J R Cole

Summary

Affiliation: Michigan State University
Country: USA

Publications

  1. doi request reprint Ribosomal Database Project: data and tools for high throughput rRNA analysis
    James R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA, Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA, Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Biological Sciences, Western Illinois University, Malcomb, IL 61455, USA and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nucleic Acids Res 42:D633-42. 2014
  2. pmc The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    J R Cole
    Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Nucleic Acids Res 37:D141-5. 2009
  3. pmc The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
    J R Cole
    Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 35:D169-72. 2007
  4. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
  5. pmc The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    J R Cole
    Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 31:442-3. 2003
  6. ncbi request reprint Inferring relatedness of a macromolecule to a sequence database without sequencing
    J Kim
    Department of Computer Science, Michigan State University, East Lansing 48824, USA
    Proc Int Conf Intell Syst Mol Biol 4:125-33. 1996
  7. pmc Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates
    T V Tsoi
    Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
    Appl Environ Microbiol 65:2151-62. 1999
  8. pmc Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov
    H De Wever
    Michigan State University, Center for Microbial Ecology, East Lansing, Michigan 48824 1325, USA
    Appl Environ Microbiol 66:2297-301. 2000
  9. pmc The RDP (Ribosomal Database Project) continues
    B L Maidak
    Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824 1325, USA
    Nucleic Acids Res 28:173-4. 2000
  10. ncbi request reprint Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments
    B Sun
    Center for Microbial Ecology and Department of Crop and Soil Sciences, Michigan State University, East Lansing 48824-1325, USA
    Int J Syst Evol Microbiol 51:365-71. 2001

Detail Information

Publications12

  1. doi request reprint Ribosomal Database Project: data and tools for high throughput rRNA analysis
    James R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA, Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA, Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Biological Sciences, Western Illinois University, Malcomb, IL 61455, USA and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nucleic Acids Res 42:D633-42. 2014
    ..In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines. ..
  2. pmc The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    J R Cole
    Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
    Nucleic Acids Res 37:D141-5. 2009
    ..Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/...
  3. pmc The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
    J R Cole
    Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 35:D169-72. 2007
    ..In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/)...
  4. pmc The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    J R Cole
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 33:D294-6. 2005
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  5. pmc The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    J R Cole
    Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
    Nucleic Acids Res 31:442-3. 2003
    ..The RDP-II email address for questions or comments is rdpstaff@msu.edu...
  6. ncbi request reprint Inferring relatedness of a macromolecule to a sequence database without sequencing
    J Kim
    Department of Computer Science, Michigan State University, East Lansing 48824, USA
    Proc Int Conf Intell Syst Mol Biol 4:125-33. 1996
    ..Furthermore, the confidence of this inferred information is strongly correlated to the minimum pairwise relatedness of any two elements in S...
  7. pmc Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates
    T V Tsoi
    Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
    Appl Environ Microbiol 65:2151-62. 1999
    ..The ohb DNA region is bordered by 14-bp imperfect inverted repeats at positions 56 to 69 and 5984 to 5997...
  8. pmc Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov
    H De Wever
    Michigan State University, Center for Microbial Ecology, East Lansing, Michigan 48824 1325, USA
    Appl Environ Microbiol 66:2297-301. 2000
    ..In view of its unique physiological characteristics, the name Trichlorobacter thiogenes is suggested for strain K1...
  9. pmc The RDP (Ribosomal Database Project) continues
    B L Maidak
    Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824 1325, USA
    Nucleic Acids Res 28:173-4. 2000
    ....
  10. ncbi request reprint Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments
    B Sun
    Center for Microbial Ecology and Department of Crop and Soil Sciences, Michigan State University, East Lansing 48824-1325, USA
    Int J Syst Evol Microbiol 51:365-71. 2001
    ..nov. The type strain is strain DCB-MT (= ATCC 700979T)...
  11. ncbi request reprint Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases
    T M Jenkins
    Dept of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824, USA
    Water Sci Technol 50:309-14. 2004
    ..The database and the VFARs established will be of use to the regulatory community as a way to assist with prioritising those organisms, which need to be regulated...