Ari Löytynoja

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc MATLIGN: a motif clustering, comparison and matching tool
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 8:189. 2007
  2. pmc An algorithm for progressive multiple alignment of sequences with insertions
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
    Proc Natl Acad Sci U S A 102:10557-62. 2005
  3. doi request reprint Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Science 320:1632-5. 2008
  4. pmc A model of evolution and structure for multiple sequence alignment
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, UK
    Philos Trans R Soc Lond B Biol Sci 363:3913-9. 2008
  5. pmc webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 11:579. 2010
  6. pmc Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Bioinformatics 28:1684-91. 2012
  7. doi request reprint Alignment methods: strategies, challenges, benchmarking, and comparative overview
    Ari Löytynoja
    European Bioinformatics Institute EMBL, Hinxton, UK
    Methods Mol Biol 855:203-35. 2012

Collaborators

Detail Information

Publications7

  1. pmc MATLIGN: a motif clustering, comparison and matching tool
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 8:189. 2007
    ..Efficient post-processing, for example, reduces the redundancy of the motifs predicted and enables them to be annotated...
  2. pmc An algorithm for progressive multiple alignment of sequences with insertions
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
    Proc Natl Acad Sci U S A 102:10557-62. 2005
    ..Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms...
  3. doi request reprint Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Science 320:1632-5. 2008
    ..These results suggest that insertions and sequence turnover are more common than is currently thought and challenge the conventional picture of sequence evolution and mechanisms of functional and structural changes...
  4. pmc A model of evolution and structure for multiple sequence alignment
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, UK
    Philos Trans R Soc Lond B Biol Sci 363:3913-9. 2008
    ....
  5. pmc webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 11:579. 2010
    ..g. by objectively selecting subsets of alignment sites...
  6. pmc Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
    Ari Löytynoja
    EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Bioinformatics 28:1684-91. 2012
    ..These do not incorporate and use phylogenetic information and are affected by the composition of the reference alignment and the phylogenetic positions of query sequences...
  7. doi request reprint Alignment methods: strategies, challenges, benchmarking, and comparative overview
    Ari Löytynoja
    European Bioinformatics Institute EMBL, Hinxton, UK
    Methods Mol Biol 855:203-35. 2012
    ..As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended...