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James Cole

Research Profile

Concepts & Ideas

Chemicals & Drugs

Procedures

Sequence Alignment

Living Beings

Phenomena

Genes & Molecular Sequences

Genes, rRNA

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Publications

TOP 3
Torey Looft; Heather K Allen; David P Alt; Darrell O Bayles; Benli Chai; James R Cole; Syed A Hashsham; Timothy A Johnson; Robert D Stedtfeld; Tiffany M Stedtfeld; Woo Jun Sul; James M Tiedje; Thaddeus B Stanton
In-feed antibiotic effects on the swine intestinal microbiome.
Woo Jun Sul; Qiong Wang; James R Cole; Ryan J Farris; Jordan A Fish; Ederson da C Jesus; James M Tiedje
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.
Dawn Field; George M Garrity; Jack Gilbert; Frank Oliver Glöckner; Lynette Hirschman; Ilene Karsch-Mizrachi; Hans-Peter Klenk; Rob Knight; Renzo Kottmann; Nikos Kyrpides; Folker Meyer; Inigo San Gil; Susanna-Assunta Sansone; Lynn M Schriml; Peter Sterk; Tatiana Tatusova; David W Ussery; Owen R White; Linda Amaral-Zettler; Guy Cochrane; James R Cole; Peter Dawyndt; John Wooley
The Genomic Standards Consortium.

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All Publications

2012: Torey Looft; Heather K Allen; David P Alt; Darrell O Bayles; Benli Chai; James R Cole; Syed A Hashsham; Timothy A Johnson; Robert D Stedtfeld; Tiffany M Stedtfeld; Woo Jun Sul; James M Tiedje; Thaddeus B Stanton
In-feed antibiotic effects on the swine intestinal microbiome.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(5):1691-6.
2011: Woo Jun Sul; Qiong Wang; James R Cole; Ryan J Farris; Jordan A Fish; Ederson da C Jesus; James M Tiedje
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(35):14637-42.
2011: Dawn Field; George M Garrity; Jack Gilbert; Frank Oliver Glöckner; Lynette Hirschman; Ilene Karsch-Mizrachi; Hans-Peter Klenk; Rob Knight; Renzo Kottmann; Nikos Kyrpides; Folker Meyer; Inigo San Gil; Susanna-Assunta Sansone; Lynn M Schriml; Peter Sterk; Tatiana Tatusova; David W Ussery; Owen R White; Linda Amaral-Zettler; Guy Cochrane; James R Cole; Peter Dawyndt; John Wooley
The Genomic Standards Consortium.
PLoS biology 2011;9(6):e1001088.
2010: Shoko Iwai; Benli Chai; Woo Jun Sul; James R Cole; Syed A Hashsham; James M Tiedje
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.
The ISME journal 2010;4(2):279-85.
2009: Carlos M Rodríguez-Minguela; Juha H A Apajalahti; Benli Chai; James R Cole; James M Tiedje
Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact.
Applied and environmental microbiology 2009;75(15):5100-10.
2008: George M Garrity; Dawn Field; Nikos Kyrpides; Lynette Hirschman; Susanna-Assunta Sansone; Samuel Angiuoli; James R Cole; Frank Oliver Glöckner; Eugene Kolker; George Kowalchuk; Mary Ann Moran; Dave Ussery; Owen R White
Toward a standards-compliant genomic and metagenomic publication record.
Omics : a journal of integrative biology 2008;12(2):157-60.
2007: Qiong Wang; George M Garrity; James M Tiedje; James R Cole
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Applied and environmental microbiology 2007;73(16):5261-7.
2007: robert stedtfeld; Samuel W Baushke; Dieter M Tourlousse; Benli Chai; James R Cole; Syed A Hashsham
Multiplex approach for screening genetic markers of microbial indicators.
Water environment research : a research publication of the Water Environment Federation 2007;79(3):260-9.
2007: robert stedtfeld; Lukas Wick; Samuel W Baushke; Dieter M Tourlousse; Amanda B Herzog; Yongmei Xia; Jean-Marie Rouillard; Joel A Klappenbach; James R Cole; Erdogan Gulari; James M Tiedje; Syed A Hashsham
Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.
Applied and environmental microbiology 2007;73(2):380-9.
2007: James R Cole; Benli Chai; RJ Farris; Qiong Wang; A S Kulam-Syed-Mohideen; Donna 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 research 2007;35(Database issue):D169-72.
2006: Timothy G Lilburn; Scott H Harrison; James R Cole; George M Garrity
Computational aspects of systematic biology.
Briefings in bioinformatics 2006;7(2):186-95.
2005: James R Cole; Benli Chai; RJ Farris; Qiong Wang; S A Kulam; Donna McGarrell; George M Garrity; James M Tiedje
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.
Nucleic acids research 2005;33(Database issue):D294-6.
2004: Tracie M Jenkins; Troy M Scott; James R Cole; Syed A Hashsham; Joan B Rose
Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases.
Water science and technology : a journal of the International Association on Water Pollution Research 2004;50(1):309-14.
2003: James R Cole; Benli Chai; Terence L Marsh; RJ Farris; Qiong Wang; S A Kulam; S Chandra; Donna 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 research 2003;31(1):442-3.
2002: Robert A Sanford; James R Cole; James M Tiedje
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium.
Applied and environmental microbiology 2002;68(2):893-900.
2001: B Sun; James R Cole; James M Tiedje
Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments.
International journal of systematic and evolutionary microbiology 2001;51(Pt 2):365-71.
2001: Joel A Klappenbach; Paul Saxman; James R Cole; Thomas M Schmidt
rrndb: the Ribosomal RNA Operon Copy Number Database.
Nucleic acids research 2001;29(1):181-4.
2001: BL Maidak; James R Cole; Timothy G Lilburn; CT Parker; Paul Saxman; RJ Farris; George M Garrity; Gary J Olsen; Thomas M Schmidt; James M Tiedje
The RDP-II (Ribosomal Database Project).
Nucleic acids research 2001;29(1):173-4.
2000: B Sun; James R Cole; Robert A Sanford; James M Tiedje
Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol.
Applied and environmental microbiology 2000;66(6):2408-13.
2000: H De Wever; James R Cole; M R Fettig; Deborah A Hogan; James M Tiedje
Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov.
Applied and environmental microbiology 2000;66(6):2297-301.
2000: BL Maidak; James R Cole; Timothy G Lilburn; CT Parker; Paul Saxman; J M Stredwick; George M Garrity; B Li; Gary J Olsen; S Pramanik; Thomas M Schmidt; James M Tiedje
The RDP (Ribosomal Database Project) continues.
Nucleic acids research 2000;28(1):173-4.
1999: Tamara V Tsoi; E G Plotnikova; James R Cole; W F Guerin; Michael Bagdasarian; James M Tiedje
Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates.
Applied and environmental microbiology 1999;65(5):2151-62.
1999: BL Maidak; James R Cole; CT Parker; George M Garrity; Niels Larsen; B Li; Timothy G Lilburn; M J McCaughey; Gary J Olsen; Ross Overbeek; S Pramanik; Thomas M Schmidt; James M Tiedje; Carl R Woese
A new version of the RDP (Ribosomal Database Project).
Nucleic acids research 1999;27(1):171-3.
1996: R A Sanford; James R Cole; Frank E Loeffler; James M Tiedje
Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate.
Applied and environmental microbiology 1996;62(10):3800-8.
1996: J Kim; James R Cole; S Pramanik
Alignment of possible secondary structures in multiple RNA sequences using simulated annealing.
Computer applications in the biosciences : CABIOS 1996;12(4):259-67.
1996: J Kim; James R Cole; E Torng; S Pramanik
Inferring relatedness of a macromolecule to a sequence database without sequencing.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():125-33.
1995: James R Cole; B Z Fathepure; James M Tiedje
Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1.
Biodegradation 1995;6(2):167-72.
1994: James R Cole; A L Cascarelli; W W Mohn; James M Tiedje
Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol.
Applied and environmental microbiology 1994;60(10):3536-42.
1992: G D Griffith; James R Cole; John F Quensen; James M Tiedje
Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.
Applied and environmental microbiology 1992;58(1):409-11.