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Items: 1 to 20 of 101

1.

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.

2.

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.

3.

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.

PMID:
29906441
4.

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.

PMID:
29700472
5.

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.

PMID:
29658782
6.

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
7.

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]

8.

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]

PMID:
29112732
9.

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.

10.

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.

11.

Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma.

Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu; Cancer Genome Atlas Research Network.

Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007.

12.

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.

13.

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
14.

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, Fenyö 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.

15.

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.

16.

Integrated genomic characterization of oesophageal carcinoma.

Cancer Genome Atlas Research Network; Analysis Working Group: Asan University; BC Cancer Agency; Brigham and Women’s Hospital; Broad Institute; Brown University; Case Western Reserve University; Dana-Farber Cancer Institute; Duke University; Greater Poland Cancer Centre; Harvard Medical School; Institute for Systems Biology; KU Leuven; Mayo Clinic; Memorial Sloan Kettering Cancer Center; National Cancer Institute; Nationwide Children’s Hospital; Stanford University; University of Alabama; University of Michigan; University of North Carolina; University of Pittsburgh; University of Rochester; University of Southern California; University of Texas MD Anderson Cancer Center; University of Washington; Van Andel Research Institute; Vanderbilt University; Washington University; Genome Sequencing Center: Broad Institute; Washington University in St. Louis; Genome Characterization Centers: BC Cancer Agency; Broad Institute; Harvard Medical School; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University; University of North Carolina; University of Southern California Epigenome Center; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Genome Data Analysis Centers: Broad Institute; Brown University:; Harvard Medical School; Institute for Systems Biology; Memorial Sloan Kettering Cancer Center; University of California Santa Cruz; University of Texas MD Anderson Cancer Center; Biospecimen Core Resource: International Genomics Consortium; Research Institute at Nationwide Children’s Hospital; Tissue Source Sites: Analytic Biologic Services; Asan Medical Center; Asterand Bioscience; Barretos Cancer Hospital; BioreclamationIVT; Botkin Municipal Clinic; Chonnam National University Medical School; Christiana Care Health System; Cureline; Duke University; Emory University; Erasmus University; Indiana University School of Medicine; Institute of Oncology of Moldova; International Genomics Consortium; Invidumed; Israelitisches Krankenhaus Hamburg; Keimyung University School of Medicine; Memorial Sloan Kettering Cancer Center; National Cancer Center Goyang; Ontario Tumour Bank; Peter MacCallum Cancer Centre; Pusan National University Medical School; Ribeirão Preto Medical School; St. Joseph’s Hospital &Medical Center; St. Petersburg Academic University; Tayside Tissue Bank; University of Dundee; University of Kansas Medical Center; University of Michigan; University of North Carolina at Chapel Hill; University of Pittsburgh School of Medicine; University of Texas MD Anderson Cancer Center; Disease Working Group: Duke University; Memorial Sloan Kettering Cancer Center; National Cancer Institute; University of Texas MD Anderson Cancer Center; Yonsei University College of Medicine; Data Coordination Center: CSRA Inc; Project Team: National Institutes of Health.

Nature. 2017 Jan 12;541(7636):169-175. doi: 10.1038/nature20805. Epub 2017 Jan 4.

17.

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.

18.

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.

19.

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.

20.

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.

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