ANDREW DAVID SMITH

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Predicting the molecular complexity of sequencing libraries
    Timothy Daley
    Department of Mathematics, University of Southern California, Los Angeles, California, USA
    Nat Methods 10:325-7. 2013
  2. pmc MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation
    Jianghan Qu
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 29:2645-6. 2013
  3. pmc A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
    Qiang Song
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 8:e81148. 2013
  4. pmc Updates to the RMAP short-read mapping software
    Andrew D Smith
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 25:2841-2. 2009

Collaborators

  • Michael Q Zhang
  • Qiang Song
  • Jianghan Qu
  • Meng Zhou
  • Elizabeth E Hong
  • Timothy Daley
  • Jun Zhou
  • Michael Kessler
  • Benjamin Decato
  • Tyler Garvin
  • Fang Fang

Detail Information

Publications4

  1. pmc Predicting the molecular complexity of sequencing libraries
    Timothy Daley
    Department of Mathematics, University of Southern California, Los Angeles, California, USA
    Nat Methods 10:325-7. 2013
    ..We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing...
  2. pmc MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation
    Jianghan Qu
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 29:2645-6. 2013
    ..Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels...
  3. pmc A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics
    Qiang Song
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 8:e81148. 2013
    ..Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database. ..
  4. pmc Updates to the RMAP short-read mapping software
    Andrew D Smith
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 25:2841-2. 2009
    ..Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads...

Research Grants1

  1. Analytic tools to examine high-resolution and genome-scale DNA methylation data
    ANDREW DAVID SMITH; Fiscal Year: 2010
    ..By providing increased capacity for analyzing methylation data, this project will assist researchers elucidate the role and mechanisms of DNA methylation in cancer and development. ..