Fabio Vandin

Summary

Affiliation: Brown University
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. pmc Accurate computation of survival statistics in genome-wide studies
    Fabio Vandin
    Department of Mathematics and Computer Science, University of Southern Denmark, Funen, Denmark Department of Computer Science, Brown University, Providence, Rhode Island, United States of America Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS Comput Biol 11:e1004071. 2015
  5. pmc Ballast: a ball-based algorithm for structural motifs
    Lu He
    Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
    J Comput Biol 20:137-51. 2013
  6. pmc Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data
    Benjamin J Raphael
    1Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
    J Comput Biol 22:510-27. 2015
  7. pmc CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer
    Mark D M Leiserson
    Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA
    Genome Biol 16:160. 2015

Collaborators

Detail Information

Publications7

  1. 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:..
  2. 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...
  3. 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...
  4. pmc Accurate computation of survival statistics in genome-wide studies
    Fabio Vandin
    Department of Mathematics and Computer Science, University of Southern Denmark, Funen, Denmark Department of Computer Science, Brown University, Providence, Rhode Island, United States of America Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
    PLoS Comput Biol 11:e1004071. 2015
    ..In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. ..
  5. pmc Ballast: a ball-based algorithm for structural motifs
    Lu He
    Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
    J Comput Biol 20:137-51. 2013
    ..By supporting generic measures of compositional and geometric similarity, Ballast provides a powerful substrate for the development of motif-matching algorithms...
  6. pmc Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data
    Benjamin J Raphael
    1Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
    J Comput Biol 22:510-27. 2015
    ..The models reconstructed with our method capture most of the current knowledge of the progression of somatic mutations in these cancer types, while also providing new insights on the tumor progression at the pathway level. ..
  7. pmc CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer
    Mark D M Leiserson
    Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA
    Genome Biol 16:160. 2015
    ..We demonstrate that CoMEt outperforms existing approaches on simulated and real data. We apply CoMEt to five different cancer types, identifying both known cancer genes and pathways, and novel putative cancer genes. ..