Vincent J Denef

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
    Ian Lo
    University of California, Berkeley, California 94720, USA
    Nature 446:537-41. 2007
  2. ncbi request reprint Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
    J Proteome Res 6:3152-61. 2007
  3. doi request reprint Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
    Vincent J Denef
    University of California, Berkeley, CA 94720, USA
    Environ Microbiol 11:313-25. 2009
  4. pmc Ecological distribution and population physiology defined by proteomics in a natural microbial community
    Ryan S Mueller
    Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA
    Mol Syst Biol 6:374. 2010
  5. pmc Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
    Vincent J Denef
    University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:2383-90. 2010
  6. pmc Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
    Christopher P Belnap
    Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    ISME J 5:1152-61. 2011
  7. pmc Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
    Alexis P Yelton
    Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    BMC Genomics 14:485. 2013
  8. doi request reprint In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
    Science 336:462-6. 2012
  9. pmc The dynamic genetic repertoire of microbial communities
    Paul Wilmes
    Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
    FEMS Microbiol Rev 33:109-32. 2009
  10. doi request reprint AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
    ISME J 4:599-610. 2010

Collaborators

Detail Information

Publications14

  1. ncbi request reprint Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
    Ian Lo
    University of California, Berkeley, California 94720, USA
    Nature 446:537-41. 2007
    ....
  2. ncbi request reprint Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
    J Proteome Res 6:3152-61. 2007
    ..4% reduction of the initial protein coverage per 1% amino acid divergence and total identification loss at 86% AAI. Consequently, shotgun proteomics is capable of cross-strain identifications but avoids most cross-species false positives...
  3. doi request reprint Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
    Vincent J Denef
    University of California, Berkeley, CA 94720, USA
    Environ Microbiol 11:313-25. 2009
    ..Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system...
  4. pmc Ecological distribution and population physiology defined by proteomics in a natural microbial community
    Ryan S Mueller
    Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA
    Mol Syst Biol 6:374. 2010
    ..This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ...
  5. pmc Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
    Vincent J Denef
    University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:2383-90. 2010
    ..In summary, the results show how subtle genetic variations can lead to distinct ecological strategies...
  6. pmc Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
    Christopher P Belnap
    Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    ISME J 5:1152-61. 2011
    ....
  7. pmc Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
    Alexis P Yelton
    Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    BMC Genomics 14:485. 2013
    ..Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order...
  8. doi request reprint In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
    Science 336:462-6. 2012
    ..The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities...
  9. pmc The dynamic genetic repertoire of microbial communities
    Paul Wilmes
    Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
    FEMS Microbiol Rev 33:109-32. 2009
    ..Finally, we highlight the importance of virus-host dynamics in generating and shaping within-population diversity...
  10. doi request reprint AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
    ISME J 4:599-610. 2010
    ..We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems...
  11. pmc Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation
    Sheri L Simmons
    Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
    PLoS Biol 6:e177. 2008
    ..Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination...
  12. pmc Persisting viral sequences shape microbial CRISPR-based immunity
    Ariel D Weinberger
    Biophysics Graduate Group, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 8:e1002475. 2012
    ..By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration...
  13. pmc Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility
    Patrick S G Chain
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 103:15280-7. 2006
    ....
  14. ncbi request reprint Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities
    Vincent J Denef
    Laboratory of Microbial Ecology and Technology, Ghent, Belgium
    Environ Microbiol 5:933-43. 2003
    ..This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment...