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Journal Articles
- 2018
[j15]Xiaole Yin
, Xiaotao Jiang, Benli Chai, Liguan Li, Ying Yang, James R. Cole, James M. Tiedje, Tong Zhang:
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. 34(13): 2263-2270 (2018)- [j14]Luis Miguel Rodriguez-Rojas, Santosh Gunturu, William T. Harvey, Ramon Rosselló-Mora, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis:
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res. 46(Webserver-Issue): W282-W288 (2018) - 2016
- [j13]Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, Tong Zhang:
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinform. 32(15): 2346-2351 (2016) - 2014
- [j12]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:
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42(Database-Issue): 633-642 (2014) - 2012
- [j11]Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown:
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc. Natl. Acad. Sci. USA 109(33): 13272-13277 (2012) - 2010
- [j10]Bostjan Murovec, James M. Tiedje, Blaz Stres:
DNA encoding for an efficient 'Omics processing. Comput. Methods Programs Biomed. 100(2): 175-190 (2010) - 2009
- [j9]Blaz Stres, James M. Tiedje, Bostjan Murovec:
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases. Bioinform. 25(12): 1556-1558 (2009) - [j8]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:
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37(Database-Issue): 141-145 (2009) - 2007
- [j7]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:
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35(Database-Issue): 169-172 (2007) - 2005
- [j6]James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, S. A. Kulam, Donna M. McGarrell, George M. Garrity, James M. Tiedje:
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33(Database-Issue): 294-296 (2005) - 2003
- [j5]John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje:
BSD: the Biodegradative Strain Database. Nucleic Acids Res. 31(1): 152-155 (2003) - [j4]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:
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31(1): 442-443 (2003) - 2001
- [j3]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:
The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29(1): 173-174 (2001) - 2000
- [j2]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:
The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28(1): 173-174 (2000) - 1999
- [j1]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:
A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27(1): 171-173 (1999)
Conference and Workshop Papers
- 2012
- [c1]Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown:
Workshop: Graph compression approaches in assembly. ICCABS 2012: 1-2
Coauthor Index
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