung L, Kolb EA, Gamis A, Smith M, Gerhard DS, Alonzo TA, Meshinchi S, Marra MA. MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia. J Clin Oncol. 2017 Dec 10;35(35):3964-3977.

Jones MR, Lim H, Shen Y, Pleasance E, Ch’ng C, Reisle C, Leelakumari S, Zhao C, Yip S, Ho J, Zhong E, Ng T, Ionescu D, Schaeffer DF, Mungall AJ, Mungall KL, Zhao R, Moore RA, Ma Y, Chia S, Ho C, Renouf DJ, Gelmon K, Jones SJM, Marra MA, Laskin J. Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer. Ann Oncol. 2017 Dec 1;28(12):3092-3097.

Grewal JK, Eirew P, Jones M, Chiu K, Tessier-Cloutier B, Karnezis AN, Karsan A, Mungall A, Zhou C, Yip S, Tinker AV, Laskin J, Marra M, Jones SJM. Detection and Genomic Characterization of a mammary-like adenocarcinoma. Cold Spring Harb Mol Case Stud. 2017 Nov 21;3(6).

The Cancer Genome Atlas Research Network.  Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017 Nov 2;171(4):950-965.e28.

Wong HL, Yang KC, Shen Y, Zhao EY, Loree JM, Kennecke HF, Kalloger SE, Karasinska JM, Lim HJ, Mungall A, Feng X, Davies JM, Schrader K, Zhou C, Karsan A, Laskin J, Marra MA, Schaeffer DF, Gorski SM, Renouf DJ. Molecular characterisation of metastatic pancreatic neuroendocrine tumours (PNETs) using whole genome and transcriptome sequencing. Cold Spring Harb Mol Case Stud. 2017 Nov 1. pii: mcs.a002329. doi: 10.1101/mcs.a002329. [Epub ahead of print]

Siu C, Wiseman S, Gakkhar S, Heravi-Moussavi A, Bilenky M, Carles A, Sierocinski T, Tam A, Zhao E, Kasaian K, Moore R, Mungall A, Walker B, Thomson T, Marra M, Hirst M, Jones SJM. Characterization of the human thyroid epigenome. J Endocrinol. 2017 Nov;235(2):153-165.

Lim EL, Trinh DL, Ries RE, Wang J, Gerbing RB, Ma Y, Topham J, Hughes M, Pleasance E, Mungall AJ, Moore R, Zhao Y, Aplenc R, Sung L, Kolb EA, Gamis A, Smith M, Gerhard DS, Alonzo TA, Meshinchi S, Marra MA. MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia. J Clin Oncol. 2017 Oct 25:JCO2017747451. doi: 10.1200/JCO.2017.74.7451. [Epub ahead of print]

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19;171(3):540-556.e25.

Gadd S,  Huff V,  Walz AL, Ooms A, Armstrong AE, Gerhard DS, Smith MA, Guidry Auvil JM,  Meerzaman D, Chen-Q-R, Hsu CH, Yan C, Nguyen C, Hu Y,  Hermida LC, Davidson T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ. A Children’s Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor. Nat Genet. 2017 Oct;49(10):1487-1494.

Mazor T, Chesnelong C, Pankov A, Jalbert L, Hong C, Hayes J, Smirnov I, Marshall R, Souza C, Shen Y, Viswanath P, Noushmehr H, Ronen S, Jones S, Marra M, Cairncross JG, Perry A, Nelson S, Chang S, Bollen A, Molinaro A, Bengtsson H, Olshen A, Weiss S, Phillips J, Luchman H, Costello J. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. Proc Natl Acad Sci U S. 2017 Oct 3;114(40):10743-10748.

Jones MR, Lim H, Shen Y, Pleasance E, Ch’ng C, Reisle C, Leelakumari S, Zhao C, Yip S, Ho J, Zhong E, Ng T, Ionescu D, Schaeffer DF, Mungall AJ, Mungall KL, Zhao R, Moore RA, Ma Y, Chia S, Ho C, Renouf DJ, Gelmon K, Jones SJM, Marra MA, Laskin J. Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer. Ann Oncol. 2017 Sep 18. doi/10.1093/annonc/mdx523. [Epub ahead of print]

Bosse KR, Raman P, Zhu Z, Lane M, Martinez D, Heitzeneder S, Rathi KW, Kendsersky NM, Randall M, Donovan L, Morrissy S, Sussman RT, Zhelev DV, Feng Y, Wang Y, Hwang J, Lopez Gardia G, Harenza JL, Wei J, Pawel B, Bhatti T, Santi M, Ganguly A, Khan J, Marra MA, Taylor MD, Dimitrov DS, Mackall C, Maris JM. Identification of GPC2 as an oncogene and candidate immunotherapeutic target in high-risk neuroblastoma. Cancer Cell. 2017 Sep 11;32(3):295-309.

Sloma I, Mitjavila-Garcia M, Feraud O, Griscelli F, Oudrhiri N, El Marsafy S, Gobbo E, Divers D, Proust A, Smadja DM, Desterke C, Carles A, Ma Y, Hirst M, Marra MA, Eaves CJ, Bennaceur-Griscelli A, Turhan AG.  Whole genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia. Exp Hematol. 2017 Sep;53:48-58.

Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13.

Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 Aug 14;32(2):204-220.e15.

Northcott PA, Buchhalter I, Morrissy S, Hovestadt V,  Groebner S, Ehrenberger T, Segura-Wang M, Zichner T, Weischenfeldt J, Schumacher S, Phillips A, Kleinheinz A, Waszak A, Erkek S, Jones D, Worst B, Kool M, Zapatka M,  Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z,  Ishaque N, Jäger-Schmidt C, Warnatz  H-J, Risch T, Amstislavskiy V, Weber U, Wolf S, Robinson G, Zhou X, Wu G, Finkelstein D, Cavalli F, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho Y-J,  Pomeroy S, Herold-Mende C, Schuhmann M, Ebinger M, Liau L, Mora J, Jabado N, Kumabe T, Witt O, Milde T, von Deimling A, Capper D, Korshunov A, Yaspo M-L, Kriwacki R, Gajjar A, Zhang  J, Beroukhim R, Fraenkel E , Korbel J, Schlesner M, Eils R, Marra M, Pfister S, Taylor M, Lichter P. The whole genome landscape of medulloblastoma subtypes. Nature. 2017 Jul 19;547(7663):311-317.

Haile S, Corbett RD, MacLeod T, Bilobram S, Smailus D, Tsao P, Kirk H, McDonald H, Pandoh P, Bala M, Hirst M, Miller D, Moore R, Mungall AJ, Schein J, Coope R, Ma Y, Zhao YJ, Holt R, Jones S, Marra M. Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing. BMC Genomics. 2017 Jul 5;18(1):515.

Chooback N, Shen Y, Jones M, Kasaian K, Martin M, Ng T, Thomson T, Marra M, Laskin J, Ho C. Carcinoma ex pleomorphic adenoma: case report and options for systemic therapy. Curr Oncol. 2017 Jun;24(3):e251-e254.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 Jun 27;19(13):2878-2880.

Cancer Genome Atlas Research Network. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell. 2017 Jun 15;169(7):1327-1341.e23. doi: 10.1016/j.cell.2017.05.046.

Haile S, Pandoh P, McDonald H, Corbett RD, Tsao P, Kirk H, MacLeod T, Jones M, Bilobram S, Brooks D, Smailus D, Steidl C, Scott D, Bala M, Hirst M, Miller D, Moore R, Mungall AJ, Coope R,  Ma Y,  Zhao YJ, Holt R, Jones S, Marra MA. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis. PLOS ONE. 2017 Jun 1;12(6):e0178706. doi: 10.1371/journal.pone.0178706.

Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal DS, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis AN, Lai D, Aniba MR, Zhang AW, Shumansky K, Siu C, Wan A, McConechy MK, Li-Chang H, Tone A, Provencher D, de Ladurantaye M, Fleury H, Okamoto A, Yanagida S, Yanaihara N, Saito M, Mungall AJ, Moore R, Marra MA, Gilks CB, Mes-Masson AM, McAlpine JN, Aparicio S, Huntsman DG, Shah SP. Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes. Nat Genet. 2017 Jun;49(6):856-865.

LeBlanc VG, Firme M, Song J, Chan SY, Lee MH, Yip S, Chittaranjan S, Marra MA. Comparative transcriptome analysis of isogenic cell line models and primary cancers links CIC loss to activation of the MAPK signalling cascade. J Pathol. 2017 Jun;242(2):206-220.

Zahir FR, Mwenifumbo JC, Chun HE, Lim EL, Van Karnebeek CDM, Couse M, Mungall KL, Lee L, Makela N, Armstrong L, Boerkoel CF, Langlois SL, McGillivray BM, Jones SJM, Friedman JM, Marra MA. Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability. BMC Genomics. 2017 May 24;18(1):403. doi: 10.1186/s12864-017-3671-0.

Ennishi D, Mottok A, Ben-Neriah S, Shulha HP, Farinha P, Chan FC, Meissner B, Boyle M, Hother C, Kridel R, Lai D, Saberi S, Bashashati A, Shah SP, Morin RD, Marra MA, Savage KJ, Sehn LH, Steidl C, Connors JM, Gascoyne RD, Scott DW. Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell of origin-specific clinical impact. Blood. 2017 May 18;129(20):2760-2770.

Tech K, Tikunov AP, Farooq H, Morrissy AS, Meidinger J, Fish T, Green SC, Liu H, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Vander Heiden MG, Taylor MD, MacDonald J, Gershon TR. Pyruvate kinase inhibits proliferation during postnatal cerebellar neurogenesis and suppresses medulloblastoma formation. Cancer Res. 2017 May 17. pii: canres.3304.2016. doi: 10.1158/0008-5472.CAN-16-3304. [Epub ahead of print]

Thibodeau ML, Reisle C, Zhao E, Martin LA, Alwelaie Y, Mungall KL, Ch’ng C, Thomas R, Ng T, Yip S, Lim H, Sun S, Young SS, Karsan A, Zhao Y, Mungall AJ, Moore RA, Renouf D, Gelmon K, Ma YP, Hayes M, Laskin J, Marra MA, Schrader KA, Jones SJM. Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud. 2017 May 16. pii: mcs.a001628. doi: 10.1101/mcs.a001628. [Epub ahead of print]

Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD. Spatial heterogeneity in medulloblastoma. Nat Genet. 2017 May;49(5):780-788.

Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384.

Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB; Cancer Genome Atlas Research Network., Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell. 2017 Mar 13;31(3):411-423.

Weymann D, Laskin J, Roscoe R, Schader KA, Chia S, Yip S, Cheung WY, Gelmon KA, Karsan A, Renouf DJ, Marra M, Regier DA. The cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers. Mol Genet Genomic Med. 2017 Mar 12;5(3):251-260.

Fishbein L, Leshchiner I, Walter V, Danilova L, Robertson AG, Johnson AR, Lichtenberg TM, Murray BA, Ghayee HK, Else T, Ling S, Jefferys SR, de Cubas AA, Wenz B, Korpershoek E, Amelio AL, Makowski L, Rathmell WK, Gimenez-Roqueplo AP, Giordano TJ, Asa SL, Tischler AS; Cancer Genome Atlas Research Network., Pacak K, Nathanson KL, Wilkerson MD. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell. 2017 Feb 13;31(2):181-193.

Cancer Genome Atlas Research Network. Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175.

Sheffield BS, Tessier-Cloutier B, Li-Chang H, Shen Y, Pleasance E, Kasaian K, Li Y, Jones SJM, Lim HJ, Renouf DJ, Huntsman DG, Yip S, Laskin J, Marra M, Schaeffer DF. Personalized oncogenomics in the management of gastrointestinal carcinomas – Early experiences from a pilot study. Curr Oncol. 2016 Dec;23(6):e571-e575.

Kridel R, Fong FC, Mottok A, Boyle M, Farinha P, Tan K, Meissner B, Bashashati A, McPherson A, Roth R, Shumansky K, Yap D, Ben-Neriah S, Rosner J, Smith MA, Nielsen C, Gine E, Telenius A, Ennishi D, Mungall A, Moore R, Morin RD, Johnson NA, Sehn LH, Tousseyn T, Dogan A, Connors JM, Scott DW, Steidl C, Marra MA, Gascoyne RD, Shah SP. Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study. PLoS Med. 2016 Dec 13;13(12):e1002197.

Topham JT, Marra MA. Sequencing Strategies to Guide Decision Making in Cancer Treatment. PLoS Med. 2016 Dec 6;13(12):e1002189.

Stunnenberg HG; International Human Epigenome Consortium., Hirst M. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 2016 Nov 17;167(5):1145-1149.

Zahir FR, Tucker T, Mayo S, Brown CJ, Lim EL, Taylor J, Marra MA, Hamdan FF, Michaud JL, Friedman JM. Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes. Am J Med Genet A. 2016 Nov;170(11):2916-2926.

LeBlanc VG and Marra MA. DNA methylation in adult diffuse gliomas. Brief Funct Genomics. 2016 Nov;15(6):491-500.

Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun HJ, Pineda G, Morris SR, Mason CN, Geron I, Barrett C, Goff DJ, Wall R, Pellecchia M, Minden M, Frazer KA, Marra MA, Crews LA, Jiang Q, Jamieson CH. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis. Cell Stem Cell. 2016 Aug 4;19(2):177-191.

McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genet. 2016 Jul;48(7):758-767.

Zheng S. Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T. Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu H-T, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, The Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 May 9;29(5): 723-736.

Chun H-Y, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Harvey D, He An, Long W, Goya R, Ng M, LeBlanc VG, Pleasance E, Thiessen N, Wong T, Chuah E, Zhao YJ, Schein JE, Gerhard DS, Taylor MD, Mungall AJ, Moore RA, Ma Y, Jones SJM, Perlman EJ, Hirst M, Marra MA. Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways. Cancer Cell.  2016 Mar 14; 29(3): 394-406.

Jones MR, Schrader KA, Shen Y, Pleasance E, Ch’ng C, Dar N, Yip S, Renouf DJ, Schein JE, Mungall AJ, Zhao Y, Moore R, Ma Y, Sheffield BS, Ng T, Jones SJM, Marra M, Laskin J, Lim H. Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer. Ann Oncol. 2016 Feb 18. pii: mdw060. [Epub ahead of print]

Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28;164(3):550-563.

Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent Clonal Selection Dominates Medulloblastoma at Recurrence. 2016 Jan 21;529(7586):351-357.

Pon JR and Marra MA. MEF2 transcription factors: developmental regulators and emerging cancer genes. Oncotarget. 2016 Jan 19;7(3):2297-2312.

Cancer Genome Atlas Network (Linehan WM). Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma. New Engl J Med. 2016 Jan 14;374(2):135-145.

Pon JR, Marra MA. Clinical correlates of molecular features in diffuse large B-cell lymphoma and and follicular lymphoma. Blood. 2016 Jan 14;127(2):181-186. doi: 10.1182/blood-2015-07-658401.

Chu A, Robertson G, Brooks D, Mungall AJ, Birol İ, Coope R, Ma Y, Jones S, Marra M. Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res. 2016 Jan 8;44(1):e3. doi: 10.1093/nar/gkv808.

Kasaian K, Wiseman SM, Walker BA, Schein JE, Zhao YJ, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJM. The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy. BMC Cancer. 2015 Dec 18;15(1):984.

Perlman EJ, Gadd S, Gerhard DS, Jennings LJ, Arold ST, Huff V, Guidry Auvil JM, Davidsen TM, Dome JS, Meerzaman D, Hsu CH, Nguyen C, Anderson JR, Ma Y, Mungall AJ, Moore RA, Marra MA, Mullighan CG, Ma J, Gastier-Foster JM, Ross N, Smith M. MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nat Commun. 2015 Dec 4;6:10013. doi: 10.1038/ncomms10013.

Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-1025.

Laskin J, Jones S, Aparicio S, Chia S, Ch’ng C, Deyell R, Eirew P, Fok A, Gelmon K, Ho C, Huntsman D, Jones M, Kasaian K, Karsan A, Leelakumari S, Li V, Lim H, Ma Y, Mar C, Martin M, Moore R, Mungall A, Mungall K, Pleasance E, Rassekh S, Renouf D, Shen YQ, Schein J, Schrader K, Tinker A, Zhao E, Yip S, Marra M. Lessons learned from the application of whole genome analysis to the treatment of patients with advanced cancers. Cold Spring Harb Mol Case Stud 1: a000570. 2015 Oct 27.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-519.

LeBlanc VG, Marra MA. Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel). 2015 Sep 23;7(3):1925-1958.

Bose P, Pleasance ED, Jones M, Shen Y, Ch’ng C, Reisle C, Schein JE, Mungall AJ, Moore R, Ma Y, Sheffield BS, Thomson T, Rasmussen S, Ng T, Yip S, Lee CW, Ho C, Laskin J, Marra MA, Jones SJ. Integrative genomic analysis of ghost cell odontogenic carcinoma. Oral Oncol. 2015 Sep;51(9):e71-5.

Pon J, Wong J, Saberi S, Moksa M, Hirst M, Marra MEF2B Mutations in Non-Hodgkin Lymphoma Dysregulate Cell Migration by Decreasing MEF2B Target Gene Activation. Nat Commun. 2015 Aug 6;6:7953. doi: 10.1038/ncomms8953.

Cancer Genome Atlas Network (Brat DJ et al). Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. New Eng J Med. 2015 Jun 25;372(26):2481-2498.

Cancer Genome Atlas Research Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-1696.

Chittaranjan S, Xu J, Kuzyk M, Dullat HK, Wilton J, De Vorkin L, Lebovitz C, Morin GB, Marra MA, Gorski S. The Drosophila TIPE family member Sigmar interacts with the Ste20-like kinase Misshapen and modulates JNK signaling, cytoskeletal remodeling and autophagy. Biol Open. 2015 Apr 2 ;4(5):672-684.

Kasaian K, Chindris A-M, Wiseman SM, Mungall KL, Zeng T, Tse K, Schein JE, Rivera M, Necela BM, Kachergus JM, Casler JD, Mungall AJ, Moore RA, Marra MA, Copland JA, Thompson EA, Smallridge RC, Jones SJM. MEN1 Mutations in Hürthle Cell (Oncocytic) Thyroid Carcinoma. J Clin Endocrinol Metab. 2015 Apr; 100(4): E611-E615.

Sheffield BS, Tinker AV, Shen Y, Hwang H, Li-Chang HH, Pleasance E, Ch’ng C, Lum A, Lorette J, McConnell YJ, Sun S, Jones SJM, Gown AM, Huntsman DG, Schaeffer DF, Churg A, Yip S, Laskin J, Marra MA, Churg A. Personalized Oncogenomics: Clinical Experience with Malignant Peritoneal Mesothelioma Using Whole Genome Sequencing. PLoS ONE. 2015 Mar 23;10(3):e0119689. doi: 10.1371/journal.pone.0119689. eCollection 2015.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Wang J, Sarkar A, Quon G, Kheradpour P, Zhang Z, Heravi-Moussavi A, Wang X, Ward LD, Liu Y, Wu Y-C, Eaton ML, Claussnitzer M, Schultz MD, Ziller MJ, Sandstrom RS, Whitaker JW, Amin V, Coarfa C, Harris RA, Shoresh N, Epstein CB, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Carles A, Eaton ML, Elliott G, Farh K-HFeizi S, Gjoneska E, Karlic R, Kim A-R, Kulkarni A, Li D, Lowdon R, Mercer TR, Neph SJ, Onuchic V, Pfenning A, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong N, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE,  Boyer L, De Jager P, Farnham PJ, Fisher SJ, Haussler D, Jones S, Li W, Marra M, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai L-H, Wang W, Waterland RA, Zhang M, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19;518(7539):317-330.

Eirew P, Ha G, Khattra J, Steif A, Yap D, Gelmon K, Chia S, Wan A, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJL, Lefebre C, Bashashati Al, Edward J, Oloumi A, Osako T, Bruna A, Sandoval J, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall A, Moore R, Zhao YJ, Lorette J, Nguyen L, Huntsman D,  Eaves C, Hansen C, Marra M, Caldas C, Shah SP, Aparicio S. Distinct patterns of genomic clonal evolution in breast cancer patient xenografts. Nature. 2015 Feb 19;518(7539):422-426.

Anglesio MS, Bashashati A, Wang YK, Senz J, Ha G, Yang W, Aniba MR, Prentice LM, Farahani H, Chang HL, Karnezis AN, Marra MA, Yong PJ, Hirst M, Gilks B, Shah SP, Huntsman DG. Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden. J Pathol.  2015 Feb 18. doi: 10.1002/path.4516. [Epub ahead of print]

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O’Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18;6:6351. doi: 10.1038/ncomms7351.

Lim EL, Trinh DL, Scott DW, Chu A, Krzywinski M, Zhao YJ, Robertson AG, Mungall AJ, Schein J, Boyle M, Mottok A, Ennishi D, Johnson NA, Steidl C, Connors JM, Morin RD, Gascoyne RD, Marra MA. Comprehensive miRNA Sequence Analysis Reveals Survival Differences in Diffuse Large B-cell Lymphoma Patients. Genome Biol. 2015 Jan 29;16(1):18. (This article made it to the cover of the journal.)

Genome Atlas Research Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576-582.

Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE. The release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015 Jan 14. pii: gr.185579.114. [Epub ahead of print]

Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB. Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Nat Commun. 2014 Nov 25;5:5442.

Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23;159(3):676-690.

Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. TITAN: Inference of copy number architectures in clonal cell populations from tumor whole genome sequence data. Genome Res. 2014 Nov;24(11):1881-1893.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; the Cancer Genome Atlas Network. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-15549.

Chittaranjan S,  Chan S, Yang C, Yang KC, Chen V,  Moradian A, Firme M, Song J, Go NE, Blough MD, Chan JA, JG Cairncross, Gorski SM, Morin GB, Yip S, Marra MA. Mutations in CIC and IDH1 cooperatively regulate 2-hydroxyglutarate levels and cell clonogenicity. Oncotarget. 2014 Sep 15;5(17):7960-7979. (This article made it to the cover of the journal.)

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-209.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ; The Cancer Genome Atlas Research Network. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-330.

Firme M and Marra MA. The Molecular Landscape of Pediatric Brain Tumours in the Next-generation Sequencing Era. (Review article) Curr Neurol Neurosci Rep. 2014 Sep;14(9):474.

Cancer Genome Atlas Research Network (Collisson EA et al). Comprehensive Molecular Profiling of Lung Adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-550.

Vanner RJ, Remke M, Gallo M, Selvadurai H, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJM, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB. Quiescent Sox2+ cells drive hierarchical growth and relapse in Sonic hedgehog subgroup medulloblastoma. Cancer Cell. 2014 Jul 14;26(1):33-47.

Jamshidi F, Pleasance E, Li Y, Shen  Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao YJ, Schein JE,  Moore RA, Rassekh R, Huntsman DG, Knowling M,  Lim H, Renouf DJ, Jones SJM,Marra MA, Nielsen TO, Laskin J, Yip S. Diagnostic Value of Next-Generation Sequencing in an Unusual Sphenoid Tumor. The Oncologist. 2014 Jun;19(6):623-630.

Tucker T, Zahir F, Griffith M, Delaney A, Chai D, Tsang E, Lemyre E, Dobrzeniecka S, Marra M, Eydoux P, Langlois S, Hamdan F, Michaud J, Friedman J. Single-exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes. Eur J Hum Genet. 2014 Jun;22(6):792-800.

Berg T, Thoene S, Yap D, Wee T, Schoeler N, Rosten P, Lim E, Bilenky M, Mungall AJ, Oellerich T, Lee S,  Lai CK, Umlandt P, Salmi A, Chang H, Yue L, Lai D, Cheng G, Morin RD, Hirst M, Serve SS, Marra MA, Morin GB, Gascoyne RD, Aparicio SA, Humphries RK.  A transgenic mouse model demonstrating the oncogenic role of mutations in the polycomb-group gene EZH2 in lymphomagenesis. Blood. 2014 May 6. [Epub ahead of print]

Ramos P, Karnezis AN, Craig DW, Sekulic A, Russell ML, Hendricks WP, Corneveaux JJ, Barrett MT, Shumansky K, Yang Y, Shah SP, Prentice LM, Marra MA, Kiefer J, Zismann VL, McEachron TA, Salhia B, Prat J, D’Angelo E, Clarke BA, Pressey JG, Farley JH, Anthony SP, Roden RB, Cunliffe HE, Huntsman DG, Trent JM. Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nat Genet. 2014 May;46(5):427-429.

Janbon G, Ormerod KL, Paulet D, Byrnes III EJ, Chatterjee G, Yadav V, Hon C-C, Billmyre RB, Brunel F, Bahn Y-S, Chen W, Chen Y, Chow EWL, Coppée Y-J, Floyd-Averette A, Gaillardin C, Gerik KJ, Goebels C, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh Y-P, Ianiri1 G, Jones S, Kodira CD, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JL, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS. Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet. 2014 Apr 17;10(4):e1004261.

Gunawardana J, Telenius A, Woolcock B, Tan KL, Ben-Neriah S, Chan FC, Lim R, Rogic S, Boyle M, Kridel R, Guiter C, Haioun C, Leroy K, Rimsza LM, Gaulard P, Savage KJ, Connors JM, Marra MA, Shah SP, Gascoyne RD, Steidl C. Recurrent Somatic Mutations of PTPN1 in Primary Mediastinal B cell lymphoma and Hodgkin Lymphoma. Nat Genet. 2014 Apr;46(4):329-335.

Zovoilis A, Mungall A, Moore R, Varhol R, Chu A, Wong T, Marra M, Jones S. The expression level of small non-coding RNAs derived from the first exon of protein coding genes is predictive of cancer status. EMBO Rep. 2014 Apr 1;15(4):402-410.

The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-322.

Shlush LI, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, Kennedy JA, Schimmer AD, Schuh AC, Yee KW, McLeod JL, Doedens M, Medeiros JJ, Marke R, Kim HJ, Lee K, McPherson JD, Hudson TJ; HALT Pan-Leukemia Gene Panel Consortium, Brown AM, Trinh QM, Stein LD, Minden MD, Wang JC, Dick JE. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014 Feb 20;506(7488):328-333.

Mack S, Witt H, Jäger N, Zuyderduyn S, Jones D, Nethery-Brokx K, Garzia L, Zayne K, Wang X, Zichner T, Stütz A, Barszcyzyk M, Pugh T, Wani K, Sill M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Kongkham P, Dubuc A, Northcott P, Shih D, Ramaswamy V, Peacock J, Remke M, Cavalli F, Clarke I, Head R, Creasy C, Verma S, Koster J, Wu X, Bertrand K, Milde T, Zuccaro J, Lau L, Faria C, Castelo-Branco P, Agnihotri S, Roberts S, Fults D, Massimi L, Cho Y-J, Van Meter T, Grajkowska W, Lach B, Kulozik A, Ryzhova M, von Deimling A, Witt O, Scherer S, Fan X, Muraszko K, Kool M, Pomeroy S, Bouffet E, Gupta N, Phillips J, Weiss W, Tabori U, Hawkins C, Rutka J, Korbel J, Lichter J, Bader G, Aldape K, Dirks P, Pfister S, Korshunov A, Piro R, Gu L, Gallo M, Zhang X, Bailey S, Lupien M, Yao Y, Sin-Chan P, Huang A, Hirst M, Marra M, Malkin D, Jabado N, Eils R, Pereira S, Taylor M. Epigenomic Alterations Define Lethal CIMP positive Ependymomas of Infancy. Nature. 2014 Feb 27;506(7489):445-450.

Johnson BE, Mazor T, Hong C, Barnes M, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Aihara J, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao YJ, Moore RA, Mungall AJ, Jones SJM, Hirst M, Marra MA, Mukasa A, Saito N, Aburatani H, Berger MS, Chang SM, Taylor BS, Costello JF. Mutational Analysis Reveals the Origin and Therapy-driven Evolution of Recurrent Glioma. Science. 2014 Jan 10;343(6167):189-193. doi: 10.1126/science.1239947.

Bosdet IE, Docking TR, Butterfield YS, Mungall AJ, Zeng T, Coope RJ, Yorida E, Chow K, Bala M, Young SS, Hirst M, Birol I, Moore RA, Jones SJ, Marra MA, Holt R, Karsan A. A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations. J Mol Diagn. 2013 Nov;15(6):796-809.

Brennan CW, Verhaak RGW, McKenna A, Campos B, Noushmehr H, Salama S, Zheng S, Chakravarty D, Sanborn JZ, Berman HS, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, WK Yung, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O’Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, TCGA Research Network. The Somatic Genomic Landscape of Glioblastoma. Cell. 2013 Oct 10;155(2):462-477.

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct;45(10):1113-1120.

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T. Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 2013 Sep;23(9):1541-1553.

Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O’Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 2013 Sep;23(9):1522-1540.

Bashashati A, Ha G, Tone A, Ding J, Prentice L, Roth A, Rosner J, Shumansky R, Kalloger S, Senz J, Yang W, McConechy M, Melnyk N, Anglesio M, Luk M, Tse K, Zeng T, Moore R, Zhao YJ, Marra M, Gilks B, Yip S, Huntsman D, Sohrab S. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol.  2013 Sep;231(1):21-34.

Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff R, Scott D, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh D, Bolger-Munro M, Taylor G, Khodabakhshi AH, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim E, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and Structural Analysis of Diffuse Large B-cell Lymphoma using Whole Genome Sequencing. Blood. 2013 Aug 15;122(7):1256-1265.

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-49.

Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O’Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 2013 Jul;45(7):836-841.

Kasaian K, Wiseman SM, Thiessen NT, Mungall KL, Corbett RD, Qian JQ,Nip KM, He A, Tse K, Chuah E, Varhol RJ, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao YJ, Hirst M, Marra MA, Walker BA, Jones SJM. Complete Genomic Landscape of a Recurring Sporadic Parathyroid Carcinoma Tumor. J Pathol. 2013 Jul;230(3):249-260.

Cancer Genome Atlas Research Network. Genomic and epigenomic landscape of adult de novo Acute Myeloid Leukemia. N J Engl Med. 2013 May 30;368(22):2059-2074.

Mwenifumbo JC and Marra MA. Cancer genome sequencing study design. Nat Rev Genet. 2013 Apr 18;14(5):321-332. doi: 10.1038/nrg3445.

Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao YJ, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Auvil JM, Gerhard DS, Hogarty MD, Jones SJ, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet. 2013 Mar;45(3):279-284. doi: 10.1038/ng.2529.

The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumors. Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412.

Ha G, Roth A, Lai D, Bashashati A, Ding J, Goya R, Giuliany R, Rosner J, Oloumi A, Shumansky K, Chin S-F, 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 Oct;22(10):1995-2007. doi: 10.1101/gr.137570.112.

The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404.

Northcott PA, Shih DJH, Peacock J, Garzia L, Morrissy S, Stütz AM, Zichner T, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DE, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli F, Wang X, Remke M, Wu X, Chiu RYB, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AGR, Thiessen N, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DTW, Witt H, Fernandez A, Kenney AM, Wechsler-Reya R, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre OO, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho B-K, Kim S-K, Wang K-C, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie YG, Di Rocco C, Massimi L, Michiels EMC, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau L, Van Meir EG, Fouladi M, Cinalli G, Garami M, Hauser P, Saad A, Iolascon A, Zollo M, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Faria CF, Chan J, Levy ML, Sorensen PHB, Meyerson M, Pomeroy SL, Cho Y-J, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJM, Korbel JO, Pfister SM, Marra MA, Taylor MD. Subgroup specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Aug 2;488(7409):49-56.

Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao YJ, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice L, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan S, Griffith M, Moradian A, Cheng SWG, Morin G, Watson P, Gelmon K, Chia S, Chin S-F, Curtis C, Rueda O, Pharoah P, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello J, Meyer IM, Eaves CE, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4;486(7403):395-399. doi: 10.1038/nature10933.

Heravi-Moussavi A, Anglesio MS, Cheng S-WG, Senz J, Yang W, Prentice L, Fejes A, 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, Zhou C, Young RH, Aparicio AS, 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 Non-Epithelial Ovarian Tumors. N Engl J Med. 2012 Jan 19;366(3):234-242.

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.

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.

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.

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 Short-read Transcriptome Sequence Data. Nat Methods. 2010 Nov;7(11):909-912.

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.

Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-1543.

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.

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.

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.

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.

International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010 Apr 15;464(7291): 993-998.

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):730-736.

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 YJ, 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.

Costello JF, Krzywinski M, Marra MA. A first look at the entire human methylomes. Nat Biotechnol. 2009 Dec;27(12):1130-1132.

Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Zhao YJ, Hirst M, Jones S, Marra MA. Next generation tag sequencing for cancer gene expression profiling. Genome Res. 2009 Oct;19(10):1825-1835.

Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao YJ, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution and RNA editing in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-813.

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra M. Circos: an Information Aesthetic for Comparative Genomics. Genome Res. 2009 Sep;19(9):1639-1645.

Shah S, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand K, Leung G, Zayed A, Mehl E, Kalloger S, Sun M, Guiliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao YJ, Zeng T, Glover JNM, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra MA, Huntsman DG. Mutation of the FOXL2 gene in granulosa cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-2729.

Hillier LH, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans. Genome Res. 2009 Apr;19(4):657-666.

Robertson AG, Bilenky M, Tam A, Zhao YJ, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. (first two are first co-authors) Genome wide relationship between histone H3 lysine 4 mono-methylation and transcription factor binding. Genome Res. 2008 Dec;18(12):1906-1917.

Morozova O and Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008 Nov;92(5):255-264.

Robertson AG, Bilenky M, Tam A, Zhao YJ, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. (first two are first co-authors) Genome wide relationship between histone H3 lysine 4 mono-methylation and transcription factor binding. Genome Res. 2008 Dec;18(12):1906-1917.

Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li I, Qian H, Farinha P, Gascoyne RD, Marra MA. Impact of Whole Genome Amplification on Analysis of Copy Number Variants. Nucleic Acids Res. 2008 Aug;36(13):e80.

Morin RD, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM, Marra MA. (first 2 are first co-authors) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008 Jul; 45(1): 81-94.

Morozova O and Marra MA. From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. Biochem Cell Biol. 2008 Apr; 86(2): 81-91.

Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao YJ, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008 Apr;18(4):610-621.

Griffith M. Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT. Marra M. ALEXA – A microarray design platform for alternative expression analysis. Nat Methods. 2008 Feb; 5(2):118.

Krzywinski M, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui A, Jones S, Schein J, Collins C, Marra MA. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol. 2007 Oct 22;8(10):R224.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao YJ, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-657.