Sorin Istrail

Summary

Affiliation: Brown University
Country: USA

Publications

  1. ncbi request reprint Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks
    Sorin Istrail
    Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
    Methods Mol Biol 674:369-99. 2010
  2. pmc HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data
    Derek Aguiar
    Department of Computer Science, Brown University, Providence RI 02912, USA
    J Comput Biol 19:577-90. 2012
  3. pmc DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
    Derek Aguiar
    Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
    Bioinformatics 28:i154-62. 2012
  4. pmc Haplotype assembly in polyploid genomes and identical by descent shared tracts
    Derek Aguiar
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Bioinformatics 29:i352-60. 2013
  5. doi request reprint The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy
    Fumei Lam
    Department of Computer Science, Brown Univerisity, Providence, Rhode Island 02912, USA
    J Comput Biol 17:767-81. 2010
  6. ncbi request reprint QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads
    Austin Huang
    Division of Infectious Disease, Computer Science Department, Brown University, Box 1910, Providence, RI 02912, USA
    In Silico Biol 11:193-201. 2011
  7. pmc Tumor haplotype assembly algorithms for cancer genomics
    Derek Aguiar
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Pac Symp Biocomput 19:3-14. 2014
  8. ncbi request reprint The regulatory genome and the computer
    Sorin Istrail
    Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
    Dev Biol 310:187-95. 2007

Collaborators

Detail Information

Publications8

  1. ncbi request reprint Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks
    Sorin Istrail
    Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
    Methods Mol Biol 674:369-99. 2010
    ..A more recent component of the CYRENE project is the Virtual Sea Urchin system (VSU), an interactive visualization tool that provides a four-dimensional (spatial and temporal) map of the gene regulatory networks of the sea urchin embryo...
  2. pmc HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data
    Derek Aguiar
    Department of Computer Science, Brown University, Providence RI 02912, USA
    J Comput Biol 19:577-90. 2012
    ..We show that HapCompass performs significantly better for a variety of data and metrics. HapCompass is freely available for download (www.brown.edu/Research/Istrail_Lab/)...
  3. pmc DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
    Derek Aguiar
    Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
    Bioinformatics 28:i154-62. 2012
    ..Identifying the genetic heterogeneity of small deletions remains a major unresolved computational problem partly due to the inability of algorithms to detect them...
  4. pmc Haplotype assembly in polyploid genomes and identical by descent shared tracts
    Derek Aguiar
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Bioinformatics 29:i352-60. 2013
    ....
  5. doi request reprint The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy
    Fumei Lam
    Department of Computer Science, Brown Univerisity, Providence, Rhode Island 02912, USA
    J Comput Biol 17:767-81. 2010
    ..We implement linear programming techniques as well as heuristics for the Directed Steiner Arborescence Problem, and use our methods to construct evolutionary histories for both simulated and real data sets...
  6. ncbi request reprint QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads
    Austin Huang
    Division of Infectious Disease, Computer Science Department, Brown University, Box 1910, Providence, RI 02912, USA
    In Silico Biol 11:193-201. 2011
    ..We demonstrate the utility of the method by applying it to simulations based on actual intra-patient clonal HIV-1 sequencing data...
  7. pmc Tumor haplotype assembly algorithms for cancer genomics
    Derek Aguiar
    Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
    Pac Symp Biocomput 19:3-14. 2014
    ..The model and algorithm are implemented in the software package HapCompass-Tumor which is available for download from http://www.brown.edu/Research/Istrail_Lab/. ..
  8. ncbi request reprint The regulatory genome and the computer
    Sorin Istrail
    Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
    Dev Biol 310:187-95. 2007
    ..The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life...