James R. Cole

22 papers A 1C 3Journal 18
YearRankTypeTitle / Venue / Authors
2018 J jnl
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.
Bioinform.
Xiaole Yin, Xiaotao Jiang, Benli Chai, Liguan Li, Ying Yang, James R. Cole, James M. Tiedje, Tong Zhang
2018 J jnl
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.
Nucleic Acids Res.
Luis Miguel Rodriguez-Rojas, Santosh Gunturu, William T. Harvey, Ramon Rosselló-Mora, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis
2016 J jnl
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database.
Bioinform.
Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, Tong Zhang
2015 C conf
Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing.
BIBE
A. K. M. Tauhidul Islam, Sakti Pramanik, Xinge Ji, James R. Cole, Qiang Zhu
2015 J jnl
Reconstructing 16S rRNA genes in metagenomic data.
Bioinform.
Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun
2014 J jnl
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.
PLoS Comput. Biol.
Yuan Zhang, Yanni Sun, James R. Cole
2014 J jnl
Ribosomal Database Project: data and tools for high throughput rRNA analysis.
Nucleic Acids Res.
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
2013 J jnl
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.
Bioinform.
Yuan Zhang, Yanni Sun, James R. Cole
2010 C conf
BLAST Tree: Fast Filtering for Genomic Sequence Classification.
BIBE
Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik
2009 J jnl
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
Nucleic Acids Res.
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
2007 J jnl
The ribosomal database project (RDP-II): introducing
Nucleic Acids Res.
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
2006 J jnl
Computational aspects of systematic biology.
Briefings Bioinform.
Timothy G. Lilburn, Scott H. Harrison, James R. Cole, George M. Garrity
2006 C conf
Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model.
BIBE
Qiang Xue, James R. Cole, Sakti Pramanik
2005 J jnl
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.
Nucleic Acids Res.
James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, S. A. Kulam, Donna M. McGarrell, George M. Garrity, James M. Tiedje
2003 J jnl
BSD: the Biodegradative Strain Database.
Nucleic Acids Res.
John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje
2003 J jnl
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.
Nucleic Acids Res.
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
2001 J jnl
The RDP-II (Ribosomal Database Project).
Nucleic Acids Res.
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
2001 J jnl
rrndb: the Ribosomal RNA Operon Copy Number Database.
Nucleic Acids Res.
Joel A. Klappenbach, Paul Saxman, James R. Cole, Thomas M. Schmidt
2000 J jnl
The RDP (Ribosomal Database Project) continues.
Nucleic Acids Res.
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
1999 J jnl
A new version of the RDP (Ribosomal Database Project).
Nucleic Acids Res.
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
1996 J jnl
Alignment of possible secondary structures in multiple RNA sequences using simulated annealing.
Comput. Appl. Biosci.
Jin Kim, James R. Cole, Sakti Pramanik
1996 A conf
Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing.
ISMB
Jin Kim, James R. Cole, Eric Torng, Sakti Pramanik