James R. Cole

According to our database, James R. Cole authored at least 22 papers between 1996 and 2018.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2018

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

Luis Miguel Rodriguez-Rojas, Santosh Gunturu, William T. Harvey, Ramon Rosselló-Mora, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis

Nucleic Acids Res., 2018

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.

Xiaole Yin, Xiaotao Jiang, Benli Chai, Liguan Li, Ying Yang, James R. Cole, James M. Tiedje, Tong Zhang

Bioinform., 2018

2016

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

Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, Tong Zhang

Bioinform., 2016

2015

Reconstructing 16S rRNA genes in metagenomic data.

Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun

Bioinform., 2015

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

A. K. M. Tauhidul Islam, Sakti Pramanik, Xinge Ji, James R. Cole, Qiang Zhu

Proceedings of the 15th IEEE International Conference on Bioinformatics and Bioengineering, 2015

2014

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

Yuan Zhang, Yanni Sun, James R. Cole

PLoS Comput. Biol., 2014

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

Nucleic Acids Res., 2014

2013

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

Yuan Zhang, Yanni Sun, James R. Cole

Bioinform., 2013

2010

BLAST Tree: Fast Filtering for Genomic Sequence Classification.

Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik

Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009

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

James R. Cole, Qiong Wang, E. 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

Nucleic Acids Res., 2009

2007

The ribosomal database project (RDP-II): introducing <i>myRDP</i> space and quality controlled public data.

James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje

Nucleic Acids Res., 2007

2006

Computational aspects of systematic biology.

Timothy G. Lilburn, Scott H. Harrison, James R. Cole, George M. Garrity

Briefings Bioinform., 2006

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

Qiang Xue, James R. Cole, Sakti Pramanik

Proceedings of the Sixth IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2006), 2006

2005

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

Nucleic Acids Res., 2005

2003

BSD: the Biodegradative Strain Database.

John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje

Nucleic Acids Res., 2003

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, S. Chandra, Donna M. McGarrell, Thomas M. Schmidt, George M. Garrity, James M. Tiedje

Nucleic Acids Res., 2003

2001

The RDP-II (Ribosomal Database Project).

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr., Paul Saxman, Ryan J. Farris, George M. Garrity, Gary J. Olsen, Thomas M. Schmidt, James M. Tiedje

Nucleic Acids Res., 2001

rrndb: the Ribosomal RNA Operon Copy Number Database.

Joel A. Klappenbach, Paul Saxman, James R. Cole, Thomas M. Schmidt

Nucleic Acids Res., 2001

2000

The RDP (Ribosomal Database Project) continues.

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr., Paul Saxman, Jason M. Stredwick, George M. Garrity, Bing Li, Gary J. Olsen, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje

Nucleic Acids Res., 2000

1999

A new version of the RDP (Ribosomal Database Project).

Bonnie L. Maidak, James R. Cole, Charles T. Parker Jr., George M. Garrity, Niels Larsen, Bing Li, Timothy G. Lilburn, Michael J. McCaughey, Gary J. Olsen, Ross A. Overbeek, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje, Carl R. Woese

Nucleic Acids Res., 1999

1996

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

Jin Kim, James R. Cole, Sakti Pramanik

Comput. Appl. Biosci., 1996

Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing.

Jin Kim, James R. Cole, Eric Torng, Sakti Pramanik

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996