Ben Raphael M
Publications
Cancer Genomics
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. (In Press).
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. (In Press)
A. Bashir A, Y.T. Liu YT, 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.
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. [Paper]
B.
Raphael, P. Pevzner (2004). Reconstructing Tumor Amplisomes. Bioinformatics, 20 Suppl 1:I265-I273. (Special ISMB/ECCB 2004
Issue) [PDF]
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].[PDF]
Computational Biology/Bioinformatics
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.
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).
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.
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.
N.C. Jones, D. Zhi, B. Raphael. (2006) AliWABA: Alignment on the Web through an A-Bruijn Approach. Nucleic Acids Research. 34:W613-6.
D.Zhi, B. Raphael, A.Price, H. Tang, P. Pevzner (2006). Identifying Repeat Domains in Large Genomes. Genome Biology, 7(1):R7. [PDF]
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.
[PDF]
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. [PDF]
Edited Volumes & Book Chapters
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.
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.
Mathematics
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.]
Ph. D. Thesis
A
Computational Investigation Of Spectral Sets And
Rational Dilations Over Multiply-Connected Domains. [Link.
PS to come.
]
