Victor Kunin

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. 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
  2. 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
  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. pmc Clustering the annotation space of proteins
    Victor Kunin
    Computational Genomics Group, EMBL EBI, Cambridge, CB10 1SO, UK
    BMC Bioinformatics 6:24. 2005
  5. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications33

  1. 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...
  2. 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...
  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. 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...
  5. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ....
  6. 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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/...
  11. pmc A bioinformatician's guide to metagenomics
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA
    Microbiol Mol Biol Rev 72:557-78, Table of Contents. 2008
    ..Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project...
  12. ncbi request reprint CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea
    Rotem Sorek
    Rotem Sorek, Victor Kunin and Philip Hugenholtz are at the Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Rev Microbiol 6:181-6. 2008
    ..CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism...
  13. 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>...
  14. doi request reprint Experimental factors affecting PCR-based estimates of microbial species richness and evenness
    Anna Engelbrektson
    Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
    ISME J 4:642-7. 2010
    ..However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities...
  15. 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
    ....
  16. 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...
  17. ncbi request reprint Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
    ..Our results underscore how complex even a 1-microl environment can be...
  18. 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...
  19. 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...
  20. doi request reprint Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Environ Microbiol 12:118-23. 2010
    ..We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere...
  21. 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...
  22. 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...
  23. 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
    ....
  24. pmc Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
    ....
  25. ncbi request reprint Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
    Hector Garcia Martin
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nat Biotechnol 24:1263-9. 2006
    ..The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems...
  26. pmc Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
    Victor Kunin
    Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
    Mol Syst Biol 4:198. 2008
    ....
  27. 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...
  28. 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)...
  29. 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...
  30. 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
  31. 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...
  32. 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...
  33. 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...