publications

Publications on PubMed.

Publications on DBLP.

2014
  • B.J. Raphael, F. Vandin (2014) Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB). (In Press)
  • B.J. Raphael, J.R. Dobson, L. Oesper, and F. Vandin (2014) Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome Medicine (In Press).
  • S.S. Sindi, B.J. Raphael (2014). Identification of Structural Variation. In Genome Analysis: Current Procedures (In Press).
  • 2013
    • B.J.Raphael (2013). Making connections: using networks to stratify human tumors (News and Views). Nature Methods 10(11):1077-8. [Publisher Link]
    • 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. (2013) Mutational landscape and significance across 12 major cancer types. Nature 502(7471):333-9. [Publisher Link]
    • M.D.M. Leiserson, J.V. Eldridge, S.Ramachandran, B.J. Raphael. Network Analysis of GWAS Data. Current Opinion in Genetics & Development (2013) 23(6):602-10. [Publisher Link]
    • The Cancer Genome Atlas Research Network. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 45(10):1113-20. [Publisher Link]
    • L. Oesper, A. Mahmoody, B.J. Raphael. (2013) THetA: Inferring intra-tumor heterogeneity from high- throughput DNA sequencing data. Genome Biology 14:R80. [Publisher Link] [Supplemental Material]
    • The Cancer Genome Atlas Research Network. (2013) Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499(7456):43-9. [Publisher Link]
    • 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. (2013) The mutational landscape of adenoid cystic carcinoma. Nature Genetics 45(7):791-8. [Publisher Link]
    • M.D.M. Leiserson, D. Bloch, R. Sharan*, B.J. Raphael*. (2013) Simultaneous Identification of Multiple Driver Pathways in Cancer. PLOS Computational Biology. May;9(5):e1003054. [Publisher Link]
    • The Cancer Genome Atlas Research Network. (2013) Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. New England Journal of Medicine. 368(22):2059-74. [Publisher Link]. [Interative visualization]
    • L. Oesper, A. Mahmoody, B.J. Raphael. (2013) Estimating Tumor Purity and Cancer Subpopulations from High-Throughput DNA Sequencing Data. 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013). [Publisher Link]
    • F. Vandin,A. Papoutsaki, B.J. Raphael*, E.Upfal*. (2013) Genome-Wide Survival Analysis of Somatic Mutations in Cancer. 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013). [Best Paper Award, RECOMB 2013] [Publisher Link]
    • L. Ding, B.J. Raphael, F. Chen, M.C. Wendl. (2013) Advances for Studying Clonal Evolution in Cancer. Cancer Letters. pii: S0304-3835(13)00034-7. [Publisher Link]
    • E. Batchelor, M.G. Kann, T.M. Przytycka, B.J. Raphael, D. Wojtowicz. (2013) Modeling cell heterogeneity: from single-cell variations to mixed cells. Pacific Symposium on Biocomputing (PSB) 2013:445-50. [Publisher Link]
    2012
    • B.J. Raphael. (2012) Structural Variation and Medical Genomics. PLOS Computational Biology.8(12): e1002821. [Publisher Link]
    • F. Vandin, E. Upfal,B.J. Raphael. (2012) Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms Mol Biol. 7(1):23. [Publisher Link]
    • A. Mahmoody, C.L. Kahn, B.J. Raphael. (2012) Reconstructing Genome Mixtures From Partial Adjacencies. Proceedings of the Tenth Annual RECOMB Satellite Workshop on Comparative Genomics.(In press).
    • L. Cao, Y. Ding, N. Hung, K. Yu, A. Ritz, B.J. Raphael, A.R. Salomon. (2012) Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells. PLOS One [Publisher Link]
    • B.J. Raphael, J. Tang (Eds.). (2012) Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings. Lecture Notes in Computer Science 7534, Springer. [Publisher Link]
    • R.H. Palmer, J.E. McGeary, S. Francazio, B.J. Raphael, A.D. Lander, A.C. Heath, V.S. Knopik. (2012) The genetics of alcohol dependence: Advancing towards systems-based approaches. Drug Alcohol Depend. 125(3):179-91. [Publisher Link]
    • 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. (2012) The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer Nature 487(7406):239-43.
    • S. Sindi, S. Onal, L. Peng, H. Wu, B.J. Raphael. (2012) An Integrative Probabilistic Model for Identification of Structural Variation in Sequencing Data. Genome Biology 13(3):R22. [Publisher link].
    • L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, B.J. Raphael (2012) Reconstructing Cancer Genome Organization. BMC Bioinformatics (Proceedings of 2nd RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq)). 13(Suppl 6):S10. Publisher Link
    • F. Vandin, E. Upfal, B.J. Raphael. (2012) Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. IEEE Computer March 2012 (vol. 45 no. 3) pp.39-46. [PDF]
    • A. Caceres, S.S Sindi, B.J Raphael, M. Caceres and J.R Gonzalez. (2012) Identification of Polymorphic Inversions from Genotypes. BMC Bioinformatics 13(1):28. Publisher Link .
    • F. Vandin, E. Upfal, B.J. Raphael. (2012) De novo Discovery of Mutated Driver Pathways in Cancer. Genome Research. 22(2):375-85. Epub 2011 Jun 7. [PDF]. Publisher Link

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

    • F. Vandin,P. Clay, E. Upfal, B.J. Raphael. (2012) Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. Pacific Symposium on Biocomputing. [PDF].
    2011
    • The Cancer Genome Atlas Research Network. (2011). Integrated Genomic Analyses of Ovarian Carcinoma. Nature. 474(7353):609-15.
    • F. Vandin, E. Upfal, B.J. Raphael. (2011) Finding Driver Pathways in Cancer: Models and Algorithms. Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI). Lecture Notes in Computer Science, Vol. 6833. 314-315.
    • 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. (2011) Integrated Genomics of Ovarian Xenograft Tumor Progression and Chemotherapy Response. BMC Cancer. Jul 22;11:308.
    • K.H. Lim, L. Ferraris, M. Filloux, B.J. Raphael, W. Fairbrother.(2011) Using positional distribution to identify splicing elements and predict mRNA processing defects in human genes. Proceedings of the National Academy of Sciences (PNAS). 108(27):11093-8.
    • A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, B.J. Raphael. (2011) Detection of Recurrent Rearrangement Breakpoints from Copy Number Data. BMC Bioinformatics 12:114. Publisher Link.
    • Vandin F, Upfal E, B.J. Raphael . (2011) Algorithms for Detecting Significantly Mutated Pathways in Cancer. Journal of Computational Biology. 18(3):507-22. [PDF]. Publisher Link.
    2010
    • T. O'Brien, A.Ritz, B.J. Raphael , and D.H. Laidlaw. (2010) Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements. IEEE Trans. on Visualization and Computer Graphics (Proc. IEEE Information Visualization Conference 2010) 16(6):918-26.
    • C.L. Kahn, B.H. Hristov, and B.J. Raphael. (2010) Parsimony and Likelihood Reconstruction of Human Segmental Duplications. Bioinformatics (Proceedings of the 9th European Conference on Computational Biology (ECCB)) 26(18):i446-52. Publisher Link
    • International Cancer Genome Consortium. (2010) International network of cancer genome projects. Nature. 464(7291):993-8. Publisher Link
    • A. Ritz, A. Bashir, and B.J. Raphael. (2010) Structural Variation Analysis with Strobe Reads. Bioinformatics. 26(10):1291-8. Publisher Link
    • F. Vandin, E. Upfal, and B.J. Raphael. (2010) Algorithms for Detecting Significantly Mutated Pathways in Cancer Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010). Paper.
    • S. Sindi and B.J. Raphael . (2010) Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. Journal of Computational Biology. 17(3):517-31. Publisher Link
    • A. Bashir, Q. Liu, B. Raphael, D. Carson, Y.T. Liu, V. Bafna. Optimizing PCR assays for DNA based cancer diagnostics. (2010) Journal of Computational Biology. 17(3):369-81. Publisher Link
    • C.L. Kahn, S. Mozes, and B.J. Raphael. (2010) Efficient Algorithms for Analyzing Segmental Duplications with Deletions and Inversions in Genomes. Algorithms for Molecular Biology . 5(1):11. Publisher Link
    2009
    • 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 A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T cell Receptor Activation. Mol Cell Proteomics. 8(11):2418-31. Publisher Link
    • C.L. Kahn, S. Mozes, and B.J. Raphael. (2009) Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI). 169-180. Publisher Link
    • S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009) A Geometric Approach for
      Classification and Comparison of Structural Variants.Bioinformatics. 25: i222-i230. (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)). Publisher Link
    • S. Sindi and B.J. Raphael. Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. (2009) Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB). Publisher Link
    • A. Bashir, Q. Liu, B.J.Raphael, D. Carson, Y.T. Liu, V. Bafna. Optimizing PCR assays for DNA based cancer diagnostics. (2009) Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB). Publisher Link
    • C.L. Kahn and B.J. Raphael. A Parsimony Approach to Analysis of Human Segmental Duplications. (2009) Pacific Symposium on Biocomputing. 14:126-137. Publisher Link. Corrected version.
    • B.T Messmer*, B.J. Raphael*, S.J Aerni, G.F Widhopf, L.Z Rassenti, T.L Toy, T.J Kipps. (2009) Computational Identification Of CDR3 Sequence Archetypes Among Immunoglobulin Sequences in Chronic Lymphocytic Leukemia . Leukemia Research . 33(3):368-76. Publisher Link *co-authors
    • A. Ritz, G. Shakhnarovich, A.R. Salomon, and B.J.Raphael. Discovery of Phosphorylation Motif Mixtures in Phosphoproteomics Data. (2009) Bioinformatics. 25(1):14-21. Publisher Link
    2008
    • C.L. Kahn and B. Raphael. Analysis of Segmental Duplications via Duplication Distance. (2008) Bioinformatics 24(16):i133-8. (Proceedings of the European Conference on Computational Biology). Publisher Link
    • A. Bashir, S. Volik, C.C. Collins, V. Bafna, B.J. Raphael. (2008) Evaluation of Paired-end Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLOS Computational Biology. 4(4):e1000051. Publisher Link
    • B. 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. (2008). A sequence based survey of the complex structural organization of tumor genomes. Genome Biology. 9(3):R59. Publisher Link
    • J. Agler, J. Harland, B. Raphael (2008). Classical Function Theory, Operator Dilation Theory, and Machine Computation on Multiply-Connected Domains. Memoirs of the American Mathematical Society. Vol. 191, No. 892. Google Books link.
    2007
    • A. Bashir A, Y.T. Liu, B. Raphael, D. Carson, V. Bafna. (2007) Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics. 23(21):2807-15.Publisher Link
    • L. Cao, K. Yu, V. Nguyen, A. Ritz, B. Raphael, Y. Kawakami, T. Kawakami, A.R. Salomon, (2007) Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling. Journal of Immunology. 179(9):5864-76. Publisher Link
    • E. Corona, B. Raphael, E. Eskin. (2007) Identifying Deletion Polymorphisms from Haplotypes. Proceedings of the 11Th Annual International Conference on Research in Computational Biology (RECOMB 2007).Publisher Link
    • 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. (2007) The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLOS Biology. 5(3):e16.Publisher Link
    • B. Raphael, S. Volik, C. Collins (2007). Analysis of Genomic Alterations in Cancer. In Genome Sequencing Technology and Algorithms. H. Tang, S. Kim, E.Mardis (eds). pp. 183-195.
    2006
    • M. Chaisson, B. Raphael, and P. Pevzner. (2006) Micro-inversions in Mammalian Evolution. Proceedings of the National Academy of Sciences, USA. 103(52):19824-9.Publisher Link
    • S. Volik, B. Raphael, et al. (2006) Decoding the Fine-scale Structure of a Breast Cancer Genome and Transcriptome. Genome Research, 16(3):394-404.Publisher Link
    • N.C. Jones, D. Zhi, B. Raphael. (2006) AliWABA: Alignment on the Web through an A-Bruijn Approach. Nucleic Acids Research. 34:W613-6.Publisher Link
    • D.Zhi, B. Raphael, A.Price, H. Tang, P. Pevzner (2006). Identifying Repeat Domains in Large Genomes. Genome Biology, 7(1):R7.Publisher Link
    • E. Eskin, T. Ideker, B. Raphael, C. Workman (eds.), (2006) Systems Biology and Regulatory Genomics. Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics. Lecture Notes in Computer Science , Vol. 4023. Springer-Verlag.
    2002- 2005
    • B. Raphael, P. Pevzner (2004). Reconstructing Tumor Amplisomes. Bioinformatics, 20 Suppl 1:I265-I273. (Special ISMB/ECCB 2004 Issue)Publisher Link
    • B. Raphael, D. Zhi, H. Tang, P. Pevzner (2004). A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Domains. Genome Research, 14(11):2336-46. Publisher Link
    • B. Raphael, L. Liu, and G. Varghese (2004). A Uniform Projection Method for the Motif Discovery Problem. IEEE Transactions on Computational Biology and Bioinformatics, 1(2):91-94.Publisher Link
    • B. Raphael, S. Volik, C. Collins, P. Pevzner (2003). Reconstructing Tumor Genome Architectures. Bioinformatics, 19 Suppl 2:II162-II171.  (Special ECCB 2003 Issue). [Recognized by the Faculty of 1000]. Publisher Link
    • B. Raphael. A Computational Investigation Of Spectral Sets And Rational Dilations Over Multiply-Connected Domains. Ph.D. Thesis. [Link. PS to come. ]