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Items: 1 to 20 of 51

1.

Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer.

Zhao EY, Shen Y, Pleasance E, Kasaian K, Leelakumari S, Jones M, Bose P, Ch'ng C, Reisle C, Eirew P, Corbett R, Mungall KL, Thiessen N, Ma Y, Schein JE, Mungall AJ, Zhao Y, Moore RA, Den Brok W, Wilson S, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Renouf D, Sun S, Schrader KA, Young S, Bosdet I, Karsan A, Laskin J, Marra MA, Jones SJM.

Clin Cancer Res. 2017 Dec 15;23(24):7521-7530. doi: 10.1158/1078-0432.CCR-17-1941.

PMID:
29246904
2.

Correction: miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer.

Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH.

Oncotarget. 2017 Mar 7;8(10):17406. doi: 10.18632/oncotarget.15921. No abstract available.

3.

Spatial heterogeneity in medulloblastoma.

Morrissy AS, Cavalli FMG, Remke M, Ramaswamy V, Shih DJH, 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 DTW, 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 SJM, Das S, Malkin D, Jabado N, Marra MA, Taylor MD.

Nat Genet. 2017 May;49(5):780-788. doi: 10.1038/ng.3838. Epub 2017 Apr 10.

4.

Putative BRAF activating fusion in a medullary thyroid cancer.

Kasaian K, Wiseman SM, Walker BA, Schein JE, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJ.

Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000729. doi: 10.1101/mcs.a000729.

5.

Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing.

Parker JD, Shen Y, Pleasance E, Li Y, Schein JE, Zhao Y, Moore R, Wegrzyn-Woltosz J, Savage KJ, Weng AP, Gascoyne RD, Jones S, Marra M, Laskin J, Karsan A.

Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000679. doi: 10.1101/mcs.a000679.

6.

miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer.

Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH.

Oncotarget. 2016 May 3;7(18):25930-48. doi: 10.18632/oncotarget.8412. Erratum in: Oncotarget. 2017 Mar 7;8(10 ):17406.

7.

Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer.

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 SJ, Marra MA, Laskin J, Lim HJ.

Ann Oncol. 2016 May;27(5):801-6. doi: 10.1093/annonc/mdw060. Epub 2016 Feb 18.

8.

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.

Chun HE, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Palmquist DL, He A, 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.

Cancer Cell. 2016 Mar 14;29(3):394-406. doi: 10.1016/j.ccell.2016.02.009.

9.

Divergent clonal selection dominates medulloblastoma at recurrence.

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.

Nature. 2016 Jan 21;529(7586):351-7. doi: 10.1038/nature16478. Epub 2016 Jan 13.

10.

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy.

Kasaian K, Wiseman SM, Walker BA, Schein JE, Zhao Y, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJ.

BMC Cancer. 2015 Dec 18;15:984. doi: 10.1186/s12885-015-1955-9.

11.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R.

N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. Epub 2015 Nov 4.

12.

Integrative genomic analysis of ghost cell odontogenic carcinoma.

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.

Oral Oncol. 2015 Sep;51(9):e71-5. doi: 10.1016/j.oraloncology.2015.06.013. Epub 2015 Jul 11. No abstract available.

PMID:
26173781
13.

MEN1 mutations in Hürthle cell (oncocytic) thyroid carcinoma.

Kasaian K, Chindris AM, 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 SJ.

J Clin Endocrinol Metab. 2015 Apr;100(4):E611-5. doi: 10.1210/jc.2014-3622. Epub 2015 Jan 27.

14.

Diagnostic value of next-generation sequencing in an unusual sphenoid tumor.

Jamshidi F, Pleasance E, Li Y, Shen Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao Y, Schein JE, Moore RA, Rassekh R, Huntsman DG, Knowling M, Lim H, Renouf DJ, Jones SJ, Marra MA, Nielsen TO, Laskin J, Yip S.

Oncologist. 2014 Jun;19(6):623-30. doi: 10.1634/theoncologist.2013-0390. Epub 2014 May 7.

15.

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Janbon G, Ormerod KL, Paulet D, Byrnes EJ 3rd, Yadav V, Chatterjee G, Mullapudi N, Hon CC, Billmyre RB, Brunel F, Bahn YS, Chen W, Chen Y, Chow EW, Coppée JY, Floyd-Averette A, Gaillardin C, Gerik KJ, Goldberg J, Gonzalez-Hilarion S, Gujja S, Hamlin JL, Hsueh YP, Ianiri G, Jones S, Kodira CD, Kozubowski L, Lam W, Marra M, Mesner LD, Mieczkowski PA, Moyrand F, Nielsen K, Proux C, Rossignol T, Schein JE, Sun S, Wollschlaeger C, Wood IA, Zeng Q, Neuvéglise C, Newlon CS, Perfect JR, Lodge JK, Idnurm A, Stajich JE, Kronstad JW, Sanyal K, Heitman J, Fraser JA, Cuomo CA, Dietrich FS.

PLoS Genet. 2014 Apr 17;10(4):e1004261. doi: 10.1371/journal.pgen.1004261. eCollection 2014 Apr.

16.

Obligate biotrophy features unraveled by the genomic analysis of rust fungi.

Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kües U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouzé P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F.

Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71. doi: 10.1073/pnas.1019315108. Epub 2011 May 2.

17.

High performance gel imaging with a commercial single lens reflex camera.

Slobodan J, Corbett R, Wye N, Schein JE, Marra MA, Coope RJ.

Rev Sci Instrum. 2011 Mar;82(3):034301. doi: 10.1063/1.3553027.

PMID:
21456768
18.

De novo transcriptome assembly with ABySS.

Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ.

Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15.

PMID:
19528083
19.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ.

Science. 2009 Apr 24;324(5926):522-8. doi: 10.1126/science.1169588.

20.

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.

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