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Items: 20

1.

Genetic Mechanisms of Immune Evasion in Colorectal Cancer.

Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U.

Cancer Discov. 2018 Jun;8(6):730-749. doi: 10.1158/2159-8290.CD-17-1327. Epub 2018 Mar 6.

PMID:
29510987
2.

The Integrated Genomic Landscape of Thymic Epithelial Tumors.

Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC; Cancer Genome Atlas Network, Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ.

Cancer Cell. 2018 Feb 12;33(2):244-258.e10. doi: 10.1016/j.ccell.2018.01.003.

PMID:
29438696
3.

Precision Oncology: The Road Ahead.

Senft D, Leiserson MDM, Ruppin E, Ronai ZA.

Trends Mol Med. 2017 Oct;23(10):874-898. doi: 10.1016/j.molmed.2017.08.003. Epub 2017 Sep 5. Review.

PMID:
28887051
4.

A weighted exact test for mutually exclusive mutations in cancer.

Leiserson MD, Reyna MA, Raphael BJ.

Bioinformatics. 2016 Sep 1;32(17):i736-i745. doi: 10.1093/bioinformatics/btw462.

5.

Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Leiserson MD, Wu HT, Vandin F, Raphael BJ.

Genome Biol. 2016 Aug 2;17(1):168. No abstract available.

6.

Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.

Leiserson MD, Vandin F, Wu HT, Raphael BJ.

Nat Genet. 2016 Feb;48(2):106-8. doi: 10.1038/ng.3491. No abstract available.

PMID:
26813760
7.

Patterns and functional implications of rare germline variants across 12 cancer types.

Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L.

Nat Commun. 2015 Dec 22;6:10086. doi: 10.1038/ncomms10086.

8.

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.

9.

CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Leiserson MD, Wu HT, Vandin F, Raphael BJ.

Genome Biol. 2015 Aug 8;16:160. doi: 10.1186/s13059-015-0700-7. Erratum in: Genome Biol. 2016;17(1):168.

10.

MAGI: visualization and collaborative annotation of genomic aberrations.

Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ.

Nat Methods. 2015 Jun;12(6):483-4. doi: 10.1038/nmeth.3412. No abstract available.

PMID:
26020500
11.

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.

Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS, Gonzalez-Perez A, Tamborero D, Cheng Y, Ryslik GA, Lopez-Bigas N, Getz G, Ding L, Raphael BJ.

Nat Genet. 2015 Feb;47(2):106-14. doi: 10.1038/ng.3168. Epub 2014 Dec 15.

12.

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM.

Cell. 2014 Aug 14;158(4):929-944. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7.

13.

Integrated analysis of germline and somatic variants in ovarian cancer.

Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L.

Nat Commun. 2014;5:3156. doi: 10.1038/ncomms4156.

14.

Network analysis of GWAS data.

Leiserson MD, Eldridge JV, Ramachandran S, Raphael BJ.

Curr Opin Genet Dev. 2013 Dec;23(6):602-10. doi: 10.1016/j.gde.2013.09.003. Epub 2013 Nov 26. Review.

15.

Mutational landscape and significance across 12 major cancer types.

Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L.

Nature. 2013 Oct 17;502(7471):333-339. doi: 10.1038/nature12634.

16.

Simultaneous identification of multiple driver pathways in cancer.

Leiserson MD, Blokh D, Sharan R, Raphael BJ.

PLoS Comput Biol. 2013;9(5):e1003054. doi: 10.1371/journal.pcbi.1003054. Epub 2013 May 23.

17.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ Jr, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G.

N Engl J Med. 2013 May 30;368(22):2059-74. doi: 10.1056/NEJMoa1301689. Epub 2013 May 1. Erratum in: N Engl J Med. 2013 Jul 4;369(1):98.

18.

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.

Gallant A, Leiserson MD, Kachalov M, Cowen LJ, Hescott BJ.

BMC Bioinformatics. 2013 Jan 18;14:23. doi: 10.1186/1471-2105-14-23.

19.

Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.

Leiserson MD, Tatar D, Cowen LJ, Hescott BJ.

J Comput Biol. 2011 Nov;18(11):1399-409. doi: 10.1089/cmb.2011.0191. Epub 2011 Sep 1.

20.

Evaluating between-pathway models with expression data.

Hescott BJ, Leiserson MD, Cowen LJ, Slonim DK.

J Comput Biol. 2010 Mar;17(3):477-87. doi: 10.1089/cmb.2009.0178.

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