James M. Tiedje

16 papers Journal 15Unranked 1
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
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
2012 J jnl
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.
Proc. Natl. Acad. Sci. USA
Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
2012 — conf
Workshop: Graph compression approaches in assembly.
ICCABS
Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
2010 J jnl
DNA encoding for an efficient 'Omics processing.
Comput. Methods Programs Biomed.
Bostjan Murovec, James M. Tiedje, Blaz Stres
2009 J jnl
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases.
Bioinform.
Blaz Stres, James M. Tiedje, Bostjan Murovec
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
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
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