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2010 – 2019
- 2018
[j18]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)- [j17]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
- [j16]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) - 2015
- [j15]Cheng Yuan, Jikai Lei, James R. Cole, Yanni Sun:
Reconstructing 16S rRNA genes in metagenomic data. Bioinform. 31(12): 35-43 (2015) - [c4]A. K. M. Tauhidul Islam, Sakti Pramanik, Xinge Ji, James R. Cole, Qiang Zhu:
Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing. BIBE 2015: 1-6 - 2014
- [j14]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) - [j13]Yuan Zhang, Yanni Sun, James R. Cole:
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data. PLoS Comput. Biol. 10(8) (2014) - 2013
- [j12]Yuan Zhang, Yanni Sun, James R. Cole:
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. Bioinform. 29(17): 2103-2111 (2013) - 2010
- [c3]Stuart King, Yanni Sun, James R. Cole, Sakti Pramanik:
BLAST Tree: Fast Filtering for Genomic Sequence Classification. BIBE 2010: 58-65
2000 – 2009
- 2009
- [j11]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
- [j10]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) - 2006
- [j9]Timothy G. Lilburn, Scott H. Harrison, James R. Cole, George M. Garrity:
Computational aspects of systematic biology. Briefings Bioinform. 7(2): 186-195 (2006) - [c2]Qiang Xue, James R. Cole, Sakti Pramanik:
Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model. BIBE 2006: 135-140 - 2005
- [j8]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
- [j7]John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje:
BSD: the Biodegradative Strain Database. Nucleic Acids Res. 31(1): 152-155 (2003) - [j6]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
- [j5]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) - [j4]Joel A. Klappenbach, Paul Saxman, James R. Cole, Thomas M. Schmidt:
rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res. 29(1): 181-184 (2001) - 2000
- [j3]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)
1990 – 1999
- 1999
- [j2]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) - 1996
- [j1]Jin Kim, James R. Cole, Sakti Pramanik:
Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. Comput. Appl. Biosci. 12(4): 259-267 (1996) - [c1]Jin Kim, James R. Cole, Eric Torng, Sakti Pramanik:
Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing. ISMB 1996: 125-133
Coauthor Index
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