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Items: 1 to 50 of 95

1.

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Myers MA, Satas G, Raphael BJ.

Cell Syst. 2019 Jun 26;8(6):514-522.e5. doi: 10.1016/j.cels.2019.05.010. Epub 2019 Jun 19.

PMID:
31229560
2.

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.

Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau DA, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, Wilson RK, Downing JR, Pappo AS, Raphael BJ, Dyer MA, Zhang J.

Mol Cancer Res. 2019 Apr;17(4):895-906. doi: 10.1158/1541-7786.MCR-18-0620. Epub 2019 Jan 16.

PMID:
30651371
3.

Hierarchical HotNet: identifying hierarchies of altered subnetworks.

Reyna MA, Leiserson MDM, Raphael BJ.

Bioinformatics. 2018 Sep 1;34(17):i972-i980. doi: 10.1093/bioinformatics/bty613.

4.

Using controls to limit false discovery in the era of big data.

Parks MM, Raphael BJ, Lawrence CE.

BMC Bioinformatics. 2018 Sep 14;19(1):323. doi: 10.1186/s12859-018-2356-2.

5.

Haplotype phasing in single-cell DNA-sequencing data.

Satas G, Raphael BJ.

Bioinformatics. 2018 Jul 1;34(13):i211-i217. doi: 10.1093/bioinformatics/bty286.

6.

Visible Machine Learning for Biomedicine.

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T.

Cell. 2018 Jun 14;173(7):1562-1565. doi: 10.1016/j.cell.2018.05.056.

7.

Inferring parsimonious migration histories for metastatic cancers.

El-Kebir M, Satas G, Raphael BJ.

Nat Genet. 2018 May;50(5):718-726. doi: 10.1038/s41588-018-0106-z. Epub 2018 Apr 26.

8.

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Zaccaria S, El-Kebir M, Klau GW, Raphael BJ.

J Comput Biol. 2018 Jul;25(7):689-708. doi: 10.1089/cmb.2017.0253. Epub 2018 Apr 16.

9.

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.

10.

Identifying simultaneous rearrangements in cancer genomes.

Oesper L, Dantas S, Raphael BJ.

Bioinformatics. 2017 Nov 27. doi: 10.1093/bioinformatics/btx745. [Epub ahead of print]

11.

Identifying structural variants using linked-read sequencing data.

Elyanow R, Wu HT, Raphael BJ.

Bioinformatics. 2017 Nov 3. doi: 10.1093/bioinformatics/btx712. [Epub ahead of print]

12.

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.

Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N.

Genome Res. 2017 Nov;27(11):1885-1894. doi: 10.1101/gr.220707.117. Epub 2017 Oct 13.

13.

Tumor phylogeny inference using tree-constrained importance sampling.

Satas G, Raphael BJ.

Bioinformatics. 2017 Jul 15;33(14):i152-i160. doi: 10.1093/bioinformatics/btx270.

14.

Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations.

Nakka P, Archer NP, Xu H, Lupo PJ, Raphael BJ, Yang JJ, Ramachandran S.

Cancer Epidemiol Biomarkers Prev. 2017 Oct;26(10):1531-1539. doi: 10.1158/1055-9965.EPI-17-0360. Epub 2017 Jul 27.

15.

Network propagation: a universal amplifier of genetic associations.

Cowen L, Ideker T, Raphael BJ, Sharan R.

Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. Review.

PMID:
28607512
16.

GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyƶ D, Raphael BJ, Wendl MC, Ding L.

Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18.

17.

Complexity and algorithms for copy-number evolution problems.

El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R.

Algorithms Mol Biol. 2017 May 16;12:13. doi: 10.1186/s13015-017-0103-2. eCollection 2017.

18.

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.

19.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, 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; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RGW.

Cancer Cell. 2016 Aug 8;30(2):363. doi: 10.1016/j.ccell.2016.07.013. Epub 2016 Aug 8. No abstract available.

20.

Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases.

Nakka P, Raphael BJ, Ramachandran S.

Genetics. 2016 Oct;204(2):783-798. Epub 2016 Aug 3.

21.

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.

22.

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures.

El-Kebir M, Satas G, Oesper L, Raphael BJ.

Cell Syst. 2016 Jul;3(1):43-53. doi: 10.1016/j.cels.2016.07.004.

23.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, 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; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RGW.

Cancer Cell. 2016 May 9;29(5):723-736. doi: 10.1016/j.ccell.2016.04.002. Erratum in: Cancer Cell. 2016 Aug 8;30(2):363.

24.

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
25.

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.

26.

On the Sample Complexity of Cancer Pathways Identification.

Vandin F, Raphael BJ, Upfal E.

J Comput Biol. 2016 Jan;23(1):30-41. doi: 10.1089/cmb.2015.0100. Epub 2015 Dec 8.

27.

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.

28.

Identification of hierarchical chromatin domains.

Weinreb C, Raphael BJ.

Bioinformatics. 2016 Jun 1;32(11):1601-9. doi: 10.1093/bioinformatics/btv485. Epub 2015 Aug 26.

29.

Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.

Doris SM, Smith DR, Beamesderfer JN, Raphael BJ, Nathanson JA, Gerbi SA.

RNA. 2015 Oct;21(10):1719-30. doi: 10.1261/rna.051144.115. Epub 2015 Aug 17.

30.

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.

31.

Pathway and network analysis of cancer genomes.

Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium.

Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440.

32.

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.

El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ.

Bioinformatics. 2015 Jun 15;31(12):i62-70. doi: 10.1093/bioinformatics/btv261.

33.

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
34.

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.

35.

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

Parks MM, Lawrence CE, Raphael BJ.

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

36.

Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data.

Raphael BJ, Vandin F.

J Comput Biol. 2015 Jun;22(6):510-27. doi: 10.1089/cmb.2014.0161. Epub 2015 Mar 18.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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
50.

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.

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