Brent Pedersen

Summary

Publications

  1. pmc Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values
    Brent S Pedersen
    Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
    Bioinformatics 28:2986-8. 2012
  2. pmc MethylCoder: software pipeline for bisulfite-treated sequences
    Brent Pedersen
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Bioinformatics 27:2435-6. 2011
  3. pmc Screening synteny blocks in pairwise genome comparisons through integer programming
    Haibao Tang
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 12:102. 2011
  4. pmc Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids
    Eric Lyons
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Physiol 148:1772-81. 2008
  5. pmc Transposed genes in Arabidopsis are often associated with flanking repeats
    Margaret R Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 6:e1000949. 2010

Detail Information

Publications5

  1. pmc Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values
    Brent S Pedersen
    Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
    Bioinformatics 28:2986-8. 2012
    ..Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications...
  2. pmc MethylCoder: software pipeline for bisulfite-treated sequences
    Brent Pedersen
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Bioinformatics 27:2435-6. 2011
    ..It is more flexible than existing software and competitive in terms of speed and memory use...
  3. pmc Screening synteny blocks in pairwise genome comparisons through integer programming
    Haibao Tang
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    BMC Bioinformatics 12:102. 2011
    ..We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events...
  4. pmc Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids
    Eric Lyons
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Physiol 148:1772-81. 2008
    ..This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically...
  5. pmc Transposed genes in Arabidopsis are often associated with flanking repeats
    Margaret R Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 6:e1000949. 2010
    ..We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition...