Benjamin J Raphael

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi 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
  2. ncbi A uniform projection method for motif discovery in DNA sequences
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:91-4. 2004
  3. ncbi A novel method for multiple alignment of sequences with repeated and shuffled elements
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2336-46. 2004
  4. ncbi 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
  5. ncbi Optimizing PCR assays for DNA-based cancer diagnostics
    Ali Bashir
    Department of Computer Science, University of California, San Diego, La Jolla, California 92129, USA
    J Comput Biol 17:369-81. 2010
  6. ncbi 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
  7. ncbi 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
  8. ncbi Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
  9. ncbi AliWABA: alignment on the web through an A-Bruijn approach
    Neil C Jones
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Nucleic Acids Res 34:W613-6. 2006
  10. ncbi Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia
    Bradley T Messmer
    The Rebecca and John Moores Cancer Center, University of California, San Diego, CA, USA
    Leuk Res 33:368-76. 2009

Collaborators

Detail Information

Publications13

  1. ncbi 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...
  2. ncbi A uniform projection method for motif discovery in DNA sequences
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 0114, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:91-4. 2004
    ..Furthermore, the uniform projection algorithm is directly applicable to other problems where the random projection algorithm has been used, including comparison of protein sequence databases...
  3. ncbi A novel method for multiple alignment of sequences with repeated and shuffled elements
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2336-46. 2004
    ..In addition, ABA is useful in the alignment of genomic sequences that contain duplications and inversions. We provide several examples illustrating the applications of ABA...
  4. ncbi 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
    ....
  5. ncbi Optimizing PCR assays for DNA-based cancer diagnostics
    Ali Bashir
    Department of Computer Science, University of California, San Diego, La Jolla, California 92129, USA
    J Comput Biol 17:369-81. 2010
    ..These results point to the development of a successful protocol for early diagnosis and monitoring of cancer. For online Supplementary Material, see www.liebertonline.com...
  6. ncbi 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...
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi AliWABA: alignment on the web through an A-Bruijn approach
    Neil C Jones
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Nucleic Acids Res 34:W613-6. 2006
    ..To facilitate the analysis of protein domains, AliWABA provides direct querying of the Conserved Domain Database. Availability: http://aba.nbcr.net/..
  10. ncbi Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia
    Bradley T Messmer
    The Rebecca and John Moores Cancer Center, University of California, San Diego, CA, USA
    Leuk Res 33:368-76. 2009
    ..Surprisingly, over 40% of the identified groups were composed of somatically mutated genes. This study significantly expands the evidence that antigen selection shapes the Ig repertoire in CLL...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...