PubMed | DBLP

publications

2014

Journal Articles
  • Structural Variation Paper Detecting independent and recurrent copy number aberrations using interval graphs

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

    Bioinformatics (To appear).

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

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

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

    Bioinformatics (To appear).

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

  • Structural Variation Paper 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
  • 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) (In Press).

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