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Results: 1 to 20 of 61

1.

Accurate computation of survival statistics in genome-wide studies.

Vandin F, Papoutsaki A, Raphael BJ, Upfal E.

PLoS Comput Biol. 2015 May 7;11(5):e1004071. doi: 10.1371/journal.pcbi.1004071. eCollection 2015 May.

2.

Detecting non-allelic homologous recombination from high-throughput sequencing data.

Parks MM, Lawrence CE, Raphael BJ.

Genome Biol. 2015 Apr 8;16(1):72. doi: 10.1186/s13059-015-0633-1.

3.

Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data.

Raphael BJ, Vandin F.

J Comput Biol. 2015 Mar 18. [Epub ahead of print]

PMID:
25785493
4.

Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes.

Weinreb C, Oesper L, Raphael BJ.

BMC Genomics. 2014;15 Suppl 6:S4. doi: 10.1186/1471-2164-15-S6-S4. Epub 2014 Oct 17.

5.

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.

PMID:
25501392
6.

Characterization of structural variants with single molecule and hybrid sequencing approaches.

Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3458-66. doi: 10.1093/bioinformatics/btu714. Epub 2014 Oct 28.

PMID:
25355789
7.

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data.

Oesper L, Satas G, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3532-40. doi: 10.1093/bioinformatics/btu651. Epub 2014 Oct 8.

PMID:
25297070
8.

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 MD, 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):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7.

PMID:
25109877
9.

Expanding the computational toolbox for mining cancer genomes.

Ding L, Wendl MC, McMichael JF, Raphael BJ.

Nat Rev Genet. 2014 Aug;15(8):556-70. doi: 10.1038/nrg3767. Epub 2014 Jul 8. Review.

10.

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.

Hajirasouliha I, Mahmoody A, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.

11.

Detecting independent and recurrent copy number aberrations using interval graphs.

Wu HT, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i195-203. doi: 10.1093/bioinformatics/btu276.

12.

Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease.

Brodsky AS, Fischer A, Miller DH, Vang S, MacLaughlan S, Wu HT, Yu J, Steinhoff M, Collins C, Smith PJ, Raphael BJ, Brard L.

PLoS One. 2014 Apr 14;9(4):e94476. doi: 10.1371/journal.pone.0094476. eCollection 2014.

13.

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.

Raphael BJ, Dobson JR, Oesper L, Vandin F.

Genome Med. 2014 Jan 30;6(1):5. doi: 10.1186/gm524. eCollection 2014. Review.

14.

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.

15.

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.

16.

Making connections: using networks to stratify human tumors.

Raphael BJ.

Nat Methods. 2013 Nov;10(11):1077-8. doi: 10.1038/nmeth.2704. No abstract available.

PMID:
24173383
17.

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 MD, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L.

Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634.

18.

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.

Oesper L, Mahmoody A, Raphael BJ.

Genome Biol. 2013 Jul 29;14(7):R80. doi: 10.1186/gb-2013-14-7-r80.

19.

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.

20.

The mutational landscape of adenoid cystic carcinoma.

Ho AS, Kannan K, Roy DM, Morris LG, Ganly I, Katabi N, Ramaswami D, Walsh LA, Eng S, Huse JT, Zhang J, Dolgalev I, Huberman K, Heguy A, Viale A, Drobnjak M, Leversha MA, Rice CE, Singh B, Iyer NG, Leemans CR, Bloemena E, Ferris RL, Seethala RR, Gross BE, Liang Y, Sinha R, Peng L, Raphael BJ, Turcan S, Gong Y, Schultz N, Kim S, Chiosea S, Shah JP, Sander C, Lee W, Chan TA.

Nat Genet. 2013 Jul;45(7):791-8. doi: 10.1038/ng.2643. Epub 2013 May 19.

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