Publications - Marco Marra

2017

 

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.

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 Sep 1;3(5). pii: a001628. doi: 10.1101/mcs.a001628.

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. doi: 10.3747/co.24.3588.

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.

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 Jun 15;77(12):3217-3230.

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.

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.

2016

Sheffield BC, 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.

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

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

Chan CK, Pan Y, Nyberg K, Marra MA, Lim EL, Jones SJM, Maar D, Gibb EA, Robertson AG, Gunaratne PH, Rowat AC. Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour. Open Biol. 2016 Nov;6(11).

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.

Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJ, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJ, Aparicio S, Hirst M, Eaves CJ. Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks. Cell Rep. 2016 Nov 15;17(8):2060-2074.

Gu Z, Churchman M, Roberts K, Li Y, Liu Y, Harvey RC, McCastlain K, Reshmi SC, Payne-Turner D, Iacobucci I, Shao Y, Chen IM, Valentine M, Pei D, Mungall KL, Mungall AJ, Ma Y, Moore R, Marra M, Stonerock E, Gastier-Foster JM, Devidas M, Dai Y, Wood B, Borowitz M, Larsen EE, Maloney K, Mattano LA Jr, Angiolillo A, Salzer WL, Burke MJ, Gianni F, Spinelli O, Radich JP, Minden MD, Moorman AV, Patel B, Fielding AK, Rowe JM, Luger SM, Bhatia R, Aldoss I, Forman SJ, Kohlschmidt J, Mrózek K, Marcucci G, Bloomfield CD, Stock W, Kornblau S, Kantarjian HM, Konopleva M, Paietta E, Willman CL, L Loh M, P Hunger S, Mullighan CG. Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia. Nat Commun. 2016 Nov 8;7:13331. 

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.

Ooms AH, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Huff V, Dome JS, Chi YY, Tian J, Geller JI, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Walz AL, van den Heuvel-Eibrink MM, de Krijger RR, Ross N, Gastier-Foster JM, Perlman EJ. Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group. Clin Cancer Res. 2016 Oct 4. [Epub ahead of print]

Costa S, Regier DA, Meissner B, Cromwell I, Ben-Neriah S, Chavez E, Hung S, Steidl C, Scott DW, Marra MA, Peacock SJ, Connors JM. A time-and-motion approach to micro-costing of high-throughput genomic assays. Curr Oncol. 2016 Oct;23(5):304-313.

Sheffield BS, Fulton R, Kalloger SE, Milne K, Geller G, Jones M, Jacquemont C, Zachara S, Zhao E, Pleasance E, Laskin J, Jones SJM, Marra MA, Yip S, Nelson BH, Gown AM, Ho C, Ionescu DN. Investigation of PD-L1 Biomarker Testing Methods for PD-1 Axis Inhibition in Non-squamous Non–small Cell Lung Cancer. J Histochem Cytochem2016 Oct;64(10):587-600.

Chong LC, Twa DD, Mottok A, Ben-Neriah S, Woolcock BW, Zhao Y, Savage KJ, Marra MA, Scott DW, Gascoyne RD, Morin RD, Mungall AJ, Steidl C. Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas. Blood.  2016 Sep 1;128(9):1206-1213.

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.

Alassiri AH, Ali RH, Shen Y, Lum A, Strahlendorf C, Deyell R, Rassekh R, Sorensen PH,Laskin J, Marra M, Yip S, Lee C-H, Ng TL. ETV6-NTRK3 is expressed in a subset of ALK-negative inflammatory myofibroblastic tumors: case series of 20 patients. Am  J Surg Pathol.  2016 Aug;40(8):1051-1061.

Grinshtein N, Rioseco CC, Marcellus R, Uehling D, Aman A, Lun X, Muto O, Podmore L, Lever J, Shen Y, Blough MD, Cairncross GJ, Robbins SM, Jones SJ, Marra MA, Al-Awar R, Senger DL, Kaplan DR. Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells. Oncotarget. 2016 Jul 18. doi: 10.18632/oncotarget.10661.

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.

Maxson JE, Ries RE, Wang YC, Gerbing RB, Kolb EA, Thompson SL, Guidry Auvil JM, Marra MA, Ma Y, Zong Z, Mungall AJ, Moore R, Long W, Gesuwan P, Davidsen TM, Hermida LC, Hughes SB, Farrar JE, Radich JP, Smith MA, Gerhard DS, Gamis AS, Alonzo TA, Meshinchi S. CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AML. Blood2016 Jun 16;127(24):3094-3098.

Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget.  2016 May 10;7(19):28169-28182.

Zhang 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.

Pan Y, Robertson AG, Pedersen L, Lim E, Hernandez-Herrera A, Rowat A, Chan C, Wen Y, Zhang X, Patil S, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Ma Y, Moore R, Schein J, Mungall A, Pecot C, Sood A, Jones S, Marra M, Gunaratne P.  miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2016 May 3;7(18):25930-25948.

Nielsen JS, Sedgwick C, Shahid A, Zong Z, Brumme ZL, Yu S, Liu L, Kroeger DR, Treon SP, Connors JM, Gascoyne RD, Berry BR, Marra MA, Morin RD, Macpherson N, Nelson BH. Toward personalized lymphoma immunotherapy: Identification of common driver mutations recognized by patient CD8+ T cells. Clin Cancer Res.  2016 May 1;22(9):2226-2236.

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 J, Marra M, Laskin J, Lim H. Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer. Ann Oncol.  2016 May;27(5):801-806.

Craig DW, Nasser S, Corbett R, Chan SK, Murray L, Legendre C, Tembe W, Adkins J, Kim N, Wong S, Baker A, Enriquez D, Pond S, Pleasance E, Mungall AJ, Moore RA, McDaniel T, Ma Y, Jones SJ, Marra MA, Carpten JD, Liang WS. A somatic reference standard for cancer genome sequencingSci Rep. 2016 Apr 20;6:24607.

Pineda G, Lennon KM, Delos Santos NP, Lambert-Fliszar F, Riso GL, Lazzari E, Marra MA, Morris S, Sakaue-Sawano A, Miyawaki A, Jamieson CH. Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche. Sci Rep. 2016 Apr 4;6:23885.

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.

Kasaian K, Wiseman SM, Walker BA, Schein JE, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJ. Putative BRAF activating fusion in a medullary thyroid cancer. Cold Spring Harb Mol Case Stud. 2016 Mar; 2(2): a000729.

Parker JD, Shen Y, Pleasance E, Li Y, Schein JE, Zhao YJ, Moore R, Wegrzyn-Woltosz J, Savage KJ, Weng AP, Gascoyne RD, Jones S, Marra M, Laskin J, Karsan A. Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing. Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000679.

Davis B, Shen Y, Poon CC, Luchman HA, Stechishin OD, Pontifex CS, Wu W, Kelly JJ, Blough MD, Terry Fox Research Institute Glioblastoma Consortium. Comparative genomic and genetic analysis of glioblastoma-derived brain tumor-initiating cells and their parent tumors. Neuro Oncol.  2016 Mar;18(3):350-360.

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. Nature. 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. 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.

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.

2015

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.

Holm F, Hellqvist E, Mason CN, Ali SA, Delos-Santos N, Barrett CL, Chun HJ, Minden MD, Moore RA, Marra MA, Runza V, Frazer KA, Sadarangani A, Jamieson CH. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15444-15449.

Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, Zhao Y, Jones SJ, Marra MA, Underhill TM, Hoodless PA. SOX9 modulates the expression of key transcription factors required for heart valve development. Development. 2015 Dec 15;142(24):4340-4350.

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.

Kridel R, Mottok A, Farinha P, Ben-Neriah S, Ennishi D, Zheng Y, Chavez EA, Shulha HP, Tan K, Chan FC, Boyle M, Meissner B, Telenius A, Sehn LH, Marra MA, Shah SP, Steidl C, Connors JM, Scott DW, Gascoyne RD. Cell-of-origin of transformed follicular lymphoma. Blood2015 Oct 29;126(18):2118-2127.

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. 2015 Oct 27 1: a000570.

Pon JR and Marra MA. MEF2 transcription factors: developmental regulators and emerging cancer genes. (Review). Oncotarget.  2015 Oct 25. doi: 10.18632/oncotarget.6223. [Epub ahead of print]

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 M. MEF2B Mutations in Non-Hodgkin Lymphoma Dysregulate Cell Migration by Decreasing Transcriptional Activation of MEF2B Target Genes. Nat Commun. 2015 Aug 6;6:7953. doi: 10.1038/ncomms8953.

Schmouth JF, Arenillas D, Corso-Diaz X, Xie YY, Bohacec S, Banks KG, Bonaguro RJ, Wong SH, Jones SJ, Marra MA, Simpson EM, Wasserman WW. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. BMC Genomics. 2015 Jul 24;16:545.

Lebovitz CB, Robertson G, Goya R, Jones S, Morin RD, Marra MA, Gorski SM. Cross-cancer profiling of molecular alterations within the human autophagy interaction network. Autophagy. 2015 Jul 24:0. [Epub ahead of print]

Cusulin C, Chesnelong C,  Bose P,  Bilenky M,  Kopciuk K,  Chan JA,  Cairncross JG,  Jones SJ,  Marra MA, Luchman HA, Weiss S.  Precursor States of Brain Tumor Initiating Cell Lines are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes. Stem Cell Reports. 2015 Jul 14;5(1):1-9.

Cancer Genome Atlas Network. 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.

Twa DD, Mottok A, Chan FC, Ben-Neriah S, Woolcock BW, Tan KL, Mungall AJ, McDonald H, Zhao Y, Lim RS, Nelson BH, Milne K, Shah SP, Morin RD, Marra MA, Scott DW, Gascoyne RD, Steidl C. Recurrent genomic rearrangements in primary testicular lymphoma. J Pathol. 2015 Jun;236(2):136-141.

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 Jun;236(2):201-209.

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. pii: BIO20148417.

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.

Sadarangani A, Pineda G, Lennon KM, Chun HY, Shih  A, Schairer AE, Court AC, Goff DJ, Prashad SL, Geron I, Wall R, McPherson JD, Moore RA, Pu M, Bao L, Jackson-Fisher A, Munchhof M, VanArsdale T, Reya T, Morris SR, Minden MD, Messer K, Mikkola HK, Marra MA, Hudson TJ, Jamieson CH. GLI2 inhibition abrogates human leukemia stem cell dormancy. J Transl Med. 2015 Mar 21;13(1):98.

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.

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 Mar;25(3):445-458.

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.

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.

Walz AL, Ooms A, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Bowlby R, Brooks D, Ma Y, Mungall AJ, Moore RA, Schein J, Marra MA, Huff V, Dome JS, Chi YY, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Jafari N, Ross N, Gastier-Foster JM, Perlman EJ. Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors. Cancer Cell. 2015 Feb 9;27(2):286-97. doi: 10.1016/j.ccell.2015.01.003.

Chan FC, Telenius A, Healy S, Ben-Neriah S, Mottok A, Lim R, Drake M, Hu S, Ding J, Ha G, Scott DW, Kridel R, Bashashati A, Rogic S, Johnson N, Morin RD, Rimsza LM, Sehn L, Connors JM, Marra MA, Gascoyne RD, Shah SP, Steidl C. An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup. Blood. 2015 Feb 5;125(6):959-966.

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 (Hayes D et al). Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576-582.

Kulic I, Robertson G, Chang L, Baker JH, Lockwood WW, Mok W, Fuller M, Fournier M, Wong N, Chou V, Robinson MD, Chun HJ, Gilks B, Kempkes B, Thomson TA, Hirst M, Minchinton AI, Lam WL, Jones S, Marra M, Karsan A. Loss of the Notch effector RBPJ promotes tumorigenesis. J Exp Med. 2015 Jan 12;212(1):37-52.

2014

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-delivered 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.

Pon JR, Marra MA. Driver and Passenger Mutations in Cancer. Annu Rev. Pathol. 2014 Oct 17. [Epub ahead of print]

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.

Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Garside V, Bilenky M, Griffith M, Morrissy AS, Robertson G, Thiessen N, Zhao YJ, Chen Q, Pan D, Jones SJM, Marra MA, Hoodless PA. Hippo Signalling Influences HNF4 and FOXA2 Enhancer Switching During Hepatocyte Differentiation. Cell Reports. 2014 Oct 9;9(1):261-271.

Cancer Genome Atlas Research Network. 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.

Dias C, Rupps R, Millar B, Choi K, Marra M, Demos M, Kratz LE, Boerkoel CF. Desmosterolosis: An illustration of diagnostic ambiguity of cholesterol synthesis disorders. Orphanet J Rare Dis. 2014 Jun 25;9(1):94. 

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 Genet2014 Jun;22(6):792-800.

Chang AC, Garside VC, Fournier M, Smrz J, Vrljicak P, Umlandt P, Fuller M, Robertson G, Zhao Y, Tam A, Jones SJ, Marra MA, Hoodless PA, Karsan A. A Notch-dependent transcriptional hierarchy promotes mesenchymal transdifferentiation in the cardiac cushion. Dev Dyn. 2014 Jul;243(7):894-905.

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.

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 Jun 19;123(25):3914-3924.

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.

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.

2013

Vojvodic M, Hansford LM, Morozova O, Blakely KM, Taylor P, Fathers KE, Moffat J, Marra M, Smith KM, Moran MF, Kaplan DR. A Phosphoproteomics Approach to Identify Candidate Kinase Inhibitor Pathway Targets in Lymphoma-Like Primary Cell Lines. Curr Drug Discov Technol. 2013 Dec;10(4):283-304.

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. doi: 10.1038/ng.2764.

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. doi: 10.1002/path.4230. 

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.

The Cancer Genome Atlas Research Network. Integrative analysis of genomic and molecular alterations in clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. doi: 10.1038/nature12222.

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):836-41. doi: 10.1038/ng.2649.  

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):249-60. doi: 10.1002/path.4203.

Wei W, Hou J,  Alder O, Ye X Lee S, Cullum R, Chu A, Zhao YJ, Warner SM, Knight DA, Yang D, Jones SJM, Marra MA, Hoodless PA. Genome-wide microRNA and mRNA profiling in mouse liver development implicates mir302b and mir20a in repressing TGFβ signaling. Hepatology. 2013 Jun;57(6):2491-2501.   

The Cancer Genome Atlas Network. The genomic and epigenomic landscape of adult de novo Acute Myeloid Leukemia. N J Engl Med. 2013 May 30;368(22):2059-2074. doi: 10.1056/NEJMoa1301689.

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

Lim E, Marra M. MicroRNA dysregulation in B-cell non-Hodgkin lymphoma. Blood Lymphat Cancer: Targets and Therapy. 2013 May 2013; 3: 25-40.

Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113.

Trinh DL, Scott DW, Morin RD, Mendez-Lago M, An J, Jones SJM, Mungall AJ, Zhao YJ, Schein J, Steidl C, Connors JM, Gascoyne RD, Marra MA. Analysis of FOXO1 mutations in Diffuse Large B-Cell Lymphoma. Blood. 2013 May 2;121(8):3666-3674.doi:10.1182blood-2013-01-479865.

Meissner B, Kridel R, Lim RS, Rogic S, Tse K, Scott DW, Moore R, Mungall AJ, Marra MA, Connors JM, Steidl C, Gascoyne RD. The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma.  (Brief Report) Blood. 2013 Apr 18;121(16):3161-3164.doi:10.1182blood-2013-01-478834.

Nolte SM, Venugopal C, McFarlane N, Morozova O, Hallett RM, O’Farrell E, Manoranjan B, Murty NK, Klurfan P, Kachur E, Provias JP, Hassell JA, Marra M, Singh SK. A cancer stem cell model for studying brain metastases from primary lung cancer. J Natl Cancer I2013 Apr 17;105(8):551-62. doi: 10.1093/jnci/djt022.

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 are associated with fluorouracil resistance in colorectal cancer. Pharmacogenomics J. 2013 Apr;13(2):148-158. doi: 10.1038/tpj.2011.65.

Dubuc AM, Remke M, Korshunov A, Northcott PA, Zhan S, Mendez-Lago M, Kool M, Jones DTW, Unterberger A, Morrissy AS, Shih D, Peacock J, Ramaswamy V, Rolider A, Witt H, Hielscher T, Hawkins C, Vibhakar R, Croul S, Rutka JT, Weiss WA, Jones SJM, Eberhart CG, Marra MA, Pfister SM, Taylor MD. Aberrant Patterns of H3K4 and H3K27 Histone Lysine Methylation Occur Across Subgroups in Medulloblastoma. Acta Neuropathol2013 Mar;125(3):373-384. doi: 10.1007/s00401-012-1070-9.

Tennant BR, Robertson AG, Beach M, Li L, Zhang X, Zhan SH, Whiting CJ, Kim A, Gottardo R, Marra MA, Jones SJM, Hoodless PA, Hoffman BG. Identification and analysis of permissive enhancers in pancreatic islets.  Diabetologia2013 Mar;56(3):542-552. doi: 10.1007/s00125-012-2797-5.

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 genomic landscape of high-risk neuroblastoma. Nat Genet. 2013 Mar;45(3):279-284. doi: 10.1038/ng.2529.

Goff DJ, Recart AC, Sadarangani A, Chun HJ, Barrett CL, Krajewska M, Leu H, Low-Marchelli J, Ma W, Shih AY, Wei J, Zhai D, Geron I, Pu M, Bao L, Chuang R, Balaian L, Gotlib J, Minden M, Martinelli G, Rusert J, Dao KH, Shazand K, Wentworth P, Smith KM, Jamieson CA, Morris SR, Goldstein LS, Hudson TJ, Marra M, Frazer KA, Pellecchia M, Reed JC, Jamieson CH. A Pan-BCL2 Inhibitor Renders Bone-Marrow-Resident Human Leukemia Stem Cells Sensitive to Tyrosine Kinase Inhibition. Cell Stem Cell. 2013 Mar 7;12(3):316-328. doi: 10.1016/j.stem.2012.12.011.

Chand D, Yamazaki Y, Ruuth K, Schönherr C, Martinsson T, Kogner P, Attiyeh EF, Maris J, Morozova O, Marra MA, Ohira M, Nakagawara A, Sandström P-E, Palmer RH, Hallberg B. Cell culture and Drosophila model systems define three classes of anaplastic lymphoma kinase mutations in neuroblastoma. Dis. Model. Mech. 2013 Mar;6(2):373-382. doi: 10.1242/dmm.010348.

Jiang Q, Crews LA, Barrett CL, Chun H-J, Court AC, Isquith JM, Zipeto MA, Goff DJ, Minden M, Sadarangani A, Rusert JM, Dao K-HT, Morris SR, Goldstein LSB, Marra MA, Frazer KA, Jamieson CHM. ADAR1 Promotes Malignant Progenitor Reprogramming in Chronic Myeloid Leukemia. Proc Natl Acad Sci USA. 2013 Jan 15;110(3):1041-1046. doi: 10.1073/pnas.1213021110.

2012

Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJM, Zhao YJ, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC.  Poly-gene Fusion Transcripts and Chromothripsis in Prostate Cancer. Gene Chromosome Canc. 2012 Dec;51(12):1144-1153. doi: 10.1002/gcc.21999.

Cheng SWG, Kuzyk MA, Moradian A, Ichu T-A, Chang VCD, Tien JF, Vollett SE, Griffith G, Marra MA, Morin GB. The interaction of CDK12/CrkRS with CYCLIN K1 is required for the phosphorylation of the C-terminal domain of RNA Pol II.  Mol Cell Biol. 2012 Nov;32(22):4691-4704. doi: 10.1128/MCB.06267-11.

Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors  JM, Gascoyne RD, Marra MA, Birol I, Jones SJM. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012 Nov;3(11):1308-1319.

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

Tsang E, Rupps R, Friedman JM, McGillivray B, Eydoux P, Marra M, Zahir F. Life-history Chronicle for a Patient with the Recently Described Chromosome 4q21 Microdeletion Syndrome. Am J Med Genet. 2012 Oct;158A(10):2606-9. doi: 10.1002/ajmg.a.35568.

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. 

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 Oct 11;31(41):4434-4446..

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.

Krzywinski M, Birol I, Jones S, Marra M. Hive Plots – Rational Approach to Visualizing Networks. Brief Bioinform. 2012 Sep;13(5):627-644.

Crisan A, Goya R, Ha G, Ding J, Prentice LM, Oloumi A, Senz J, Zeng T, Tse K, Delaney A, Marra MA, Huntsman DG, Hirst M, Aparicio S, Shah S. Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with Co-NAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors. PLoS One. 2012;7(8):e41551. doi: 10.1371/journal.pone.0041551.

Roberts KG, Morin R, Zhang J, Hirst M, Zhao YJ, Su X, Chen S-C, Payne-Turner D, Churchman M, Chen X, Harvey R, Kasap C, Yan C, Becksfort J, Finney R, Teachey D, Maude S, Tse K,  Moore R, Jones S, Mungall K, Birol I, Edmonson M, Hu Y, Buetow K, Chen I-M, Carol W, Wei L, Ma J, Kleppe M, Levine R, Garcia-Manero G, Larsen E, Shah N, Devidas M, Reaman G, Smith M, Paugh S, Evans W, Grupp S, Jeha S, Pui C-H, Gerhard D, Downing J, Willman C, Loh M, Hunger S, Marra M, Mullighan C. Novel genetic alterations activating kinase and cytokine receptor signaling in high risk acute lymphoblastic leukemia. Cancer Cell. 2012 Aug 14;22(2):153-166.

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.

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;7(7):e40815.

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.

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. 2012 Jul 15;28(14):1923-1924.

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 YJ, 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 May 3. doi: 10.1002/path.4047.

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 Jun;71(6):845-9. doi: 10.1002/ana.23610.

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, Lücke1 T, Bokenkamp A, Marra MA, van Lohuizen M, Lewis DB, Shaw C, Boerkoel CF. Penetrance of SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. Hum Mol Genet. 2012 Jun 1;21(11):2572-2587.

Schuetz JM, Johnson NA, Morin RD, Scott DW, Tan K, Ben-Nierah S, Boyle M, Slack GW, Marra MA, Connors JM, Brooks-Wilson AR, Gascoyne RD. BCL2 mutations in diffuse large B-cell lymphoma. Leukemia. 2011 Dec 22. doi: 10.1038/leu.2011.378.

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 24;119(21):4949-4952.

Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Fazli L, Hurtado-Coll A, Butterfield YS, 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 case of hybrid and aggressive prostate cancer. J Pathol. 2012 May;227(1):53-61. doi: 10.1002/path.3987.

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. Genet Med. 2012 May;14(5):520-6. doi: 10.1038/gim.2011.26.

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.

Roth A, Morin R, Ding J, 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 DataBioinformatics. 2012 Apr 1;28(7):907-913.

Chu JS, Johnsen RC, Chua SY, Tu D, Dennison M, Marra M, Jones SJ, Baillie DL, Rose AM.  Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs. Genetics. 2012 Apr;190(4):1225-1233.

Dubuc AM, Morrissy AS, Kloosterhof NK, Northcott PA, Yu EP, 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;123(4):485-499. doi: 10.1007/s00401-012-0959-7.

Northcott PA, Shih DJH, Remke M, Cho Y-J, 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 Apr;123(4):615-626.

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. Mol Cancer Ther. 2012 Mar;11(3):775-83.

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 Mar 1;119(9):1963-1971.

Mo F, Wyatt A, Wu C, Lapuk A, Marra M, Gleave M, Volik S, Collins C. Next generation sequencing of  prostate tumours provides independent evidence of XMRV contamination. J Clin Microbiol. 2012 Feb;50(2):536-537.

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.

Lee CH, Ou WB, 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 SJ, Marra MA, Shah SP, van de Rijn M, Huntsman DG, Dal Cin P, Debiec-Rychter M, Nucci MR, Fletcher JA. 4-3-3 Fusion Oncogenes in High-grade Endometrial Stromal Sarcoma. Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):929-934.

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. 2012 Jan 15;18(2):167-175.

Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ,  Eydoux P, Babul-Hirji R, Chitayat D, An J, Marra MA, FORGE Canada Consortium, Boycott KM, Weaver DD, Jones SJ. Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet. 2012 Jan 13;90(1):110-118. 

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 YJ, Mungall AJ, Jones SJM, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC mutations, IDH mutations and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol. 2012 Jan;226(1):7-16.doi: 10.1002/path.2995.

2011

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 Sep 22;118(12):3350-3358.

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.

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 23;108(34):13999-14004.

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.

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.

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.

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.

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.

McPherson AW, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MGF, Griffith M, Heravi-Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SdeFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.  PLOS Comput Biol. 2011 May;7(5):e1001138.

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.

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.

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.

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.

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.

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.

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.

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.

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.

2010

Hirst M, Marra MA. Next Generation Sequencing Based Approaches to Epigenomics. Brief Funct Genomics. 2010 Dec;9(5-6):455-465.

The modENCODE Consortium. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-1797.

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.

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.

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.

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.

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.

Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ. Cell. 2010 Oct 29;143(3):367-378.

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.

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.

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.

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 Methods2010 Oct;7(10):843-847.

Romanuik TL, Wang G, Morozova O, Delaney A, Marra MA, Sadar MD. LNCaP Atlas: Gene expression associated with in vivo progression to castration-recurrent prostate cancer. BMC Med Genomics. 2010 Sep 24;3(1):43.

Smith KM, Datti A, Fujitani M, Grinshtein N, Zhang L, Morozova O, Blakely KM, Rotenberg SA, Hansford LM, Miller FD, Yeger H, Irwin MS, Moffat J, Marra MA, Baruchel S, Wrana JL, Kaplan DR. Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens. EMBO Mol Med. 2010 Sep;2(9):371-384.

Morozova O, Vojvodic M, Grinshtein N, Hansford L, Blakely K, Maslova A, Hirst M, Cezard T, Morin R, Moore R, Smith K, Miller F, Taylor P, Thiessen N, Varhol R, Zhao YJ, Jones S, Moffat J, Kislinger T, Moran M, Kaplan D, Marra M. Systems-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma. Clin Cancer Res. 2010 Sep 15;16(18):4572-4582.

Petriv OI, Kuchenbauer F, Delaney AD, Lecault V, White A, Kent D, Marmolejo L, Heuser M, Berg T, Copley M, Ruschmann J, Sekulovic S, Antignano F, Kuroda E, Ho V, Benz C, Halim T, Giambra V, Krystal G, Takei CJF, Weng AP, Eaves C, Piret J, Marra MA, Humphries RK, Hansen CL. Comprehensive microRNA Expression Profiling of the Hematopoietic Hierarchy. Proc Natl Acad Sci USA2010 Aug 31;107(35):15443-15448.

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.

Cheung KJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE. High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer. 2010 Aug;49(8):669-681.

Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao YJ, Hirst M, Verchere B, Helgason CD, Marra MA, Jones SJM, Hoodless PA. H3K4me1 Profiles Distinguish Functional Classes of Transcription Factor Binding Sites. Genome Res.  2010 Aug;20(8):1037-1051. 

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.

Wong RTF, Flibotte S, Corbett R, Saeedi P, Jones SJM, Marra MA, Schein JE, Birol I. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Transactions on Automation Science and Engineering. 2010 Jul; 7(3): 706-708.

Flibotte S ,Edgley ML, Chaudhry I,Taylor J, Neil SE, Rogula A,  Zapf R, Hirst M, Butterfield Y, Jones SJ,  Marra MA, Barstead RJ, Moerman DG. Whole-Genome profiling of mutagenesis in Caenorhabditis elegans. Genetics2010 Jun;185(2):431-441.

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.

Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod. 2010 Jul;16(7):463-471.

Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Feb 23;11(1):131.

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. (Featured in News and Views, Nat Genet.  2010 Feb;42(2):100-101.)  

Vrljicak P, Chang A, Morozova O, Wederell E, Niessen K, Marra M, Karsan A, Hoodless P. Genomic Analysis Distinguishes Phases of Early Development of the Mouse Atrio-Ventricular Canal. Physiol Genomics. 2010 Feb 4;40(3):150-157.

Starczynowski DT, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, Hirst M, Hogge D, Marra M, Wells RA, Buckstein R, Lam W, Humphries RK, Karsan A. Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype. Nat Med. 2010 Jan;16(1):49-58.

2009

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

The MGC Project Teams. The Completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-2333.

Biernaskie J, Paris M, Morozova O, Fagan BM, Marra M, Pevny L, Miller FD. SKPs derive from hair follicle precursors and exhibit properties of adult dermal stem cells. Cell Stem Cell. 2009 Dec 4;5(6):610-623.

Lehman AM, Friedman JM, Zahir FH,  Eydoux P, Marra MA, Prisman L, Tsang E, Armstrong L. A characteristic syndrome associated with microduplication of 8q12, inclusive of CHD7. Eur J Med Genet. 2009 Nov-Dec;52(6):436-439.

Birol I, Jackman S, Nielsen C, Qian J, Varhol R, Stazyk G, Zhao YJ, Hirst M, Schein J, Horsman D, Connors J, Gascoyne R, Marra M, Jones S. De novo Transcriptome Assembly with AbySS. Bioinformatics. 2009 Nov 1;25(21):2872-2877.

Friedman JM,  Adam S, Arbour L,  Armstrong L, Baross A, Birch P, Boerkoel C, Chan S, Chai D, Delaney AD, Flibotte S,  Gibson WT, Langlois S,  Lemyre E, Li HI, MacLeod P, Mathers J, Michaud JL, McGillivray BC, Patel MS, Qian H,  Rouleau GA, Van Allen MI,  Yong S-L,  Zahir FR,  Eydoux P, Marra MA. Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500K SNP array genomic hybridization. BMC Genomics. 2009 Nov 16;10:526.

Romanuik TL, Wang G, Holt RA, Jones SJM, Marra MA, Sadar MD. Identification of novel androgen-responsive genes by deep sequencing of LongSAGE libraries. BMC Genomics. 2009 Oct 15;10(1):476.  

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.

DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo assembly of a genome sequence for the filamentous fungus, Grosmannia clavigera, assembled using Sanger, 454 and Illumina sequence data. Genome Biol. 2009 Sep 11;10(9):R94.

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.

Halaschek-Wiener J, Amirabbasi-Beik M, Monfared N, Pieczyk M, Sailer C, Kollar A, Turnbull R, Agalaridis G, Yamada S, Oliveira L, Collins J, Meneilly G, Marra MA, Madden KM, Le ND, Connors JM, Brooks-Wilson AR. Genetic variation in healthy oldest-old. PloS One. 2009 Aug 14;4(8):e6641.

Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet. 2009;10:135-151.

Pugh T, Keyes M,  Barclay L, Delaney A,  Krzywinski M, Thomas D, Yang C,  Agranovich A, McKenzie M, Morris WJ, Moore M, Marra MA. Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients. Clin Cancer Res. 2009 Aug 1;15(15):5008-5016. 

Tucker T, Marra M, Friedman JM. Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine. Am J Hum Genet. 14 Aug 2009;85(2):142-154.

Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Alvarado AS, Kim JK, Rajewsky N. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11546-11551. 

Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM,  Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet. 2009 Jun;5(6):e1000537.

 

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.

Wang X, Zhao JY, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics. 2009 May 9;10:213. 

Zahir FR, Langlois S, Gall K, Eydoux P, Marra MA, Friedman JM. A novel de novo 1.1 Mb duplication of 17q21.33 associated with cognitive impairment and other anomalies. Am J Med Genet A. 2009 Jun;149A(6):1257-62.

Bovine Genome Sequencing and Analysis Consortium (incl Holt RA, Jones SJ, Marra MA, Moore R). The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-528. 

Kent DG, Copley MR, Benz C, Wöhrer S, Dykstra BJ, Ma E, Cheyne J, Zhao YJ, Bowie M, Zhao Y, Gasparetto M, Delaney A, Smith C, Marra M, Eaves CJ.  New Candidate Regulators of Hematopoietic Stem Cells with High Self-renewal Activity. Blood. 2009 Apr 17.

Hillier LH, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans. Genome Res2009 Apr;19(4):657-666.  

McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol. 2009;Mar 15;327(2):551-565.

Hirst M and Marra MA. Epigenetics and human disease. Int J Biochem Cell Biol. 2009 Jan;41(1):136-146. 

 

2008

Robertson AG, Bilenky M. Tam A, Zhao YJ, Zeng T. Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Eukirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM (first two are first co-authros). 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. (#1 most downloaded article from Genomics for 2008).

Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008 Nov;18(11):1787-1797. 

Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, and Slukvin I. Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis. Exp Hematol. 2008 Oct;36(10):1377-1389.

Ralph SG, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJM, Marra MA. Douglas CJ, Ridland K, Bohlmann. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics. 2008 Oct 14;9(1):484.

Morozova O, Morozov V, Hoffman B, Helgason CD, Marra MA. A seriation approach for visualization-driven discovery of co-expression pattern in Serial Analysis of Gene Expression (SAGE) data. PLOS ONE. 2008 Sep 12;3(9):e3205.

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. 

Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA. Global Analysis of In Vivo FoxA2 Binding Sites in Mouse Adult Liver Using Massively Parallel Sequencing. Nucleic Acids Res.  2008 Aug;36(14):4549-64. Epub 2008 Jul 8.

D'Souza CA, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y, Lee LLC, Bilenky M, Portales-Casamar E, He A, Wasseman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJM. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008 Jul 14;9(1):66.

Shin H, Hirst M, Bainbridge M, Magrini V, Mardis E, Moerman DG, Marra MA. Baillie DL, Jones SJM. Transcriptome analysis of C. elegans on novel expressed sequence tags (ESTs). BMC Biology. 2008 Jul 8;6(1):30.

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

Raouf A, Zhao Y, To K, Stingl HJ, Delaney A, Barbara M, Iscove N, Jones S, McKinney S, Emerman J, Aparicio S, Marra M, Eaves C. Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell. 2008 Jul 3;3(1):109-118. 

Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Hoodless PA, Jones S, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol. 2008 Jun 14;9(6):R99. 

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

Zahir F, Baross A, Delaney AD, Eydoux P, Ferdinandez ND, Marra M. Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1a. J Med Genet. 2008 Apr;45(4):239-243. Epub 2007 Dec 5.

Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao Y, 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;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;5(2):118.

Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J. Analysis of 6,464 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics. 2008;9(1):57.

2007

Zahir F, Baross A, Delaney AD, Eydoux P, Ferdinandez ND, Marra M, Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1a. J Med Genet. 2007.

Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martínez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table Grape (Muscat Hamburg) and discovery of new candidate genes with possible roles in berry development. Gene. 2007;402(1-2):40-50.

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 A. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol. 2007;8(10):R224.

Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA. Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. BMC Bioinformatics. 2007;8(1):368.

Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O’Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ. Identification and analysis of internal promoters in Caenorhabditis elegans operons. Genome Res. 2007;17(10):1478-1485.

Stratford AL, Habibi G, Astanehe A, Jiang H, Hu K, Park E, Shadeo A, Buys TP, Lam W, Pugh T, Marra M, Nielsen TO, Klinge U, Mertens PR, Aparicio S, Dunn SE. Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer providing a potential target for therapy. Breast Cancer Res. 2007;99(5):R61.

Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastis D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, Mckay S, Okada HM, Pan J, Shultz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High Throughput In Vivo Analysis of Gene Expression in C. Elegans. PloS Biology. 2007;5(9):e237.

Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol. 2007;8(8):R165.

Hou J, Charters AM, Lee SC, Zhao Y, Wu MK, Jones SJM, Marra MA , Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev Biol. 2007;7(1):92.

Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol. 2007;42(8):825-39.

Pugh TJ, Bebb G, Barclay L, Sutcliffe M, Fee J, Salski C, O’Connor R, Ho C, Murray N, Melosky B, English J, Vielkind J, Horsman D, Laskin JJ, Marra MA. Correlations of EGFR mutations and increases in EGFR and copy number to gefitinib response in a retrospective analysis of lung cancer patients. BMC Cancer. 2007;7(1):128.

Etchberger JF, Lorch A, Sleumer M, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Dev. 2007;21(31):1653-1674.

Hu G, Linning R, Joseph C, McCallum B, Banks T, Cloutier S, Butterfield Y, Liu J, Kirkpatrick R, Stott J, Yang G, Smailus D, Jones S, Marra M, Schein J, Bakkeren G. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Mol Plant Pathol. 2007;8(4):451-467.

Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Mokda M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu A-L, Pandoh P, McDonald H, Asano J, Dhalla N,Ma K, Lee S, Ally A, Chalal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of 9 human embryonic stem cell lines. Genome Biol. 2007;8(6):R113.

Margulies EH, Coope GM, Asimenos G, Thomas DJ, Dewey CN, Siepe A, Birney E, Keepe D, Schwart AS, Hou M, Taylot J, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Schuler G, Church D, Rosenbloom KR, Kent J, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center,Washington University Genome Sequencing Center, Broad Institute. UCSC Genome Browser Team, British Columbia Cancer Agency Genome Sciences Centre (Field MA, Moore RA, Mathewson CA, Schein JE,and Marra MA), et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007;17(6):760-774.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, 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;4(8):651-657.

Zahir F, Firth HV, Baross A, Delaney AD, Eydoux P, Gibson WT, Langlois S, Martin H, Willat L, Marra M, Friedman JM. A Novel Deletion14q11.2 Syndrome Identified By Array Genomic Hybridization. J Med Genet. 2007.

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD,Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform and Broad Institute Whole Genome Assembly Team and , Marshall Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, and Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007;447(7141):167-177.

Kelleher CT, Chiu R. Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Pradhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J. 2007.

Rhesus Macaque Genome Sequencing and Analysis Consortium (incl Jones SM, Marra MA, and Schein JE). Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-234.

Zhao Y, Raouf A, Kent D, Khattra J, Delaney A, Schnerch A, Asano J, MacDonald H, Chan C, Jones S, Marra MA, Eaves CJ. A modified PCR-LongSAGE protocol identifies novel transcripts in human CD34+ bone marrow cells. Stem Cells. 2007.

McGhee JD. Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 2007;302(2):627-645.

Quayle SN, Heidi H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJM, Marra MA, Sadar MD. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007;8:32.

McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD,Yang G, Stott JM, Schein JE. Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis D. The complete genome of Rhodococcus sp. RHA1: insights into a catabolic powerhouse. Proc Natl Acad Sci USA. 2006;103(42):15582-15587.

Bainbridge M, Warren R, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis E, Sadar M, Siddiqui A, Marra M, Jones S. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006;7:246.

Menten B, Buysse K, Zahir F, Hellemans J, Hamilton SJ, Costa T, Fagerstrom C, Anadiotis G, Kingsbury D, McGillivray BC, Marra MA, Friedman JM, Speleman F, Mortier G. Osteopoikilosis, short stature and mental retardation as key features of a new microdeletion syndrome on 12q14. BJ Med Genet. 2007 Jan 12.

Robertson N, Oveisi-Fordorei M, Zuyderduyn S, Varhol R, Fjell C, Marra MA, Jones SJM, Siddiqui AS. DiscoverySpace: an interactive data analysis application. Genome Biol. 2007;8(1):R6.

2006

Khattra J, Delaney AD, Zhao Y, Siddiqui A, Hirst M, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu A, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Jones S, Holt R, Hoodless P, Marra MA. Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells and cell lines. Genome Res. 2006 Dec 22;7(12):R126.

Chen N, Mah A, Blacque OE, Chu J, Phgora K, Bakhoum MW, Newbury CRH, Khattra J, Chan S, Go A, Efimenko E, Johnsen R, Phirke P, Swoboda P, Marra M, Moerman DG, Leroux MR, Baillie DL, Stein LD. Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol. 2006;7(12):R126.

Lonergan KM, Chari R, deLeeuw RJ, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam WL. Identification of Novel Lung Genes in Bronchial Epithelium by Serial Analysis of Gene Expression. Am J Respir Cell Mol Biol. 2006;35(6):651-661.

Sea Urchin Genome Sequencing Consortium (incl. I. Bosdet, Shin H, Schein J and Marra MA). The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science. 2006;314(5801):941-952.

Tuskan GA, DiFazio SP, Hessten U, Jansson S, Rombauts S, Putnam N, Sterck L, Bohlmann J, Schein J, Ralph S, Aets A, Bhalerao R, Bhalerao P, Blaudez D, 85 other authors, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313(5793):1596-1604.

Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006;79(3):500-513.

Bakkeren G, Jiang G, Warren R, Butterfield Y, Shin H, Chiu R, Linning R, Schein J, Lee N, Hu G, Kupfer DM, Tang Y, Roe BA, Jones S, Marra M, Kronstad JW. Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals. Fungal Genet Biol. 2006;43(9):655-666.

Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J. Conifer defense against iInsects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell Environ. 2006;29(8):1545-1570.

Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJM, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006;34(12):e83.

Wang G, Jones SJM, Marra MA, Sadar MD. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 2006 Jun 5;7311-7323.

Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, 35 other authors, Marra MA, Jones SJM, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis. Genome Res. 2006;16(6):796-803.

Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJM. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 2006;16:768-775.

Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, 15 other authors, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpa x deltoids) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Mol Ecol. 2006;15(5):1275-1297.

Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, Holt RA. Identification by full coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 2006;16(2):173-182.

2005

Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, 38 other authors, Marra M. A mouse altas of gene expression: Large-scale digital gene expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci USA. 2005;102(51):18485-18490.

Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, Chiu R, Schein JE, Marra MA, Womack JE, Lewin HA. A high-resolution whole-genome cattle-human comparative map reveals new details of mammalian chromosome evolution. Proc Natl Acad Sci USA. 2005;102(51):18526-18531.

Larraya LM, Boyce K, So A, Steen BR, Jones S, Marra M, Kronstad J. Serial Analysis of Gene Expression Reveals Conserved Links Between Protein Kinase A, Ribosome Biogenesis and Phosphate Metabolism in Ustilago maydis. Eukaryot Cell. 2005;4(12):2029-2043.

Pavy N, Paule C, Parsons L, Crow JA, Morency M-J, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics. 2005;6:144.

Smailus DE, Marziali A, Dextras P, Marra MA, Holt RA. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing. Genome Res. 2005;15:1447-1450.

Ng SHS, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJM, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005;86(4):396-404.

Ivens AC, Peacock C, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Marra M et al. The Genome of the Kinetoplastid parasite, Leishmania major. Science. 2005;309(5733):436-442.

Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 Mutants using Serial Analysis of Gene Expression. Genome Res. 2005;15(5)603-615.

Blacque OE, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJM, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional Genomics of the Cilium, A Sensory Organelle. Curr Biol. 2005;15(10):935-941.

Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. Management and Visualization of Whole Genome Shotgun Assemblies using SAM. Biotechiques. 2005;38:715-720.

Hillier LW, Graves TA, 110 other authors, Marra MA et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005;434(7034):724-731.

Lian TS, Simmer M, D’Souza CD, Steen BR, Zuyderduyn S, Jones S, Marra M, Kronstad J. Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Mol Microbiol. 2005;55(5):1452-1472>.

Loftus B, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamethevan J, Miranda M, Anderson I, Fraser JA, Allen J, Bosdet I, Brent MR, Chiu R, Doering TL, Donlin, MJ, D’Souza C. Fox DS, Grinberg V, Fu J, Fukushima M, Haas B, Huang JC, Janbon G, Jones S, Krzywinski MI, Kwon-Chung J, Lengeler KB, Maiti R, Marra M et al. The genome and transcriptone of Cryptococcus neoformans, a basidiomycetous fungal pathogen of humans. Science. 2005;307(5713):1321-1324.

Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA. High-throughput Sequencing: A Failure Mode Analysis. BMC Genomics. 2005;6(1):2.

2004

Hirst M, Astell C, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Paetzel M. A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columbia. Emerg Infect Dis. 2004;10(12):2192-2195.

Warren R, Hsiao WWL, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Butterfield Y, Schein JE, Shin H, Khattra J, Smailus D, Holt R, Siddiqui A, Jones S, Marra M, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional characterization of catabolic plasmid from PCB-degrading Rhodococcus sp. RHA1. J Bacteriol. 2004;186(22)7783-7795.

The ENCODE Project Consortium (including Marra M). The ENCODE (ENCyclopedia of DNA Elements) Project. Science. 2004;306(5696):636-640.

The MGC Project Team (including Marra M). The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Res. 2004;(10B):2121-2127.

Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Siddiqui A, Jones S, Holt R, Marra M. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Res. 2004(10B):2083-2092.

Anglesio MS, Evdokimova V, Melnyk N, Zhang L, Fernandez CV, Grundy PE, Leach S, Marra MA, Brooks-Wilson AR, Penninger J, Sorensen PHB. Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilm’s tumor versus normal kidney. Hum Mol Genet. 2004;13(18):2061-2074.

Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Tsai M, Albertson D, Lam W, Choy C-O, Osoegawa K, Zhao S, de Jong P, Schein J, Jones S, Marra M. A Set of BAC Clones Spanning the Human Genome. Nucleic Acids Res. 2004;32(12):3651-3660.

Flibotte S, Chiu R, Fjell C, Krzywinski M, Schein JE, Shin Heesun, Marra MA. Automated ordering of fingerprinted clones. Bioinformatics. 2004;20(8):1264-1271.

MacAulay C, Lonergan K, Chi B, Zuyderduyn S, Shein J, Tsao M, LeRiche J, Jones S, Marra M, Lam S, Lam WL. Serial analysis of gene expression profiles of developmental stages in non-small cell lung carcinoma. Chest. 2004;125(5 Suppl):97S.

Henderson L-J, Okamoto I, Lestou VS, Robichaud M, Chhanabhai M, Gascoyne RD, Klasa RJ, Connors JM, Marra MA, Horsman DE, Lam WL. Delineation of a minimal region of deletion at 6q16.3 in follicular lymphoma and construction of a BAC contig spanning a 6 megabase region of 6q16-q22. Genes Chromosomes Cancer. 2004;40:60-65.

Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, 39 other authors, Marra M, Schein J. Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome. Genome Res. 2004;14(4):766-779.

Baross A, Schertzer M, Zuyderduyn SD, Jones SJM, Marra MA, Lansdorp PM. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer. 2004 Apr;39(4):298-310.

Rat Genome Sequencing Project Consortium (including Marra M). Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Nature. 2004;428(6982):493-521.

Ishkanian AS, Malloff C, Watson S, deLeeuw R, Chi B, Coe B, Albertson DG, Pinkel D, Marra M , Ling V, MacAulay C, Lam WL. A tiling resolution DNA Microarray with complete coverage of the human genome. Nat Genet. 2004;36(3):299-303.

Rise ML, von Schalburg KR, Brown GD, Mawer, MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SRM, Smailus DE, Jones SJM, Schein J, Marra MA, Butterfield YSN, Stott J, Ng SHS, Davidson WS, Koop BF. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Intespecific Hybridization Characteristics. Genome Res. 2004;14:478-490.

McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M et al. Gene Expression Profiling of Cells, Tissues and Developmental Stages of the Nematode C. elegans. Cold Spring Harb Symp Quant Biol. 2004;159-169.

Kingsley D, Zhu B, DeJong P, Schein J, Marra M, Peichel K, Amemiya C, Schluter D, Balabhadra S, Friedlander B, Cha YM, Dickson M, Grimwood J, Schmutz J, Talbot WS, Myers R. New genomic tools for molecular studies of evolutionary change in sticklebacks. Behavior. 2004;141:1331-1344.

2003

Steen BR, Zuyderduyn S, Toffaletti DL, Marra M, Jones SJM, Perfect JR, Kronstad J. Analysis of Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot Cell. 2003;2(6):1336-1349.

Stein LD, Bao Z, Blasier D, Blumenthal T, Brent M, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fulton L, Fulton R, Griffiths-Jones S, Harris T, Hillier L, Kamath R, Kuwabara P, Marra M et al. The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biol. 2003;1(2):E45.

Boon K, Edwards JB, Siu I-M, Olschner D, Eberhart CG, Marra MA, Strausberg RL, Riggins GJ. Comparison of Medulloblastoma and Normal Neural Transcriptomes Identifies a Restricted Set of Activated Genes. Oncogene. 2003;22(48):7687-7694.

Hillier LW, Fulton RS, 72 other authors, Marra MA et al. The DNA sequence of human chromosome 7. Nature. 2003;424(6945):157-164.

Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE) - A tool for visualizing clone fingerprint maps. Genome Res. 2003;13(6):1244-1249.

Pleasance ED, Marra MA, Jones SJM. Assessment of SAGE in transcript identification based on a new method of tag-to-gene mapping. Genome Res. 2003;13(6):1203-1215.

Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A et al. The genome sequence of the SARS-associated coronavirus. Science. 2003;300(5624):1399-1404.

Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003;13(5)940-953.

Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Jones SJM, Marra MA. A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death. Curr Biol. 2003;13(4):358-363.

S.S. Moore, C. Hansen, J.L. Willimans, A. Fu, Y. Meng, C. Li, Y Zhang, B.S.D. Urquhart, Marra M, J Schein, B. Benkel, P. J. de Jong, K. Osoegawa, B.W. Kirkpatrick and C.A. Gill. A comparative map of bovine chromosome 19 based on a combination of mapping on a bacterial artificial chromosome scaffold map, a whole genome radiation hybrid panel and the human draft sequence. Cytogenet Genome Res. 2003;102:32-38.

2002

Mammalian Gene Collection Program Consortium (including Marra M). Generation and initial analysis of more than 14,000 non-redundant, full-length human and mouse cDNA sequences by the NIH Mammalian Gene Collection Program. Proc Natl Acad Sci USA. 2002;99(26):16899-16903.

Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu A, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on the MegaBACE 1000 automated sequencer. Biotechniques. 2002;33:532-4,536,538-539.

Steen BR, Lian T, Zuyderduyn S, MacDonald K, Marra M, Jones SJM, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 2002;12:1386-1400.

Schein J, Tangen K, Chiu R, Shin H, Lengeler KB, MacDonald K, Bosdet I, Heitman J, Jones SJM, Marra M, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002;12:1445-53.

Gregory SG, Sekhon M, 83 other authors, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature. 2002; 418:743-750.

Mattman A, Huntsman D, Lockitch G, Langlois S, Buskard N, Ralston D, Butterfield Y, Rodrigues P, Jones S, Porto G, Marra M, De Sousa M, Vatcher G. Transferrin Receptor 2 (TFR2) and HFE Mutational Analysis in Non-C282Y Iron Overload:Identification of a Novel TfR2 mutation associated with Iron Overload and Leukopenia. Blood. 2002;100:1075-1077.

Butterfield YSN, Marra MA, Asano JK, Chan SY, Guin R, Kryzwinski MI, Lee SS, MacDonald KWK, Mathewson CA, Olson TE, Pandoh PK, Prabhu A, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJM. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res. 2002;30:2460-2468.

Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res. 2002;1;30:2469-2477.

Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJM. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002;18:484-485.

Gorski S, Marra M. Programmed cell death takes flight: Genetic and genomic approaches to gene discovery in Drosophila. Physiol Genomics. 2002; 9:59-69.

2001

Cai W-W, Chow C-W, Damani S, Gregory SG, Marra M, Bradley A. An SSLP marker-anchored BAC framework map of the mouse genome. Communication. Nat Genet. 2001;29:133-134.

Clark MD, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson, SL. An oligonucleotide fingerprint normalised and Expressed Sequence Tag characterised zebrafish cDNA library. Genome Res. 2001;11:1594-1602.

Jones SJM, Riddle D, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. Changes in gene expression associated with developmental arrest and longevity in C. elegans. Genome Res. 2001;11:1346-1352.

Gower NJD, Temple GR, Schein JE, Marra M, Walker DS, Baylis HA. Dissection of the promoter region of the inositol 1,4,5-trisphosphate receptor gene, itr-1, in C. elegans: A molecular basis for cell-specific expression of IP3R isoforms. J Mol Biol. 2001;306(2):145-157.

McPherson JD, Marra M et al. A physical map of the human genome. Nature. 2001; 409:934-941.

The International Human Genome Sequencing Consortium (including Marra M). Initial sequencing and analysis of the human genome. Nature. 2001;409:860-921.

Wendl MC, Marra MA, Hillier LW, Chinwalla AT, Wilson RK, Waterston RH. Theories and applications for sequencing randomly selected clones. Genome Res. 2001;11:274-280.

2000

The Arabidopsis Genome Initiative (including Marra M). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796-815.

Kazusa DNA Research Institute, the Cold Spring Harbor and Washington University Sequencing Consortium, the European Union Arabidopsis Genome Sequencing Consortium and Institute of Plant Genetics and Crop Plant Research (IPK). Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 2000;408:823-826.

Loging WT, Lal A, Siu IM, Loney TL, Wikstrand CJ, Marra MA, Prange C, Bigner DD, Strausberg RL, Riggins GJ. Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening. Genome Res. 2000;10(9):1393-1402.

Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, Brown MR, Buetow KH, Chuaqui RF, Cole KA, Duray PH, Englert CR, Gillespie JW, Greenhut S, Grouse L, Hillier LW, Katz KS, Klausner RD, Kuznetzov V, Lash AE, Lennon G, Linehan WM, Liotta LA, Marra MA, Munson PJ, Ornstein DK, Prabhu VV, Prange C, Schuler GD, Soares MB, Tolstoshev CM, Vocke CD, Waterston RH. Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications. Am J Pathol. 2000;156(4):1109-1115.

Aamodt E, Shen L, Marra M, Schein J, Rose B and McDermott J. Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae. Gene 2000;243:67-74.

The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000;100:377-386.

1999

The European Union Arabidopsis Genome Sequencing Consortium, The Cold Spring Harbor, Washington University in St. Louis, and PE Biosystems Arabidopsis Sequencing Consortium. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999;402:769-776.

Copenhaver GP, Nickel K, Kuromori T, Benito M-I, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, McCombie WR, Martienssen RA, Marra M, Preuss D. Genetic definition and sequence analysis of Arabidopsis centromeres. Science. 1999;286:2468-2474.

Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak N, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A Public Database for Gene Expression in Human Cancers. Cancer Res. 1999;59: 5403-5407.

Ellsworth RE, Ionasescu V, Searby C, Sheffield VC, Braden VV, Kucaba TA, McPherson JD, Marra MA, Green ED. The CMT2D Locus: Refined genetic position, construction of a bacterial-based physical map, and evidence of allelic heterogeneity with distal spinal muscular atrophy. Genome Res. 1999;9:568-574.

Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gun C, McCombie WR, McDonald K, McPherson J, Mudd N, Parnell L, Schein J, Seim R, Shelby P, Waterston R, Wilson R. A map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet. 1999;22:265-270.

Mozo T, Dewar K, Dunn P, Ecker J, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet. 1999;22:271-275.

The C. elegans Genome Sequencing Consortium, Washington University Genome Sequencing Center, St. Louis U.S.A. and the Sanger Centre, Hinxton, U.K. How the worm was won: The C. elegans genome sequencing project. Trends Genet. 1999;15:51-58.

Marra M, Hillier L, K et al. An encyclopedia of mouse genes. Nat Genet. 1999;21:191-194.

Marra MA, Kucaba TA, Hillier LW, Waterston RH. High-throughput plasmid DNA purification for three cents per sample. Nucleic Acids Res. 1999;27:e37 (1-6).

Thacker C, Marra MA, Jones A, Baillie DL, Rose AM. Functional genomics in Caenorhabditis elegans: an approach involving comparisons of sequences from related nematodes. Genome Res. 1999;9:348-359.

Streit A, Li W, Robertson B, Schein J, Kamal IH, Marra M, Wood WB. Homologs of the Caenorhabditis elegans Masculinizing Gene her-1 in C. briggsae and the Filarial Parasite Brugia malayi. Genetics. 1999;152:1573-1584.

Vatcher GP, Barbazuk WB, O'Neil NJ, Marra MA, Ha T, Baillie DL. Identification and characterization of a serine hydroxymethyltransferase isoform in Caenorhabditis briggsae. Gene. 1999;230:137-144.

1998

The Sanger Centre and the Washington University Genome Sequencing Center. Toward a complete human genome sequence. Genome Res. 1998; 8:1097-1108.

The C. elegans Genome Sequencing Consortium (incl Marra M), Washington University Genome Sequencing Center, St. Louis U.S.A., and the Sanger Center, Hinxton, U.K. Genome sequence of the nematode Caenorhabditis elegans. A platform for investigating biology. Science. 1998;282:2012-2018.

Manger ID, Hehl A, Parmley S, Sibley LD, Marra MA. Hillier L, Waterston RH, Boothroyd JC. Expressed sequence tag analysis of the bradyzoite stage of toxoplasma gondii: Identification of developmentally regulated gene. Infect Immun. 1998;66:1632-1637.

Ajioka J, Boothroyd JC, Brunk BP, Hehl L, Manger ID, Overton GC, Marra MA. Roos D, Wan KL, Waterston RH, Sibley LD. Gene discovery by EST sequencing to toxoplasma gondii reveals sequences restricted to the apicomplexa. Genome Res. 1998;8:18-28.

Marra MA, Hillier L, Waterston RH. Expressed sequence tags - ESTablishing bridges between genomes. Trends Genet. 1998;14:4-7.

1997

Marra MA, Kucaba TK, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH. High throughput fingerprint analysis of large-insert clones. Genome Res. 1997;7:1072-1084.

Chissoe SL, Marra MA, Hillier L, Brinkman R, Wilson RK, Waterston RH. Representation of cloned genomic sequences in two sequencing vectors: Colleration of DNA sequence and subclone distribution. Nucleic Acids Res. 1997;25:2960-2966.

1996

Marra MA, Weinstock LA, Mardis ER. End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res. 1996;6:1118-1122.

Hillier L, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W, Hawkins M, Hultman M, Kucaba T, Lacy M, Le M, Le N, Mardis E, Moore B, Morris M, Parsons J, Prange C, Rifkin L, Rohlfing T, Schellenberg K, Soares MB, Tan F, Thierry-Mieg J, Trevaskis E, Underwood K, Wohldman P, Waterston R, Wilson RK, Marra MA. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 1996 Sep;(6)9:807-828.

1994

Marra MA, Baillie DL. Recovery of duplications by drug resistance selection in Caenorhabditis elegans. Genome. 1994;37:701-705.

McKim KS. Mathewson C, Marra MA, Wakarchuk MF, Baillie DL. The Caenorhabditis elegans unc-60 gene encodes proteins homologous to a family of actin-binding proteins. Mol Gen Genet. 1994;242:346-357. 

1993

Schein JE, Marra MA, Benien GM, Fields C, Baillie DL. The use of deficiencies to determine essential gene content in the let-56 - unc-22 region of Caenorhabditis elegans. Genome. 1993;36:1148-1156.

Marra MA, Prasad SS, Baillie DL, Molecular analysis of two genes between let-653 in the unc-22(IV) region of C. elegans. Mol Gen Genet. 1993;236:289-298.

 

Book Chapters

Tucker T, Marra M, Friedman, JM. Massively Parallel Sequencing. Molecular Analysis & Genome Discovery, Second Edition. Edited by Ralph Rapley and Stuart Harbron.  2012 John Wiley & Sons, Ltd. Published 2012 by John Wiley & Sons, Ltd. 

Morrissy AS,  Zhao YJ, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Pradhu A-L, Tam A, Hirst M, Marra M. Tag-seq: Next generation tag sequencing for gene expression profiling. 2010. Tag-based Approaches for Next Generation Sequencing. Part 1. Chapter 14.  Wiley-VCH, Germany.  In press

Morin RD, Zhao YJ, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra MA.  Preparation and Analysis of MicroRNA Libraries Using the Illumina Massively Parallel Sequencing Technology. RNAi and microRNA-Mediated Gene Regulation in Stem Cells. Methods in Molecular Biology, Zhang, Baohong, Stellwag, Edmund J. (Eds.). 1st Edition. 2010 Sep. Vol 650 Section III, pp 173-199. 

Morrissy SA, Zhao YJ, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Prabhu A-L, Tam A, Hirst M, Marra MA. Digital Gene Expression by Tag Sequencing on the Illumina Genome Analyzer. Curr Protoc Hum Genet. 2010 Apr; Chapter 11:Unit 11.11.1-36.

Pugh TJ and Marra MA. Trisomy 9. Encyclopedia of Molecular Mechanisms of Disease. 2008.

Petrescu AS and Marra MA. Genomic approaches for identifying mammalian cis-encoded antisense transcripts. Res Adv Nucleic Acids Res. 2, 2008.

Delaney AD, Qian H, Friedman JM, Marra MA. Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation. Curr Protoc Hum Genet. 2008 Oct; Chapter 8: Unit 8:13.

Griffith M and Marra MA. Alternative expression analysis: Experimental and bioinformatic approaches for the analysis of transcript diversity. Genes, Genomes and Genomics. Thangadurai D, Tang W, Papavassiliou AG, Anupama M (eds), Regency Publications New Delhi, India, 2007; Vol 2, pp. 199-250.

Mathewson CA, Schein JE, Marra MA. Large-scale BAC clone restriction digest fingerprinting. Curr Prot Human Genet. D. Smith (ed) John Wiley and Sons, Inc., Hoboken, NJ, 26 Apr 2007;pp. 5.19.1-5.19.21.

Halaschek-Weiner JV, Marra MA, Brooks-Wilson AR. (2005) Gene Expression Analysis in Pharmacogenetics and Pharmacogenomics. Pharmacogenomics 2nd Edition. Kalow W, Meyer UA, Tyndale RF (eds) Marcel Dekker Inc. New York, USA, Vol. 156, pp. 389-406.

Astell CR, Holt RA, Jones SJM, Marra MA.(2005) Genome Organization and Structural Aspects of the SARS-related Virus. Adv Infect Dis. Schmidt A, Wolff MH, Weber O (eds), Birkhauser Verlag, Basel, Switzerland, Vol. I, pp. 101-128.

Schein J, Kucaba T, Sekhon M, Smailus D, Waterston R, Marra M.(2004) High throughput BAC fingerprinting. Meth Mol Biol. Zhao S, Stodolsky M (eds), Humana Press, Clifton, NJ, Vol. 255, pp. 143-156.

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