Adrian Schneider

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. pmc Empirical codon substitution matrix
    Adrian Schneider
    Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland
    BMC Bioinformatics 6:134. 2005
  2. doi request reprint Support patterns from different outgroups provide a strong phylogenetic signal
    Adrian Schneider
    ETH Zurich, Department of Computer Science, Zurich, Switzerland
    Mol Biol Evol 26:1259-72. 2009
  3. ncbi request reprint SynPAM-a distance measure based on synonymous codon substitutions
    Adrian Schneider
    ETH Zurich, Institute of Computational Science, Universitaetsstrasse, Zurich, Switzerland
    IEEE/ACM Trans Comput Biol Bioinform 4:553-60. 2007
  4. ncbi request reprint OMA Browser--exploring orthologous relations across 352 complete genomes
    Adrian Schneider
    Institute of Computational Science, ETH Zurich, Switzerland
    Bioinformatics 23:2180-2. 2007
  5. pmc A phylogenomic study of human, dog, and mouse
    Gina Cannarozzi
    Institute of Computational Science, ETH Zurich, Zurich, Switzerland
    PLoS Comput Biol 3:e2. 2007
  6. pmc Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
    Christophe Dessimoz
    ETH Zurich, Institute of Computational Science, 8092 Zurich, Switzerland
    BMC Bioinformatics 7:529. 2006
  7. doi request reprint Improving phylogenetic inference with a semiempirical amino acid substitution model
    Stefan Zoller
    Computational Biochemistry Research Group, ETH Zurich, Zurich, Switzerland
    Mol Biol Evol 30:469-79. 2013
  8. doi request reprint A new semiempirical codon substitution model based on principal component analysis of mammalian sequences
    Stefan Zoller
    Department of Computer Science, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    Mol Biol Evol 29:271-7. 2012
  9. pmc OMA 2011: orthology inference among 1000 complete genomes
    Adrian M Altenhoff
    ETH Zurich, Computer Science, Universitätstr 6, 8092 Zurich, Switzerland
    Nucleic Acids Res 39:D289-94. 2011
  10. doi request reprint Empirical analysis of the most relevant parameters of codon substitution models
    Stefan Zoller
    Computer Science Department, ETH Zurich, Zurich, Switzerland
    J Mol Evol 70:605-12. 2010

Detail Information

Publications10

  1. pmc Empirical codon substitution matrix
    Adrian Schneider
    Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland
    BMC Bioinformatics 6:134. 2005
    ..Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution...
  2. doi request reprint Support patterns from different outgroups provide a strong phylogenetic signal
    Adrian Schneider
    ETH Zurich, Department of Computer Science, Zurich, Switzerland
    Mol Biol Evol 26:1259-72. 2009
    ..It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade...
  3. ncbi request reprint SynPAM-a distance measure based on synonymous codon substitutions
    Adrian Schneider
    ETH Zurich, Institute of Computational Science, Universitaetsstrasse, Zurich, Switzerland
    IEEE/ACM Trans Comput Biol Bioinform 4:553-60. 2007
    ..Comparisons with established measures of synonymous distance indicate that SynPAM has less variance and yields useful results over a longer time range...
  4. ncbi request reprint OMA Browser--exploring orthologous relations across 352 complete genomes
    Adrian Schneider
    Institute of Computational Science, ETH Zurich, Switzerland
    Bioinformatics 23:2180-2. 2007
    ..Several large-scale efforts with various methodologies and scope tackle this problem, including OMA (the Orthologous MAtrix project)...
  5. pmc A phylogenomic study of human, dog, and mouse
    Gina Cannarozzi
    Institute of Computational Science, ETH Zurich, Zurich, Switzerland
    PLoS Comput Biol 3:e2. 2007
    ....
  6. pmc Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
    Christophe Dessimoz
    ETH Zurich, Institute of Computational Science, 8092 Zurich, Switzerland
    BMC Bioinformatics 7:529. 2006
    ..The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming...
  7. doi request reprint Improving phylogenetic inference with a semiempirical amino acid substitution model
    Stefan Zoller
    Computational Biochemistry Research Group, ETH Zurich, Zurich, Switzerland
    Mol Biol Evol 30:469-79. 2013
    ....
  8. doi request reprint A new semiempirical codon substitution model based on principal component analysis of mammalian sequences
    Stefan Zoller
    Department of Computer Science, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    Mol Biol Evol 29:271-7. 2012
    ....
  9. pmc OMA 2011: orthology inference among 1000 complete genomes
    Adrian M Altenhoff
    ETH Zurich, Computer Science, Universitätstr 6, 8092 Zurich, Switzerland
    Nucleic Acids Res 39:D289-94. 2011
    ..In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org...
  10. doi request reprint Empirical analysis of the most relevant parameters of codon substitution models
    Stefan Zoller
    Computer Science Department, ETH Zurich, Zurich, Switzerland
    J Mol Evol 70:605-12. 2010
    ..For the third and subsequent PCs no simple descriptions could be found...