James R. Cole

发表

Jin Kim, James R. Cole, Eric Torng, 1996, ISMB.

ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database

Tong Zhang, James R. Cole, Bing Li, 2016, Bioinform..

Experimental Testbed for Testing a Robotics Based Identification Method

Ou Ma, James R. Cole, Jeremy J. Bruggemann, 2008 .

BSD: the Biodegradative Strain Database

James R. Cole, Paul Saxman, James M. Tiedje, 2003, Nucleic Acids Res..

Alignment of possible secondary structures in multiple RNA sequences using simulated annealing

James R. Cole, Sakti Pramanik, Jin Kim, 1996, Comput. Appl. Biosci..

Computational aspects of systematic biology

James R. Cole, George M. Garrity, Timothy G. Lilburn, 2006, Briefings Bioinform..

Computational aspects of systematic

James R. Cole, George M. Garrity, Scott H. Harrison, 2006 .

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

Yuan Zhang, James R. Cole, Yanni Sun, 2014, PLoS Comput. Biol..

Reconstructing 16S rRNA genes in metagenomic data

James R. Cole, Cheng Yuan, Jikai Lei, 2015, Bioinform..

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

James R. Cole, Qiong Wang, George M. Garrity, 2006, Nucleic Acids Res..

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

James R. Cole, Qiong Wang, George M. Garrity, 2004, Nucleic Acids Res..

Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model

James R. Cole, Sakti Pramanik, Qiang Xue, 2006, Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06).

ARGs‐OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

Tong Zhang, James R. Cole, Ying Yang, 2018, Bioinform..

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads

Yuan Zhang, James R. Cole, Yanni Sun, 2013, Bioinform..

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

James R. Cole, Qiong Wang, George M. Garrity, 2003, Nucleic Acids Res..

rrndb: the Ribosomal RNA Operon Copy Number Database

James R. Cole, Paul Saxman, Thomas M. Schmidt, 2001, Nucleic Acids Res..

Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing

James R. Cole, Sakti Pramanik, Qiang Zhu, 2015, 2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE).

The RDP (Ribosomal Database Project) continues

James R. Cole, Sakti Pramanik, Bing Li, 2000, Nucleic Acids Res..

SERDP and ESTCP Expert Panel Workshop on Research and Development Needs for the Environmental Remediation Application of Molecular Biological Tools

James R. Cole, Hans F. Stroo, Andrea Leeson, 2005 .

BLAST Tree: Fast Filtering for Genomic Sequence Classification

James R. Cole, Sakti Pramanik, Yanni Sun, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

A new version of the RDP (Ribosomal Database Project)

James R. Cole, Sakti Pramanik, Bing Li, 1999, Nucleic Acids Res..

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

James R. Cole, Qiong Wang, George M. Garrity, 2008, Nucleic Acids Res..

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

James R. Cole, William T. Harvey, James M. Tiedje, 2018, Nucleic Acids Res..

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

James R. Cole, James M. Tiedje, Yanni Sun, 2019, Front. Genet..

Ribosomal Database Project: data and tools for high throughput rRNA analysis

James R. Cole, Qiong Wang, Benli Chai, 2013, Nucleic Acids Res..

Taxonomic Outline of the Bacteria and Archaea: Formerly the Taxonomic Outline of the Prokaryotes

James R. Cole, Timothy Lilburn, George M. Garrity, 2007 .

Part 10 - The Bacteria: Phylum Actinobacteria, Class "Actinobacteria"

James R. Cole, Timothy Lilburn, George M. Garrity, 2007 .

How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

James R. Cole, Nikos C. Kyrpides, Konstantinos T. Konstantinidis, 2018, Applied and Environmental Microbiology.

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

James R. Cole, Timothy A. Johnson, Syed A. Hashsham, 2016, mBio.

Corrigendum: ''RNAcentral : a hub of information for non-coding RNA sequences'' [Nucleic acids research, 47 (2019) D1, p. D221-D229]

Robert D. Finn, James R. Cole, Alex Bateman, 2019 .

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

James R. Cole, Benli Chai, Woo Jun Sul, 2009, The ISME Journal.

Towards richer descriptions of our collection of genomes andmetagenomes

Robert Stevens, Victor Markowitz, James R. Cole, 2006 .

Genomic Standards Consortium Projects

Renzo Kottmann, Pelin Yilmaz, Folker Meyer, 2014, Standards in genomic sciences.

Introduction to the Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7

James R. Cole, Timothy Lilburn, George M. Garrity, 2007 .

Development of soil metadata standards for international DNA sequence databases.

James R. Cole, R. J. Gilkes, N. Prakongkep, 2010 .

Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 9 – The Bacteria : Phylum “ Firmicutes ” : Class “ Bacilli ”

James R. Cole, George M. Garrity, Timothy G. Lilburn, 2007 .

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming

James R. Cole, Kai Xue, Ye Deng, 2016 .

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Andreas Wilke, Renzo Kottmann, Pelin Yilmaz, 2010 .

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

Marcus J. Claesson, James R. Cole, Orla O'Sullivan, 2010, Nucleic acids research.