PubMed | Google Scholar | DBLP

publications

This list of publications is almost definitely out of date.
Recent lists of publications are available at Google Scholar, PubMed, or DBLP.

Preprints and In press

  • structured-anomalies Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies

    U. Chitra, K. Ding, J.C.H. Lee, B.J. Raphael

    ICML 2021 [In Press]

    arXiv preprint Software

2022

Journal Articles

  • PASTE Alignment and Integration of Spatial Transcriptomics Data

    R. Zeira, M. Land, A. Strzalkowski, B.J. Raphael

    Nature Methods (May. 16, 2022).

    Publication Software

2021

Conference Proceedings

  • CND-aliquoting Genome Halving and Aliquoting under the Copy Number Distance

    R. Zeira, G. Mon, B.J. Raphael

    WABI 2021, LIPIcs (July 22, 2021)

    Publication

    Software

2020

Journal Articles

  • STARCH STARCH: Copy number and clone inference from spatial transcriptomics data

    R. Elyanow, R. Zeira, M. Land, B.J. Raphael

    Physical Biology 18 035001 (Oct 2020)

    Publication

    Software

  • WCND Copy number evolution with weighted aberrations in cancer

    R. Zeira, B.J. Raphael

    ISMB 2020, Bioinformatics (July 13, 2020).

    Publication Software

  • SBMClone Identifying tumor clones in sparse single-cell mutation data

    M.A. Myers*, S. Zaccaria*, B.J. Raphael

    ISMB 2020, Bioinformatics (July 13, 2020).

    Publication Software

  • SCARLET Single-cell tumor phylogeny inference with copy-number constrained mutation losses

    G Satas, S Zaccaria, G Mon, BJ Raphael

    RECOMB 2020 [In Press]

    bioRxiv (Nov. 26, 2019). doi.org/10.1101/840355

    bioRxiv preprint Software

  • NetMix NetMix: A network-structured mixture model for less biased identification of altered subnetworks

    M.A. Reyna*, U. Chitra*, R Elyanow, BJ Raphael

    RECOMB 2020, Journal of Computational Biology (May 20, 2021)

    Publication Software

  • HATCHet Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

    S Zaccaria and BJ Raphael

    bioRxiv (Dec. 17, 2018) doi.org/10.1101/496174

    bioRxiv preprint Software

  • RCK Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

    S Aganezov, BJ Raphael

    bioRxiv (Feb. 25, 2019)

    bioRxiv preprint Software

  • ICGCPCAWGNetworks Pathway and network analysis of more than 2,500 whole cancer genomes

    M.A. Reyna, …, J. Reimand, J.M. Stuart, B.J. Raphael on behalf of the PCAWG Drivers and Functional Annotation Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes

    bioRxiv (Aug. 7, 2018) doi.org/10.1101/385294

    bioRxiv preprint

  • netNMF-sc netNMF-sc: Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis

    R Elyanow, B Dumitrascu, B Engelgardt, BJ Raphael

    Genome Research (Jan. 28, 2020).

    Publication Software

  • AMLStJudesBlood Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia

    B. Li, S.W. Brady, X. Ma, S. Shen, Y. Zhang, Y. Li, K. Szlachta, L. Dong, Y. Liu, F. Yang, N. Wang, D.A. Flasch, M.A. Myers, H.L. Mulder, L. Ding, Y. Liu, L. Tian, K. Hagiwara, K. Xu, X. Zhou, E. Sioson, T. Wang, L. Yang, J. Zhao, H. Zhang, Y. Shao, H. Sun, L. Sun, J. Cai, H. Sun, T. Lin, L. Du, H. Li, M. Rusch, M.N. Edmonson, J. Easton, X. Zhu, J. Zhang, C. Cheng, B.J. Raphael, J. Tang, J.R. Downing, L.B. Alexandrov, B.S. Zhou, C. Pui, J.J. Yang, J. Zhang

    Blood (2020). 135 (1), 41-55.

2019

Journal Articles

  • CALDER CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples

    M.A. Myers, G. Satas, B.J. Raphael

    RECOMB 2019, Cell Systems (2019). 8 (6), 514-522.e5.

    Publication Software

  • OsteoSarBrady The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

    S W Brady, X Ma, A Bahrami, G Satas, G. Wu, S Newman, M Rusch, D K Putnam, H L Mulder, D Yergeau, M N Edmonson, J Easton, L B Alexandrov, X Chen, E R Mardis, R K Wilson, J R Downing, A S Pappo, B J Raphael, M A Dyer, J Zhang

    Molecular Cancer Research (2019)

Conference Proceedings

  • ICML2019 Random Walks on Hypergraphs with Edge-Dependent Vertex Weights

    U. Chitra, B.J. Raphael

    International Conference on Machine Learning (ICML) 2019.

    Proceedings arXiv preprint

2018

Journal Articles

  • HierarchicalHotNet Hierarchical HotNet: identifying hierarchies of altered subnetworks

    M.A. Reyna, M.D.M. Leiserson, B.J. Raphael

    ECCB 2018/Bioinformatics, 34(17):i972-i980.

    Software

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

    M.M. Parks, B.J. Raphael, C.E. Lawrence.

    BMC Bioinformatics (2018) 19 (1), 323.

  • MACHINA Inferring parsimonious migration histories for metastatic cancers

    M. El-Kebir, G. Satas, B.J. Raphael

    Nature Genetics. 50, 718–726

    Software

  • SC-Hap Haplotype phasing in single-cell DNA-sequencing data

    G. Satas, B.J. Raphael

    ISMB 2018, Bioinformatics. 34 (13), i211-i217

    Software

  • PanCanAtlasCell Pathogenic germline variants in 10,389 adult cancers

    K Huang, RJ Mashl, Y Wu, DI Ritter, J Wang, C Oh, M Paczkowska, … .

    Cell (2018) 173 (2), 355-370. e14.

  • VisibleML Visible Machine Learning for Biomedicine

    K.Y. Michael, J. Ma, J. Fisher, J.F. Kreisberg, B.J. Raphael, T Ideker

    Cell (2018) 173 (7), 1562-1565.

  • Grasso2018 Genetic mechanisms of immune evasion in colorectal cancer

    C.S. Grasso, … B.J. Raphael ….[52 total authors], U Peters.

    Cancer Discovery (2018) 8 (6), 730-749.

  • ThymomaTCGA The Integrated Genomic Landscape of Thymic Epithelial Tumors

    M. Radovich, 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, B.J. Raphael, 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) 33(2):244-258.e10.

  • JCB2018CNT Phylogenetic Copy-Number Factorization of Multiple Tumor Samples

    S. Zaccaria*, M. El-Kebir*, G.W. Klau, B.J. Raphael

    Journal of Computational Biology (2018) 25(7):689-708.

    Software

Edited Volumes

  • RECOMBProceddings Proceedings of Research in Computational Molecular Biology: 22nd Annual International Conference, RECOMB 2018

    B.J. Raphael (Ed).
    (2018) , Paris, France, April 21-24, 2018.

2017

Journal Articles

  • LinkedReadSV Identifying structural variants using linked-read sequencing data

    R Elyanow, HT Wu, BJ Raphael

    RECOMB Computational Cancer Biology 2017, Bioinformatics (2017) 34, (2), 353–360.

    Software

  • ChromothripsisCCB Identifying Simultaneous Rearrangements in Cancer Genomes

    L Oesper, S Dantas, BJ Raphael

    RECOMB Computational Cancer Biology 2017 and Bioinformatics, (2), 346-352.

    bioRxiv preprint Software

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

    J Kuipers, K Jahn, BJ Raphael, N Beerenwinkel

    Genome research

  • ISMB2017 Tumor Phylogeny Inference Using Tree-Constrained Importance Sampling

    G. Satas, B.J. Raphael

    ISMB 2017, Bioinformatics. 33(14), i152-i160.

    Software

  • TCGAPDAC Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma

    BJ Raphael, RH Hruban, AJ Aguirre, TCGA Research Network

    Cancer Cell 32 (2), 185-203. e13

  • NetworkPropagationReview Network propagation: a universal amplifier of genetic associations

    L Cowen, T Ideker, BJ Raphael, R Sharan

    Nature Reviews Genetics (2017) 18(9):551-562.

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

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

    Genome Research, gr. 211656.116

  • CNTAMB Complexity and algorithms for copy-number evolution problems

    M El-Kebir, BJ Raphael, R Shamir, R Sharan, S Zaccaria, M Zehavi, R Zeira Algorithms for Molecular Biology 12 (1), 13

  • PegasusALL Novel gene and network associations found for lymphoblastic leukemia using case-control and family-based studies in multi-ethnic populations

    P Nakka, NP Archer, H Xu, PJ Lupo, BJ Raphael, JJ Yang, S Ramachandran Cancer Epidemiology and Prevention Biomarkers (10):1531-1539

    Software

  • TCGAESCA Integrated genomic characterization of oesophageal carcinoma

    The Cancer Genome Atlas Research Network

    Nature, 541(7636):169-175.

Conference Proceedings

  • RECOMB2017 The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-Sample Bulk Sequencing Tumor Data

    S. Zaccaria, M. El-Kebir, G.W. Klau, B.J. Raphael

    RECOMB 2017.

    Software

2016

Journal Articles

  • WExT A Weighted Exact Test for Mutually Exclusive Mutations in Cancer

    M.D.M. Leiserson, M.A. Reyna, B.J. Raphael

    ECCB 2016/Bioinformatics, 32(17):i736-i745.

    Website Software Release arXiv preprint

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

    P.Nakka, B.J. Raphael*, S Ramachandran*

    Genetics, (2016) 204(2):783-798.

  • elKebirCELLSYSTEMS Inferring the Mutational History of a Tumor using Multi-State Perfect Phylogeny Mixtures

    M. El-Kebir*, G. Satas*, L. Oesper, B.J. Raphael

    Cell Systems, (2016) 3(1):43-53.

    Website Software Release

  • SampleComplexityJournal On the Sample Complexity of Cancer Pathways Identification

    F. Vandin, B.J. Raphael, E.Upfal.

    Journal of Computational Biology, (2016) 23(1):30-41.

  • TCGA_ACC 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 MC, 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 RG.

    Cancer Cell, (2016) 29(5):723-36.

  • TCGAKIRP Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

    The Cancer Genome Atlas Research Network

    New England Journal of Medicine, (2016) 374(2):135-45.

Conference Proceedings

  • CNT Copy-Number Evolution Problems: Complexity and Algorithms

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

    WABI 2016

  • elKebirRECOMB2016 Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing

    M. El-Kebir, G. Satas, L. Oesper, B.J. Raphael

    RECOMB 2016

    arXiv preprint

2015

Journal Articles

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

    Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MDM, 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.

    Nature Communications, (2015) 6:10086.

  • TADTree Identification of hierarchical chromatin domains

    C. Weinreb and B.J. Raphael

    Bioinformatics, (2015) pii: btv485.

    Website

  • CoMEtGenomeBiology Comet: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

    M.D.M. Leiserson*, H-T. Wu*, F. Vandin, B.J. Raphael

    Genome Biology (2015) 16:160.

    Website Software Release arXiv preprint

  • GerbiRNA Universal and Domain-Specific Sequences in 23S-28S Ribosomal RNA Identified by Computational Phylogenetics.

    S.M. Doris, D.R. Smith, J.N. Beamesderfer, B.J. Raphael, J.A. Nathanson, S.A. Gerbi

    RNA, (2015) 21(10):1719-30.

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

    M. El-Kebir*, L. Oesper*, H. Acheson-Field, B.J. Raphael

    Bioinformatics (Special Issue: Proceedings of ISMB), (2015) 31(12):i62-i70.

    Website Software Release

  • ICGCPathways Pathway and network analysis of cancer genomes.

    Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium

    Nature Methods, (2015) 12(7):615-621.

  • MAGI MAGI: visualization and collaborative annotation of genomic aberrations

    M.D.M Leiserson, C.C. Gramazio, J. Hu, H-T. Wu, D.H. Laidlaw, B.J Raphael

    Nature Methods, (2015) 12(6):483-484.

    Website Software Release

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

    M. Parks, C.E. Lawrence,B.J. Raphael

    Genome Biology, (2015) 8;16(1):72.

    Software Release

  • Survival PLOS CB Accurate Computation of Survival Statistics in Genome-wide Studies

    F. Vandin, A. Papoutsaki, B.J. Raphael*, E. Upfal*

    PLOS Computational Biology, (2015) 11(5):e1004071.

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

    B.J. Raphael, F. Vandin

    Journal of Computational Biology, (2015) 22(6):510-27.

  • HotNet2 Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

    M.D.M Leiserson*, F. Vandin*, H. Wu, J.R. Dobson, J.V. Eldridge, J.L. Thomas, A. Papoutsaki, Y. Kim, B. Niu, M. McLellan, M.S. Lawrence, A. Gonzalez-Perez, D. Tamborero, Y. Cheng, G.A. Ryslik, N. Lopez-Bigas, G. Getz, L. Ding, B.J Raphael

    Nature Genetics, (2015) 47(2):106-114.

    Website Software Release

Conference Proceedings

  • CoMEtRECOMB Comet: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

    M.D.M. Leiserson*, H-T. Wu*, F. Vandin, B.J. Raphael

    19th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2015)

    Website Software Release arXiv preprint

  • SampleComplexity On the Sample Complexity of Cancer Pathways Identification

    F. Vandin, B.J. Raphael, E. Upfal

    19th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2015) Lecture Notes in Computer Science Volume 9029, 2015, pp 326-337.

Book Chapters

  • CombinationsBookChapter Analyzing Combinations of Somatic Mutations in Cancer Genomes
    M.D.M. Leiserson and B.J. Raphael

    In Integrating Omics Data G.C.Tseng, D. Ghosh, X.J. Zhou (Eds). Cambridge University Press (2015)

2014

Journal Articles

  • Ritz Single Molecule Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches

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

    Bioinformatics, (2014) 30(24):3458-66.

    Software Release

  • THetA2 Paper Quantifying Tumor Heterogeneity in Whole-Genome and Whole-Exome Sequencing Data

    L. Oesper, G. Satas, B.J. Raphael

    Bioinformatics, (2014) 30(24):3532-40.

    Software Release

  • TCGA Thyroid Integrated Genomic Characterization of Papillary Thyroid Carcinoma

    The Cancer Genomic Atlas Research Network

    Cell, (2014) 159(3):676-90.

  • Chromothripsis Paper

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

    C. Weinreb, L. Oesper, B.J. Raphael

    BMC Genomics, (2014) 15(Suppl 6):S4.

    Special issue for the 12th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics (RECOMB-CG 2014) PubLink

  • Pan-Cancer Subtypes

    Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
    K.A. Hoadley, C. Yau, D.M. Wolf, A.D. Cherniack, D. Tamborero, S. Ng, M.D.M. Leiserson, B. Niu, M.D. McLellan, V. Uzunangelov, J. Zhang, C. Kandoth, R. Akbani, H. Shen, L. Omberg, A. Chu, A.A. Margolin, L.J. van’t Veer, N. Lopez-Bigas, P.W. Laird, B.J. Raphael, L. Ding, A.G. Robertson, L.A. Byers, G.B. Mills, J.N. Weinstein, C. Van Waes, Z. Chen, E.A. Collisson, The Cancer Genome Atlas Research Network, C.C. Benz, C.M. Perou, J.M. Stuart

    Cell, 158(4):929-944. PubLink

  • NRG Review Expanding the computational toolbox for mining cancer genomes.

    L. Ding, M.C. Wendl, J.F. McMichael, B.J. Raphael

    Nature Reviews Genetics. (2014) 15(8):556-70.

  • TCGA STAD Comprehensive molecular characterization of gastric adenocarcinoma

    The Cancer Genome Atlas Research Network

    Nature 513:202-209.

    PubLink

  • RAIG Paper Detecting independent and recurrent copy number aberrations using interval graphs

    H. Wu, I. Hajirasouliha, B.J. Raphael

    Bioinformatics 30 (12), i195-i203.

    Special issue for the 22nd Annual International Conference on Intelligent Systems in Molecular Biology (ISMB 2014)

    PubLink Website Software Release

  • Structural Variation Paper A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

    I. Hajirasouliha, A. Mahmoody, B.J. Raphael

    Bioinformatics 30 (12), i78-i86.

    Special issue for the 22nd Annual International Conference on Intelligent Systems in Molecular Biology (ISMB 2014)

    PubLink

  • Brodsky PLOSOne Paper Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease

    A.S. Brodsky, A. Fischer, D.H. Miller, S.Vang, S.Maclaughlan, H.T. Wu, J.Yu, M.Steinhoff, C.Collins, P.J.Smith, B.J. Raphael, L.Brard

    PLoS One. (2014) 9(4):e94476.

  • Genome Medicine Review Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

    B.J. Raphael, J.R. Dobson, L. Oesper, F. Vandin

    Genome Medicine

    PDF

  • Network GWAS Paper Integrated analysis of germline and somatic variants in ovarian cancer

    K.L. Kanchi, K.J. Johnson, C. Lu, M.D. McLellan, M.D.M. Leiserson, M.C. Wendl, Q. Zhang, D.C. Koboldt, M. Xie, C. Kandoth, J.F. McMichael, M.A. Wyczalkowski, D.E. Larson, H.K. Schmidt, C.A. Miller, R.S. Fulton, P.T. Spellman, E.R. Mardis, T.E. Druley, T.A Graubert, P.J. Goodfellow, B.J. Raphael, R. K. Wilson, L. Ding

    Nature Communications

    PubLink

  • Structural Variation Paper Identification of Structural Variation

    S.S. Sindi, B.J. Raphael

    Genome Analysis: Current Procedures (In Press)

Conference Proceedings

  • WABI2014 Paper Reconstructing mutational history in multiply sampled tumors using perfect phylogeny mixtures

    I. Hajirasouliha, B.J. Raphael

    14th Workshop on Algorithms in Bioinformatics (WABI) (2014) Lecture Notes in Computer Science Volume 8701, 2014, pp 354-367.

  • RECOMB2014 Paper Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data

    B.J. Raphael, F. Vandin

    18th Annual International Conference on Research in Computational Molecular Biology (RECOMB) (2014) Lecture Notes in Computer Science Volume 8394, 2014, pp 250-264.

2013

Journal Articles

  • Network GWAS Paper Network analysis of GWAS data

    M.D.M. Leiserson, J.V. Eldridge, S. Ramachandran, B.J. Raphael

    Current Opinion in Genetics & Development

    PubLink

  • TCGA Pan-can Mutations Paper Mutational landscape and significance across 12 major cancer types

    C. Kandoth, M.D. McLellan, F. Vandin, K. Ye, B. Niu, C. Lu, M. Xie, Q. Zhang, J.F. McMichael, M.A. Wyczalkowski, M.D.M. Leiserson, C.A. Miller, J.S. Welch, M.J. Walter, M.C. Wendl, T.J. Ley, R.K. Wilson, B.J. Raphael, L. Ding

    Nature

    PubLink

  • TCGA Pan-can Paper The Cancer Genome Atlas Pan-Cancer analysis project

    The Cancer Genome Atlas Research Network, J.N. Weinstein, E.A. Collisson, G.B. Mills, K.R. Mills Shaw, B.A. Ozenberger, K. Ellrott, I. Shmulevich, C. Sander, J.M. Stuart

    Nature Genetics

    PubLink

  • Nature Methods News and Views Making connections: using networks to stratify human tumors (News and Views)

    B.J. Raphael

    Nature Methods

    PubLink

  • THeTA Paper THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

    L. Oesper, A. Mahmoody, B.J. Raphael

    Genome Biology

    PubLink Software Release

  • TCGA Renal Cell Paper Comprehensive molecular characterization of clear cell renal cell carcinoma

    The Cancer Genome Atlas Research Network

    Nature

    PubLink

  • ACC Paper 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

    Nature Genetics

    PubLink

  • Multi-Dendrix Paper Simultaneous Identification of Multiple Driver Pathways in Cancer

    M.D.M. Leiserson, D. Blokh, R. Sharan, B.J. Raphael

    PLoS Computational Biology

    PubLink Software Release Website

  • TCGA AML Paper Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

    The Cancer Genome Atlas Research Network

    New England Journal of Medicine

    PubLink Interactive Visualization

  • Clonal Evolution Paper Advances for Studying Clonal Evolution in Cancer

    L. Ding, B.J. Raphael, F. Chen, M.C. Wendl

    Cancer Letters

    PubLink

Conference Proceedings

  • THeTA RECOMB Paper Inferring Intra-Tumor Heterogeneity from High-Throughput DNA Sequencing Data

    L. Oesper, A. Mahmoody, B.J. Raphael

    17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013)

    PubLink

  • Survival RECOMB Paper Genome-Wide Survival Analysis of Somatic Mutations in Cancer

    F. Vandin, A. Papoutsaki, B.J. Raphael, E. Upfal

    17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013) — Best Paper Award

    PubLink Software Release

  • PSB Heterogeneity Paper Modeling cell heterogeneity: from single-cell variations to mixed cells

    E. Batchelor, M.G. Kann, T.M. Przytycka, B.J. Raphael, D. Wojtowicz

    Pacific Symposium on Biocomputing (PSB)

    PubLink

2012

Journal Articles

  • Structural Variation & Medical Genomics Chapter Structural Variation and Medical Genomics

    B.J. Raphael

    PLOS Computational Biology

    PubLink

  • AMB Driver Pathways Paper Finding Driver Pathways in Cancer: Models and Algorithms

    F. Vandin, E. Upfal, B.J. Raphael

    Algorithms for Molecular Biology

    PubLink

  • Quantitative Phosphoproteomics Paper Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells

    L. Cao, Y. Ding, N. Hung, K. Yu, A. Ritz, B.J. Raphael, A.R. Salomon

    PLOS One

    PubLink

  • Alcohol Genetics Paper The genetics of alcohol dependence: Advancing towards systems-based approaches

    R.H. Palmer, J.E. McGeary, S. Francazio, B.J. Raphael, A.D. Lander, A.C. Heath, V.S. Knopik

    Drug and Alcohol Dependence

    PubLink

  • Prostate Cancer Paper The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

    C. Grasso, Y. Wu, D. Robinson, X. Cao, S. Dhanasekaran, A. Khan, M. Quist, X. Jing, R. Lonigro, J.C. Brenner, I. Asangani, B. Ateeq, S. Chun, J. Siddiqui, L. Sam, M. Anstett, R. Mehra, J. Prensner, N. Palanisamy, G. Ryslik, F. Vandin, B.J. Raphael, L. Kunju, D. Rhodes, K. Pienta, A. M. Chinnaiyan, S.A. Tomlins

    Nature

    PubLink

  • GASVPro Paper An Integrative Probabilistic Model for Identification of Structural Variation in Sequencing Data

    S. Sindi, S. Onal, L. Peng, H. Wu, B.J. Raphael

    Genome Biology

    PubLink Software Release

  • IEEE Driver Pathways Paper Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer

    F. Vandin, E. Upfal, B.J. Raphael

    IEEE Computer

    PDF

  • Polymorphic Inversions Paper Identification of Polymorphic Inversions from Genotypes

    A. Caceres, S.S Sindi, B.J Raphael, M. Caceres and J.R Gonzalez

    BMC Bioinformatics

    PubLink

  • Dendrix Paper De novo Discovery of Mutated Driver Pathways in Cancer

    F. Vandin, E. Upfal, B.J. Raphael

    Genome Research

    PubLink Software Release

    [Preliminary version at 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011)]

Conference Proceedings

  • Genome Mixtures Paper Reconstructing Genome Mixtures From Partial Adjacencies

    A. Mahmoody, C.L. Kahn, B.J. Raphael

    Proceedings of the Tenth Annual RECOMB Satellite Workshop on Comparative Genomics

    PubLink

  • WABI Proceedings Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings.

    B.J. Raphael, J. Tang (Eds.)

    Lecture Notes in Computer Science

    PubLink

  • PREGO Paper Reconstructing Cancer Genome Organization

    L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, B.J. Raphael

    BMC Bioinformatics (Proceedings of 2nd RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq))

    PubLink Software Release

  • HotNet Survival Paper Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer

    F. Vandin, P. Clay, E. Upfal, B.J. Raphael

    Pacific Symposium on Biocomputing

    PDF

2011

Journal Articles

  • TCGA Ovarian Paper Integrated Genomic Analyses of Ovarian Carcinoma

    The Cancer Genome Atlas Research Network

    Nature

    PubLink

  • Ovarian BMC Cancer Paper Integrated Genomics of Ovarian Xenograft Tumor Progression and Chemotherapy Response

    A. Stuckey, A. Fischer, D.H. Miller, S. Hillenmeyer, K.K. Kim, A. Ritz, R.K. Singh, B.J. Raphael, L. Brard and A.S. Brodsky

    BMC Cancer

    PubLink

  • RNA Splicing Paper Using positional distribution to identify splicing elements and predict mRNA processing defects in human genes

    K.H. Lim, L. Ferraris, M. Filloux, B.J. Raphael, W. Fairbrother

    Proceedings of the National Academy of Sciences (PNAS)

    PubLink

  • NBC Paper Detection of Recurrent Rearrangement Breakpoints from Copy Number Data

    A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, B.J. Raphael

    BMC Bioinformatics

    PubLink Software Release

  • HotNet Paper Algorithms for Detecting Significantly Mutated Pathways in Cancer

    F. Vandin, E. Upfal, B.J. Raphael

    Journal of Computational Biology

    PubLink Software Release

Conference Proceedings

  • WABI Driver Pathways Paper Finding Driver Pathways in Cancer: Models and Algorithms

    F. Vandin, E. Upfal, B.J. Raphael

    Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI)

2010

Journal Articles

  • Gremlin Paper Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements

    T. O’Brien, A. Ritz, B.J. Raphael, D.H. Laidlaw

    IEEE Transactions on Visualization and Computer Graphics

    PubLink Software Release

  • Bioinformatics Parsimony Paper Parsimony and Likelihood Reconstruction of Human Segmental Duplications

    C.L. Kahn, B.H. Hristov, and B.J. Raphael

    Bioinformatics

    PubLink

    [Preliminary version at the 9th European Conference on Computational Biology (ECCB)

  • ICGC Paper International network of cancer genome projects

    International Cancer Genome Consortium

    Nature

    PubLink

  • HITSEQ Structural Analysis Paper Structural Variation Analysis with Strobe Reads

    A. Ritz, A. Bashir, and B.J. Raphael

    Bioinformatics

    PubLink

  • Inversion Prediction Paper Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data

    S. Sindi and B.J. Raphael

    Journal of Computational Biology

    PubLink

  • PCR Assays Paper Optimizing PCR assays for DNA based cancer diagnostics

    A. Bashir, Q. Liu, B.J. Raphael, D. Carson, Y.T. Liu, V. Bafna

    Journal of Computational Biology

    PubLink

  • Segmental Duplications Paper Efficient Algorithms for Analyzing Segmental Duplications with Deletions and Inversions in Genomes

    C.L. Kahn, S. Mozes, and B.J. Raphael

    Algorithms for Molecular Biology

    PubLink

Conference Proceedings

  • HotNet RECOMB Paper Algorithms for Detecting Significantly Mutated Pathways in Cancer

    F. Vandin, E. Upfal, and B.J. Raphael

    Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010)

    PDF

2009

Journal Articles

  • Nguyen2009 Paper A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T cell Receptor Activation

    V. Nguyen, L. Cao, J.T. Lin, N. Hung, A. Ritz, K. Yu, R. Jianu, S.P. Ulin, B.J. Raphael, D.H. Laidlaw, L.Brossay, A.R. Salomon

    Molecular Cell Proteomics

    PubLink

  • Sindi2009 Paper A Geometric Approach for Classification and Comparison of Structural Variants

    S. Sindi, E. Helman, A. Bashir, B.J. Raphael

    Bioinformatics

    PubLink

    [Special issue for the Joint 17th Annual International Conference on Intelligent Systems in Molecular Biology and 8th Annual International European Conference on Computational Biology (ISMB/ECCB 09)]

  • Messmer2009 Paper Computational Identification Of CDR3 Sequence Archetypes Among Immunoglobulin Sequences in Chronic Lymphocytic Leukemia

    B.T Messmer, B.J. Raphael, S.J Aerni, G.F Widhopf, L.Z Rassenti, T.L Toy, T.J Kipps

    Leukemia Research

    PubLink

  • Ritz2009 Paper Discovery of Phosphorylation Motif Mixtures in Phosphoproteomics Data

    A. Ritz, G. Shakhnarovich, A.R. Salomon, and B.J. Raphael

    Bioinformatics

    PubLink Software Release

Conference Proceedings

  • Kahn2009 Paper Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes

    C.L. Kahn, S. Mozes, and B.J. Raphael

    Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI)

    PubLink

  • Sindi2009 Paper Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data

    S. Sindi, B.J. Raphael

    Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB)

    PubLink

  • Bashir2009 Paper Optimizing PCR assays for DNA based cancer diagnostics

    A. Bashir, Q. Liu, B.J. Raphael, D. Carson, Y.T. Liu, V. Bafna

    Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB)

    PubLink

  • Kahn2009 Paper A Parsimony Approach to Analysis of Human Segmental Duplications

    C.L. Kahn, B.J. Raphael

    Pacific Symposium on Biocomputing

    PubLink Corrected version

2008

Journal Articles

  • Kahn2008 Paper Analysis of Segmental Duplications via Duplication Distance

    C.L. Kahn, B.J. Raphael

    Bioinformatics (Proceedings of the European Conference on Computational Biology)

    PubLink

  • Kahn2008 Paper Evaluation of Paired-end Sequencing Strategies for Detection of Genome Rearrangements in Cancer

    A. Bashir, S. Volik, C.C. Collins, V. Bafna, B.J. Raphael

    PLoS Computational Biology

    PubLink

  • Raphael2008 Paper A sequence-based survey of the complex structural organization of tumor genomes

    B.J. Raphael, S. Volik, Guiqing Huang, F.Waldman, J. Costello, S.Aerni, R.P. Brown, A. Bashir, K. Pienta, G. Mills, K. Bajsarowicz, P. Paris, Q. Tao, W. Kuo, J.W. Gray, J. Cheng, M. Nefedov, P. de Jong, and C. Collins

    Genome Biology

    PubLink

  • Agler2008 Paper Classical Function Theory, Operator Dilation Theory, and Machine Computation on Multiply-Connected Domains

    J. Agler, J. Harland, B.J. Raphael

    Memoirs of the American Mathematical Society

    Google Books Link

2007

Journal Articles

  • Bashir2007 Paper Optimization of primer design for the detection of variable genomic lesions in cancer

    A. Bashir A, Y.T. Liu, B.J. Raphael, D. Carson, V. Bafna

    Bioinformatics

    PubLink

  • Cao2007 Paper Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling

    L. Cao, K. Yu, V. Nguyen, A. Ritz, B.J. Raphael, Y. Kawakami, T. Kawakami, A.R. Salomon

    Journal of Immunology

    PubLink

  • Yooseph2007 Paper The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

    S. Yooseph, G. Sutton, D.B. Rusch, A.L. Halpern, S.J. Williamson, K.Remington, J.A. Eisen, K..B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C.S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B.J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J.E. Dixon, S. S. Taylor, R.L. Strausberg, M. Frazier, J.C. Venter

    PLoS Biology

    PubLink

  • Raphael2007 Paper Analysis of Genomic Alterations in Cancer

    B.J. Raphael, S. Volik, C. Collins

    Genome Sequencing Technology and Algorithms, H. Tang, S. Kim, E. Mardis (eds)

    PubLink

Conference Proceedings

  • Corona2007 Paper Identifying Deletion Polymorphisms from Haplotypes

    E. Corona, B.J. Raphael, E. Eskin

    Proceedings of the 11Th Annual International Conference on Research in Computational Biology (RECOMB 2007)

    PubLink

2006

Journal Articles

  • Chaisson2006 Paper Micro-inversions in Mammalian Evolution

    M. Chaisson, B.J. Raphael, and P. Pevzner

    Proceedings of the National Academy of Sciences, USA

    PubLink

  • Volik2006 Paper Decoding the Fine-scale Structure of a Breast Cancer Genome and Transcriptome

    S. Volik, B.J. Raphael, et al.

    Genome Research

    PubLink

  • Jones2006 Paper AliWABA: Alignment on the Web through an A-Bruijn Approach

    N.C. Jones, D. Zhi, B.J. Raphael

    Nucleic Acids Research

    PubLink

  • Zhi2006 Paper Identifying Repeat Domains in Large Genomes

    D.Zhi, B.J. Raphael, A.Price, H. Tang, P. Pevzner

    Genome Biology

    PubLink

Conference Proceedings

  • Eskin2006 Paper Systems Biology and Regulatory Genomics. Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics

    E. Eskin, T. Ideker, B.J. Raphael, C. Workman (eds.)

    Lecture Notes in Computer Science

2002 - 2005

Journal Articles

  • Raphael2004 Paper Reconstructing Tumor Amplisomes

    B.J. Raphael, P. Pevzner

    Bioinformatics

    PubLink

  • Raphael2004 Paper A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Domains

    B.J. Raphael, D. Zhi, H. Tang, P. Pevzner

    Genome Research

    PubLink

  • Raphael2004 Paper A Uniform Projection Method for the Motif Discovery Problem

    B.J. Raphael, L. Liu, and G. Varghese

    IEEE Transactions on Computational Biology and Bioinformatics

    PubLink

  • Raphael2003 Paper Reconstructing Tumor Genome Architectures

    B.J. Raphael, S. Volik, C. Collins, P. Pevzner

    Bioinformatics (Special ECCB 2003 Issue)

    PubLink

    [Recognized by the Faculty of 1000]

Other Publications

  • Raphael2002 Paper A Computational Investigation Of Spectral Sets And Rational Dilations Over Multiply-Connected Domains

    B.J. Raphael

    Ph.D. Thesis

    Link