J
James R. Cole
Researcher at Michigan State University
Publications - 115
Citations - 41975
James R. Cole is an academic researcher from Michigan State University. The author has contributed to research in topics: Metagenomics & Tundra. The author has an hindex of 49, co-authored 115 publications receiving 36048 citations. Previous affiliations of James R. Cole include Great Lakes Bioenergy Research Center & Los Alamos National Laboratory.
Papers
More filters
Journal ArticleDOI
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Journal ArticleDOI
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
James R. Cole,Qiong Wang,Erick Cardenas,Jordan A. Fish,Benli Chai,Ryan J. Farris,A. S. Kulam-Syed-Mohideen,Donna M. McGarrell,Terry L. Marsh,George M. Garrity,James M. Tiedje +10 more
TL;DR: An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
Journal ArticleDOI
Ribosomal Database Project: data and tools for high throughput rRNA analysis
James R. Cole,Qiong Wang,Jordan A. Fish,Benli Chai,Donna M. McGarrell,Yanni Sun,C. Titus Brown,Andrea Porras-Alfaro,Cheryl R. Kuske,James M. Tiedje +9 more
TL;DR: RDP now includes a collection of fungal large subunit rRNA genes, and 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.
Journal ArticleDOI
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
James R. Cole,Benli Chai,Ryan J. Farris,Qiong Wang,S. A. Kulam,Donna M. McGarrell,George M. Garrity,James M. Tiedje +7 more
TL;DR: The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data.
Journal ArticleDOI
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
James R. Cole,Benli Chai,Terry L. Marsh,Ryan J. Farris,Qiong Wang,S. A. Kulam,Sadanandavalli Retnaswami Chandra,Donna M. McGarrell,Thomas M. Schmidt,George M. Garrity,James M. Tiedje +10 more
TL;DR: The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community and debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences.