Victor Kunin

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Clustering the annotation space of proteins
    Victor Kunin
    Computational Genomics Group, EMBL EBI, Cambridge, CB10 1SO, UK
    BMC Bioinformatics 6:24. 2005
  2. ncbi request reprint Functional evolution of the yeast protein interaction network
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge, UK
    Mol Biol Evol 21:1171-6. 2004
  3. ncbi request reprint CoGenT++: an extensive and extensible data environment for computational genomics
    Leon Goldovsky
    Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:3806-10. 2005
  4. ncbi request reprint MagicMatch--cross-referencing sequence identifiers across databases
    Mike Smith
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:3429-30. 2005
  5. ncbi request reprint GeneTRACE-reconstruction of gene content of ancestral species
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 19:1412-6. 2003
  6. pmc Protein families and TRIBES in genome sequence space
    Anton J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:4632-8. 2003
  7. ncbi request reprint COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
    Paul Janssen
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Welcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Bioinformatics 19:1451-2. 2003
  8. pmc Measuring genome conservation across taxa: divided strains and united kingdoms
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:616-21. 2005
  9. ncbi request reprint A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective
    Christos A Ouzounis
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Res Microbiol 157:57-68. 2006
  10. ncbi request reprint The properties of protein family space depend on experimental design
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:2618-22. 2005

Collaborators

Detail Information

Publications24

  1. pmc Clustering the annotation space of proteins
    Victor Kunin
    Computational Genomics Group, EMBL EBI, Cambridge, CB10 1SO, UK
    BMC Bioinformatics 6:24. 2005
    ..Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas...
  2. ncbi request reprint Functional evolution of the yeast protein interaction network
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge, UK
    Mol Biol Evol 21:1171-6. 2004
    ..We propose that the understanding of the mechanisms that generate the scale-free protein interaction network, and possibly other biological networks, requires consideration of protein function...
  3. ncbi request reprint CoGenT++: an extensive and extensible data environment for computational genomics
    Leon Goldovsky
    Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:3806-10. 2005
    ..CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility...
  4. ncbi request reprint MagicMatch--cross-referencing sequence identifiers across databases
    Mike Smith
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:3429-30. 2005
    ..At present, mapping of sequence identifiers across databases is a daunting, time-consuming and computationally expensive process, usually achieved by sequence similarity searches with strict threshold values...
  5. ncbi request reprint GeneTRACE-reconstruction of gene content of ancestral species
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 19:1412-6. 2003
    ....
  6. pmc Protein families and TRIBES in genome sequence space
    Anton J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:4632-8. 2003
    ..Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/...
  7. ncbi request reprint COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
    Paul Janssen
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Welcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Bioinformatics 19:1451-2. 2003
    ..For its design we have implemented an extremely simple yet powerful schema to allow linking of genome sequence data to other resources...
  8. pmc Measuring genome conservation across taxa: divided strains and united kingdoms
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:616-21. 2005
    ..All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>...
  9. ncbi request reprint A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective
    Christos A Ouzounis
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Res Microbiol 157:57-68. 2006
    ....
  10. ncbi request reprint The properties of protein family space depend on experimental design
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Bioinformatics 21:2618-22. 2005
    ..Databases of protein families often exhibit drastically different properties of the protein family space...
  11. ncbi request reprint Classification schemes for protein structure and function
    Christos A Ouzounis
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nat Rev Genet 4:508-19. 2003
    ....
  12. pmc Denoising inferred functional association networks obtained by gene fusion analysis
    Atanas Kamburov
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    BMC Genomics 8:460. 2007
    ..The precision of this method typically improves with an ever-increasing number of reference genomes...
  13. pmc The balance of driving forces during genome evolution in prokaryotes
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Genome Res 13:1589-94. 2003
    ..This approach indicates that it is possible to trace genome content history and quantify the factors that shape contemporary prokaryotic genomes...
  14. pmc Myriads of protein families, and still counting
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK
    Genome Biol 4:401. 2003
    ..From the historical record of genome sequencing, we show that the rate of discovery of new families has remained constant over time, indicating that our knowledge of sequence space is far from complete...
  15. pmc The net of life: reconstructing the microbial phylogenetic network
    Victor Kunin
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, United Kingdom
    Genome Res 15:954-9. 2005
    ..We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs...
  16. pmc Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
    Peter D Karp
    Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 33:6083-9. 2005
    ..Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing...
  17. pmc Beyond 100 genomes
    Paul Janssen
    Genome Biol 4:402. 2003
    ..An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments...
  18. ncbi request reprint An experimental metagenome data management and analysis system
    Victor M Markowitz
    Biological Data Management and Technology Center, Lawrence Berkeley National Lab, USA
    Bioinformatics 22:e359-67. 2006
    ..IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m...
  19. ncbi request reprint TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities
    Shengyin Gu
    Institute for Data Analysis and Visualization IDAV, Department of Computer Science, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
    Bioinformatics 23:764-6. 2007
    ..AVAILABILITY: The program, detailed tutorial and examples are available online (http:/genome.lbl.gov/vista/TreeQVista)...
  20. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  21. pmc A bacterial metapopulation adapts locally to phage predation despite global dispersal
    Victor Kunin
    Microbial Ecology Program, Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Genome Res 18:293-7. 2008
    ..Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally...
  22. pmc Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications
    Paul Janssen
    Belgian Nuclear Research Centre, Belgium
    EMBO Rep 6:397-9. 2005
  23. pmc Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes
    Yang Liu
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520 8114, USA
    Genome Biol 5:R64. 2004
    ..Pseudogenes often manifest themselves as disabled copies of known genes. In prokaryotes, it was generally believed (with a few well-known exceptions) that they were rare...
  24. pmc A korarchaeal genome reveals insights into the evolution of the Archaea
    James G Elkins
    Lehrstuhl fur Mikrobiologie und Archaeenzentrum, Universitat Regensburg, D 93053 Regensburg, Germany
    Proc Natl Acad Sci U S A 105:8102-7. 2008
    ..In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form...