Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing. - Jin Kim 002; James R. Cole; Eric Torng; Sakti Pramanik (ISMB, 1996)

Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. - Jin Kim 002; James R. Cole; Sakti Pramanik (Comput. Appl. Biosci., 1996)

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; et al. (Nucleic Acids Res., 1999)

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)

rrndb: the Ribosomal RNA Operon Copy Number Database. - Joel A. Klappenbach; Paul Saxman; James R. Cole; Thomas M. Schmidt (Nucleic Acids Res., 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)

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)

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): 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)

Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model. - Qiang Xue; James R. Cole; Sakti Pramanik (BIBE, 2006)

Computational aspects of systematic biology. - Timothy G. Lilburn; Scott H. Harrison; James R. Cole; George M. Garrity (Briefings Bioinform., 2006)

The ribosomal database project (RDP-II): introducing myRDP 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)

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)

BLAST Tree: Fast Filtering for Genomic Sequence Classification. - Stuart King; Yanni Sun; James R. Cole; Sakti Pramanik (BIBE, 2010)

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. - Yuan Zhang; Yanni Sun; James R. Cole (Bioinform., 2013)

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)

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)

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 001 (BIBE, 2015)

Reconstructing 16S rRNA genes in metagenomic data. - Cheng Yuan 001; Jikai Lei; James R. Cole; Yanni Sun (Bioinform., 2015)

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)

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)

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)