Raphael Lab - Ben Raphael - Brown University Department of Computer Science - Center for Computational Molecular Biology

2009

• S. Sindi and B.J. Raphael . (2010) Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. Journal of Computational Biology. (In Press)
• C.L. Kahn, S. Mozes, and B.J. Raphael . (2009) Efficient Algorithms for Analyzing Segmental Duplications with Deletions and Inversions in Genomes. Algorithms for Molecular Biology . (In Press)
• C.L. Kahn, S. Mozes, and B. 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.
• 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. (In Press)
• S. Sindi, E. Helman, A. Bashir, B. 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. 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. 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. 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. 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. 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. [PDF, WARNING: This paper is long - you might want to see the Table of Contents first.]

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. ]