Alexey E Kazakov

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi request reprint Bioinformatics classification and functional analysis of PhoH homologs
    Alexei E Kazakov
    Integrated Genomics Inc, Moscow, Russia
    In Silico Biol 3:3-15. 2003
  2. pmc Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes
    Alexey E Kazakov
    Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:29-38. 2013
  3. pmc Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
    Dmitry A Ravcheev
    Sanford Burnham Medical Research Institute, La Jolla, California, USA
    J Bacteriol 194:1145-57. 2012
  4. pmc Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus
    Dmitry A Rodionov
    Sanford Burnham Medical Research Institute, La Jolla, California, USA
    BMC Genomics 12:S3. 2011
  5. pmc Comparative genomics of the dormancy regulons in mycobacteria
    Anna Gerasimova
    Energy Bioscience Institute, University of California, Berkeley, California 94720, USA
    J Bacteriol 193:3446-52. 2011
  6. pmc RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley 94710, CA, USA
    BMC Genomics 14:745. 2013
  7. pmc New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria
    Alexey E Kazakov
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:4466-75. 2013
  8. pmc RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
    Michael J Cipriano
    Department of Microbiology, University of California Davis, Davis, CA 95616, USA
    BMC Genomics 14:213. 2013
  9. pmc RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:W299-307. 2010

Detail Information

Publications9

  1. ncbi request reprint Bioinformatics classification and functional analysis of PhoH homologs
    Alexei E Kazakov
    Integrated Genomics Inc, Moscow, Russia
    In Silico Biol 3:3-15. 2003
    ..EC-PhoH orthologs are classified in a third group, specific for Enterobacteria. Functional role of PhoH homologs in the lipid and RNA metabolism and proposed interrelation of PhoH paralogs in one organism are discussed...
  2. pmc Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes
    Alexey E Kazakov
    Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:29-38. 2013
    ..The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp)...
  3. pmc Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
    Dmitry A Ravcheev
    Sanford Burnham Medical Research Institute, La Jolla, California, USA
    J Bacteriol 194:1145-57. 2012
    ..The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima...
  4. pmc Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus
    Dmitry A Rodionov
    Sanford Burnham Medical Research Institute, La Jolla, California, USA
    BMC Genomics 12:S3. 2011
    ..The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria...
  5. pmc Comparative genomics of the dormancy regulons in mycobacteria
    Anna Gerasimova
    Energy Bioscience Institute, University of California, Berkeley, California 94720, USA
    J Bacteriol 193:3446-52. 2011
    ..abscessus. Analysis of large gene families encoding USPs, nitroreductases, and DGATs demonstrates a mosaic distribution of regulated and nonregulated members, suggesting frequent acquisition and loss of DosR-binding sites...
  6. pmc RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley 94710, CA, USA
    BMC Genomics 14:745. 2013
    ..The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches)...
  7. pmc New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria
    Alexey E Kazakov
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    J Bacteriol 195:4466-75. 2013
    ..To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases. ..
  8. pmc RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes
    Michael J Cipriano
    Department of Microbiology, University of California Davis, Davis, CA 95616, USA
    BMC Genomics 14:213. 2013
    ..Additionally, confirming computationally inferred regulons by experimental data is critically important...
  9. pmc RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
    Pavel S Novichkov
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Nucleic Acids Res 38:W299-307. 2010
    ..An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov...