Research Topics
| Victor KuninSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
| Collaborators
|
Detail Information
Publications
The properties of protein family space depend on experimental designVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:2618-22. 2005..We conclude that these properties are complementary rather than contradictory, while describing the protein universe from different perspectives...
Evolutionary conservation of sequence and secondary structures in CRISPR repeatsVictor 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...- CoGenT++: an extensive and extensible data environment for computational genomicsLeon Goldovsky
Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:3806-10. 2005..Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing... - Clustering the annotation space of proteinsVictor 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... - A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaDongying Wu
DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 462:1056-60. 2009.... - A bacterial metapopulation adapts locally to phage predation despite global dispersalVictor 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... - The net of life: reconstructing the microbial phylogenetic networkVictor 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... - MagicMatch--cross-referencing sequence identifiers across databasesMike Smith
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 21:3429-30. 2005..The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer... - GeneTRACE-reconstruction of gene content of ancestral speciesVictor Kunin
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Bioinformatics 19:1412-6. 2003.... - Protein families and TRIBES in genome sequence spaceAnton 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/... - A bioinformatician's guide to metagenomicsVictor 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... - CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaeaRotem 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... - Measuring genome conservation across taxa: divided strains and united kingdomsVictor 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>... 
Experimental factors affecting PCR-based estimates of microbial species richness and evennessAnna 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...- A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspectiveChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Res Microbiol 157:57-68. 2006.... - Denoising inferred functional association networks obtained by gene fusion analysisAtanas 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... - Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termiteFalk 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... - Functional evolution of the yeast protein interaction networkVictor 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... - COmplete GENome Tracking (COGENT): a flexible data environment for computational genomicsPaul 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. AVAILABILITY: http://maine.ebi.ac.uk:8000/services/cogent/.. - Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesVictor 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... - The balance of driving forces during genome evolution in prokaryotesVictor 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... - An experimental metagenome data management and analysis systemVictor 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... - Classification schemes for protein structure and functionChristos A Ouzounis
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
Nat Rev Genet 4:508-19. 2003.... - Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix oreniiKonstantinos Mavromatis
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e4192. 2009.... - Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communitiesHector 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... - Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial matVictor Kunin
Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA
Mol Syst Biol 4:198. 2008.... - Myriads of protein families, and still countingVictor 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... - TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilitiesShengyin 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)... - A korarchaeal genome reveals insights into the evolution of the ArchaeaJames 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... - Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publicationsPaul Janssen
Belgian Nuclear Research Centre, Belgium
EMBO Rep 6:397-9. 2005 - Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genesYang 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... - Beyond 100 genomesPaul Janssen
Genome Biol 4:402. 2003..An overview of these genomes reveals certain interesting trends and provides valuable insights into possible future developments... - Expansion of the BioCyc collection of pathway/genome databases to 160 genomesPeter 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...