Andreas Heger

Summary

Affiliation: University of Helsinki
Country: Finland

Publications

  1. ncbi request reprint Exhaustive enumeration of protein domain families
    Andreas Heger
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 328:749-67. 2003
  2. pmc ADDA: a domain database with global coverage of the protein universe
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
    Nucleic Acids Res 33:D188-91. 2005
  3. ncbi request reprint Accurate detection of very sparse sequence motifs
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, Finland
    J Comput Biol 11:843-57. 2004
  4. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
  5. doi request reprint Pfam: the protein families database
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 Viikinkaari 5, 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE 17121 Solna, Sweden
    Nucleic Acids Res 42:D222-30. 2014
  6. pmc The Pfam protein families database
    Marco Punta
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nucleic Acids Res 40:D290-301. 2012
  7. ncbi request reprint The global trace graph, a novel paradigm for searching protein sequence databases
    Andreas Heger
    Institute of Biotechnology, P O Box 56 Viikinkaari 5, FI 00014 University of Helsinki, Finland
    Bioinformatics 23:2361-7. 2007
  8. pmc Insights into hominid evolution from the gorilla genome sequence
    Aylwyn Scally
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 483:169-75. 2012
  9. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008
  10. pmc PairsDB atlas of protein sequence space
    Andreas Heger
    MRC Functional Genetics Unit, University of Oxford, UK
    Nucleic Acids Res 36:D276-80. 2008

Detail Information

Publications14

  1. ncbi request reprint Exhaustive enumeration of protein domain families
    Andreas Heger
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 328:749-67. 2003
    ..The data are publicly available at ftp://ftp.ebi.ac.uk/pub/contrib/heger/adda...
  2. pmc ADDA: a domain database with global coverage of the protein universe
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
    Nucleic Acids Res 33:D188-91. 2005
    ..The data are freely available for downloading and querying via a web interface (http://ekhidna.biocenter.helsinki.fi:9801/sqgraph/pairsdb)...
  3. ncbi request reprint Accurate detection of very sparse sequence motifs
    Andreas Heger
    Institute of Biotechnology, University of Helsinki, Finland
    J Comput Biol 11:843-57. 2004
    ....
  4. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/)...
  5. doi request reprint Pfam: the protein families database
    Robert D Finn
    HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 Viikinkaari 5, 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE 17121 Solna, Sweden
    Nucleic Acids Res 42:D222-30. 2014
    ..Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. ..
  6. pmc The Pfam protein families database
    Marco Punta
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nucleic Acids Res 40:D290-301. 2012
    ..Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam...
  7. ncbi request reprint The global trace graph, a novel paradigm for searching protein sequence databases
    Andreas Heger
    Institute of Biotechnology, P O Box 56 Viikinkaari 5, FI 00014 University of Helsinki, Finland
    Bioinformatics 23:2361-7. 2007
    ..The evolutionary signal can be difficult to detect because functional sites may consist of non-contiguous residues while segments in-between may be mutated without affecting fold or function...
  8. pmc Insights into hominid evolution from the gorilla genome sequence
    Aylwyn Scally
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 483:169-75. 2012
    ..The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution...
  9. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008
    ..Gene predictions, multiple alignments and phylogenetic trees are freely available to browse and download from http://genserv.anat.ox.ac.uk/clades. Further genomes and clades will be added in the future...
  10. pmc PairsDB atlas of protein sequence space
    Andreas Heger
    MRC Functional Genetics Unit, University of Oxford, UK
    Nucleic Acids Res 36:D276-80. 2008
    ..Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites...
  11. ncbi request reprint Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins
    Andreas Heger
    Institute of Biotechnology, P O Box 56, 00014 University of Helsinki Finland
    Bioinformatics 19:i130-7. 2003
    ..The targeted patterns-as gleaned from structure comparisons-are too sparse for statistically significant signals of sequence similarity and accurate multiple sequence alignment...
  12. pmc Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 18:298-309. 2008
    ..Alignment errors are inevitable, and should be considered when drawing conclusions from alignments. Software and alignments to assist researchers in doing this are provided at http://genserv.anat.ox.ac.uk/grape/...
  13. pmc Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
    Christina M Laukaitis
    Department of Medical Genetics, University of Washington, Seattle, USA and Division of Human Biology, Fred Hutchinson CancerResearch Center, Seattle, USA
    BMC Evol Biol 8:46. 2008
    ..Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents and mammals...
  14. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...