ANDREW DAVID SMITH
Affiliation: University of Southern California
- Predicting the molecular complexity of sequencing librariesTimothy 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...
- MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylationJianghan 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...
- A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomicsQiang 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. ..
- Updates to the RMAP short-read mapping softwareAndrew 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...
- Analytic tools to examine high-resolution and genome-scale DNA methylation dataANDREW 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. ..