Adam C Siepel

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi An algorithm to enumerate sorting reversals for signed permutations
    Adam C Siepel
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    J Comput Biol 10:575-97. 2003
  2. ncbi Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA
    Mol Biol Evol 21:468-88. 2004
  3. ncbi Combining phylogenetic and hidden Markov models in biosequence analysis
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
    J Comput Biol 11:413-28. 2004
  4. ncbi Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
  5. ncbi Computational screening of conserved genomic DNA in search of functional noncoding elements
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nat Methods 2:535-45. 2005
  6. ncbi Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters
    Miltiadis Kininis
    Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, USA
    Mol Cell Biol 27:5090-104. 2007

Collaborators

Detail Information

Publications6

  1. ncbi An algorithm to enumerate sorting reversals for signed permutations
    Adam C Siepel
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    J Comput Biol 10:575-97. 2003
    ..An implementation of the algorithm is available at www.cse.ucsc.edu/~acs...
  2. ncbi Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA
    Mol Biol Evol 21:468-88. 2004
    ..Estimates based on about 3 million sites in coding regions demonstrate that amino acid substitution rates can be learned at the nucleotide level, and suggest that context effects across codon boundaries are significant...
  3. ncbi Combining phylogenetic and hidden Markov models in biosequence analysis
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
    J Comput Biol 11:413-28. 2004
    ....
  4. ncbi Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  5. ncbi Computational screening of conserved genomic DNA in search of functional noncoding elements
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nat Methods 2:535-45. 2005
  6. ncbi Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters
    Miltiadis Kininis
    Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, USA
    Mol Cell Biol 27:5090-104. 2007
    ..These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors...