Benjamin J Raphael

Summary

Affiliation: Brown University
Country: USA

Publications

  1. pmc Chapter 6: Structural variation and medical genomics
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS Comput Biol 8:e1002821. 2012
  2. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
  3. pmc Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells
    Lulu Cao
    Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 7:e46725. 2012
  4. pmc De novo discovery of mutated driver pathways in cancer
    Fabio Vandin
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
    Genome Res 22:375-85. 2012
  5. pmc An integrative probabilistic model for identification of structural variation in sequencing data
    Suzanne S Sindi
    Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Genome Biol 13:R22. 2012
  6. doi request reprint Structural variation analysis with strobe reads
    Anna Ritz
    Department of Computer Science, Brown University, Providence, RI 02912, USA
    Bioinformatics 26:1291-8. 2010
  7. pmc Integrated genomics of ovarian xenograft tumor progression and chemotherapy response
    Ashley Stuckey
    Molecular Therapeutics Laboratory, Program in Women s Oncology, Department of Obstetrics and Gynecology, Women and Infants7 Hospital, Alpert Medical School of Brown University, Providence, RI 02905, USA
    BMC Cancer 11:308. 2011
  8. pmc Reconstructing genome mixtures from partial adjacencies
    Ahmad Mahmoody
    Department of Computer Science, Brown University, Providence, RI, USA
    BMC Bioinformatics 13:S9. 2012
  9. doi request reprint Gremlin: an interactive visualization model for analyzing genomic rearrangements
    Trevor M O'Brien
    Computer Science Department, Brown University, Providence, RI 02912, USA
    IEEE Trans Vis Comput Graph 16:918-26. 2010
  10. pmc Parsimony and likelihood reconstruction of human segmental duplications
    Crystal L Kahn
    Department of Computer Science, Brown University, Providence, RI 02912, USA
    Bioinformatics 26:i446-52. 2010

Collaborators

Detail Information

Publications27

  1. pmc Chapter 6: Structural variation and medical genomics
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS Comput Biol 8:e1002821. 2012
    ..We describe the genomic technologies and computational techniques currently used to measure SVs, focusing on applications in human and cancer genomics...
  2. pmc A sequence-based survey of the complex structural organization of tumor genomes
    Benjamin J Raphael
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
    Genome Biol 9:R59. 2008
    ..The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes...
  3. pmc Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells
    Lulu Cao
    Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
    PLoS ONE 7:e46725. 2012
    ..Altogether our data suggests unique modes of regulation of positive and negative feedback pathways in T cells by SLP-76, reconfirming its central role in the pathway...
  4. pmc De novo discovery of mutated driver pathways in cancer
    Fabio Vandin
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
    Genome Res 22:375-85. 2012
    ..Our Dendrix algorithms scale to whole-genome analysis of thousands of patients and thus will prove useful for larger data sets to come from The Cancer Genome Atlas (TCGA) and other large-scale cancer genome sequencing projects...
  5. pmc An integrative probabilistic model for identification of structural variation in sequencing data
    Suzanne S Sindi
    Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Genome Biol 13:R22. 2012
    ..GASVPro outperforms existing methods with a 50-90% improvement in specificity on deletions and a 50% improvement on inversions...
  6. doi request reprint Structural variation analysis with strobe reads
    Anna Ritz
    Department of Computer Science, Brown University, Providence, RI 02912, USA
    Bioinformatics 26:1291-8. 2010
    ..Strobe sequencing holds promise for unraveling complex variants that have been difficult to characterize with current sequencing technologies...
  7. pmc Integrated genomics of ovarian xenograft tumor progression and chemotherapy response
    Ashley Stuckey
    Molecular Therapeutics Laboratory, Program in Women s Oncology, Department of Obstetrics and Gynecology, Women and Infants7 Hospital, Alpert Medical School of Brown University, Providence, RI 02905, USA
    BMC Cancer 11:308. 2011
    ..In this study we identify genes and gene networks important for the efficacy of a pre-clinical anti-tumor therapeutic, MT19c...
  8. pmc Reconstructing genome mixtures from partial adjacencies
    Ahmad Mahmoody
    Department of Computer Science, Brown University, Providence, RI, USA
    BMC Bioinformatics 13:S9. 2012
    ..These results lay the foundation for future algorithmic studies of the k-MCP and the application of these algorithms to real cancer sequencing data...
  9. doi request reprint Gremlin: an interactive visualization model for analyzing genomic rearrangements
    Trevor M O'Brien
    Computer Science Department, Brown University, Providence, RI 02912, USA
    IEEE Trans Vis Comput Graph 16:918-26. 2010
    ....
  10. pmc Parsimony and likelihood reconstruction of human segmental duplications
    Crystal L Kahn
    Department of Computer Science, Brown University, Providence, RI 02912, USA
    Bioinformatics 26:i446-52. 2010
    ..Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task...
  11. pmc Reconstructing cancer genomes from paired-end sequencing data
    Layla Oesper
    Department of Computer Science, Brown University, Providence, RI, USA
    BMC Bioinformatics 13:S10. 2012
    ..We present an efficient algorithm for reconstructing the block organization of a cancer genome from paired-end DNA sequencing data...
  12. pmc Detection of recurrent rearrangement breakpoints from copy number data
    Anna Ritz
    Department of Computer Science, Brown University, Providence, RI, USA
    BMC Bioinformatics 12:114. 2011
    ..Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant...
  13. pmc A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation
    Vinh Nguyen
    Department of Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
    Mol Cell Proteomics 8:2418-31. 2009
    ..These methods are adaptable to any cell culture signaling system in which isogenic wild type and mutant cells have been or can be derived using any available phosphopeptide enrichment strategy...
  14. pmc Finding driver pathways in cancer: models and algorithms
    Fabio Vandin
    Department of Computer Science, and Center for Computational Molecular Biology Brown University, 115 Waterman St, 4th Flr, Providence, RI 02912, USA
    Algorithms Mol Biol 7:23. 2012
    ..abstract:..
  15. pmc Discovery of phosphorylation motif mixtures in phosphoproteomics data
    Anna Ritz
    Department of Computer Science, Brown University, Toyota Technological Institute at Chicago, Chicago, IL, USA
    Bioinformatics 25:14-21. 2009
    ..Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells. Phosphorylation sites on proteins are determined in part through particular patterns, or motifs, present in the amino acid sequence...
  16. doi request reprint Analysis of segmental duplications via duplication distance
    Crystal L Kahn
    Department of Computer Science, Brown University, Providence, RI, USA
    Bioinformatics 24:i133-8. 2008
    ..A major difficulty in analyzing segmental duplications is that many duplications are complex mosaics of fragments of numerous other segmental duplications...
  17. doi request reprint Identification and frequency estimation of inversion polymorphisms from haplotype data
    Suzanne S Sindi
    Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 17:517-31. 2010
    ..Many of these correspond to known inversions or have other evidence supporting them, and the predicted inversion frequencies largely agree with the limited information presently available...
  18. pmc Quantitative time-resolved phosphoproteomic analysis of mast cell signaling
    Lulu Cao
    Department of Chemistry, Brown University, Providence, RI 02912, USA
    J Immunol 179:5864-76. 2007
    ....
  19. pmc Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes
    Kian Huat Lim
    Department of Molecular and Cellular Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA
    Proc Natl Acad Sci U S A 108:11093-8. 2011
    ..This category together with mutations in the canonical splicing signals suggest that approximately one third of all disease-causing mutations alter pre-mRNA splicing...
  20. doi request reprint Algorithms for detecting significantly mutated pathways in cancer
    Fabio Vandin
    Department of Computer Science, Brown University, Providence, Rhode Island, USA
    J Comput Biol 18:507-22. 2011
    ..We anticipate that our approach will find increasing use as cancer genome studies increase in size and scope...
  21. pmc A geometric approach for classification and comparison of structural variants
    Suzanne Sindi
    Division of Applied Mathematics, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
    Bioinformatics 25:i222-30. 2009
    ..Consequently, most reported human structural variants are poorly defined and not readily compared across different studies and measurement techniques...
  22. pmc Decoding the fine-scale structure of a breast cancer genome and transcriptome
    Stanislav Volik
    Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
    Genome Res 16:394-404. 2006
    ..Given these properties, ESP could play an important role in a tumor genome project...
  23. pmc Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
    ..Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries...
  24. ncbi request reprint Optimization of primer design for the detection of variable genomic lesions in cancer
    Ali Bashir
    Bioinformatics Program, University of California, San Diego, CA, USA
    Bioinformatics 23:2807-15. 2007
    ..We use these test results to help set design parameters for larger problems. We can achieve near-optimal designs for regions close to 1 Mb...
  25. ncbi request reprint Reconstructing tumor amplisomes
    Benjamin J Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 20:i265-73. 2004
    ....
  26. pmc Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer
    Ali Bashir
    Bioinformatics Graduate Program, University of California San Diego, San Diego, California, United States of America
    PLoS Comput Biol 4:e1000051. 2008
    ..These results will be useful in calibrating future cancer sequencing efforts, particularly large-scale studies of many cancer genomes that are enabled by next-generation sequencing technologies...
  27. ncbi request reprint Reconstructing tumor genome architectures
    Benjamin J Raphael
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093 0114, USA
    Bioinformatics 19:ii162-71. 2003
    ..Our results assist in the ongoing ESP analysis of MCF7 tumors by suggesting additional ESP experiments for the completion of a reliable reconstruction of the MCF7 tumor genome, and by focusing BAC re-sequencing efforts...