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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.

Yin X, Jiang XT, Chai B, Li L, Yang Y, Cole JR, Tiedje JM, Zhang T.

Bioinformatics. 2018 Feb 2. doi: 10.1093/bioinformatics/bty053. [Epub ahead of print]


How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT.

Appl Environ Microbiol. 2018 Mar 1;84(6). pii: e00014-18. doi: 10.1128/AEM.00014-18. Print 2018 Mar 15.


Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.

Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA.

Front Microbiol. 2017 Sep 7;8:1708. doi: 10.3389/fmicb.2017.01708. eCollection 2017.


Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, Zhou J.

Glob Chang Biol. 2018 Jan;24(1):297-307. doi: 10.1111/gcb.13820. Epub 2017 Sep 1.


Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers.

Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA.

J Environ Manage. 2017 Aug 1;198(Pt 1):213-220. doi: 10.1016/j.jenvman.2017.04.079. Epub 2017 Apr 29.


Virulence factor activity relationships (VFARs): a bioinformatics perspective.

Waseem H, Williams MR, Stedtfeld T, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA.

Environ Sci Process Impacts. 2017 Mar 22;19(3):247-260. doi: 10.1039/c6em00689b. Review.


Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay.

Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM.

PLoS One. 2016 Jun 16;11(6):e0157008. doi: 10.1371/journal.pone.0157008. eCollection 2016.


ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database.

Yang Y, Jiang X, Chai B, Ma L, Li B, Zhang A, Cole JR, Tiedje JM, Zhang T.

Bioinformatics. 2016 Aug 1;32(15):2346-51. doi: 10.1093/bioinformatics/btw136. Epub 2016 Mar 12.


Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.

Johnson TA, Stedtfeld RD, Wang Q, Cole JR, Hashsham SA, Looft T, Zhu YG, Tiedje JM.

MBio. 2016 Apr 12;7(2):e02214-15. doi: 10.1128/mBio.02214-15.


Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.

Deshpande V, Wang Q, Greenfield P, Charleston M, Porras-Alfaro A, Kuske CR, Cole JR, Midgley DJ, Tran-Dinh N.

Mycologia. 2016 Jan-Feb;108(1):1-5. doi: 10.3852/14-293. Epub 2015 Nov 9.


Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.

Guo J, Cole JR, Zhang Q, Brown CT, Tiedje JM.

Appl Environ Microbiol. 2015 Oct 16;82(1):157-66. doi: 10.1128/AEM.02772-15. Print 2016 Jan 1.


Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils.

Penton CR, St Louis D, Pham A, Cole JR, Wu L, Luo Y, Schuur EA, Zhou J, Tiedje JM.

Front Microbiol. 2015 Jul 21;6:746. doi: 10.3389/fmicb.2015.00746. eCollection 2015.


Xander: employing a novel method for efficient gene-targeted metagenomic assembly.

Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR.

Microbiome. 2015 Aug 5;3:32. doi: 10.1186/s40168-015-0093-6. eCollection 2015.


Supplementation of monensin and Optimase to beef cows consuming low-quality forage during late gestation and early lactation.

Linneen SK, McGee AL, Cole JR, Jennings JS, Stein DR, Horn GW, Lalman DL.

J Anim Sci. 2015 Jun;93(6):3076-83. doi: 10.2527/jas.2014-8406.


Genomic standards consortium projects.

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.


A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

Zhang Y, Sun Y, Cole JR.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003737. doi: 10.1371/journal.pcbi.1003737. eCollection 2014 Aug.


History and impact of RDP: a legacy from Carl Woese to microbiology.

Cole JR, Tiedje JM.

RNA Biol. 2014;11(3):239-43. doi: 10.4161/rna.28306. Epub 2014 Feb 27. Review.


A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM.

Microbiome. 2013 Mar 4;1(1):8. doi: 10.1186/2049-2618-1-8.


Ribosomal Database Project: data and tools for high throughput rRNA analysis.

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244. Epub 2013 Nov 27.


FunGene: the functional gene pipeline and repository.

Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, Cole JR.

Front Microbiol. 2013 Oct 1;4:291. doi: 10.3389/fmicb.2013.00291. eCollection 2013.


Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.

Penton CR, Johnson TA, Quensen JF 3rd, Iwai S, Cole JR, Tiedje JM.

Front Microbiol. 2013 Sep 17;4:279. doi: 10.3389/fmicb.2013.00279. eCollection 2013.


Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.

Wang Q, Quensen JF 3rd, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR.

MBio. 2013 Sep 17;4(5):e00592-13. doi: 10.1128/mBio.00592-13.


Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions.

Penton CR, St Louis D, Cole JR, Luo Y, Wu L, Schuur EA, Zhou J, Tiedje JM.

Appl Environ Microbiol. 2013 Nov;79(22):7063-72. doi: 10.1128/AEM.01702-13. Epub 2013 Sep 6.


A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.

Zhang Y, Sun Y, Cole JR.

Bioinformatics. 2013 Sep 1;29(17):2103-11. doi: 10.1093/bioinformatics/btt357. Epub 2013 Jun 19.


Continued Competency Assessment. Does it have a necessary role in dentistry?

Cole JR 2nd, Findley JS, Martin MM Jr, Cole JS, Dodge WW, Winder RL, Young SK, Glover JF, Kalkwarf KL.

J Am Coll Dent. 2012 Fall;79(3):13-9.


Continued Competency Assessment. Its history and role in the health professions.

Dodge WW, Winder RL, Young SK, Cole JR 2nd, Findley JS, Martin MM Jr, Cole JS, Glover JF, Kalkwarf KL.

J Am Coll Dent. 2012 Fall;79(3):5-12.


Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms.

Lan Y, Wang Q, Cole JR, Rosen GL.

PLoS One. 2012;7(3):e32491. doi: 10.1371/journal.pone.0032491. Epub 2012 Mar 5.


Expression of the aryl hydrocarbon receptor is not required for the proliferation, migration, invasion, or estrogen-dependent tumorigenesis of MCF-7 breast cancer cells.

Spink BC, Bennett JA, Lostritto N, Cole JR, Spink DC.

Mol Carcinog. 2013 Jul;52(7):544-54. doi: 10.1002/mc.21889. Epub 2012 Mar 2.


In-feed antibiotic effects on the swine intestinal microbiome.

Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, Sul WJ, Stedtfeld TM, Chai B, Cole JR, Hashsham SA, Tiedje JM, Stanton TB.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1691-6. doi: 10.1073/pnas.1120238109. Epub 2012 Jan 17.


RNAcentral: A vision for an international database of RNA sequences.

Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.

RNA. 2011 Nov;17(11):1941-6. doi: 10.1261/rna.2750811. Epub 2011 Sep 22.


Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.

Sul WJ, Cole JR, Jesus Eda C, Wang Q, Farris RJ, Fish JA, Tiedje JM.

Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14637-42. doi: 10.1073/pnas.1111435108. Epub 2011 Aug 22.


The Genomic Standards Consortium.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.

PLoS Biol. 2011 Jun;9(6):e1001088. doi: 10.1371/journal.pbio.1001088. Epub 2011 Jun 21.


Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.


Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.

Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW.

Nucleic Acids Res. 2010 Dec;38(22):e200. doi: 10.1093/nar/gkq873. Epub 2010 Sep 29.


Genomics. Genome project standards in a new era of sequencing.

Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC.

Science. 2009 Oct 9;326(5950):236-7. doi: 10.1126/science.1180614. No abstract available.


Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.

Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM.

ISME J. 2010 Feb;4(2):279-85. doi: 10.1038/ismej.2009.104. Epub 2009 Sep 24.


Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact.

Rodríguez-Minguela CM, Apajalahti JH, Chai B, Cole JR, Tiedje JM.

Appl Environ Microbiol. 2009 Aug;75(15):5100-10. doi: 10.1128/AEM.00133-09. Epub 2009 Jun 5.


Fluorescence enhancement by Au nanostructures: nanoshells and nanorods.

Bardhan R, Grady NK, Cole JR, Joshi A, Halas NJ.

ACS Nano. 2009 Mar 24;3(3):744-52. doi: 10.1021/nn900001q.


Construct validity of the Neuropsychological Screening Battery for Hispanics (NeSBHIS) in a neurological sample.

Bender HA, Cole JR, Aponte-Samalot M, Cruz-Laureano D, Myers L, Vazquez BR, Barr WB.

J Int Neuropsychol Soc. 2009 Mar;15(2):217-24. doi: 10.1017/S1355617709090250. Epub 2009 Feb 12.


The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.


Toward a standards-compliant genomic and metagenomic publication record.

Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O.

OMICS. 2008 Jun;12(2):157-60. doi: 10.1089/omi.2008.A2B2.


Does faculty development enhance teaching effectiveness?

Hendricson WD, Anderson E, Andrieu SC, Chadwick DG, Cole JR, George MC, Glickman GN, Glover JF, Goldberg JS, Haden NK, Kalkwarf KL, Meyerowitz C, Neumann LM, Pyle M, Tedesco LA, Valachovic RW, Weaver RG, Winder RL, Young SK.

J Dent Educ. 2007 Dec;71(12):1513-33.


Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

Wang Q, Garrity GM, Tiedje JM, Cole JR.

Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.


Multiplex approach for screening genetic markers of microbial indicators.

Stedtfeld RD, Baushke S, Tourlousse D, Chai B, Cole JR, Hashsham SA.

Water Environ Res. 2007 Mar;79(3):260-9.



Carducci MD, Gu X, Cole JR, Hruby VJ.

Acta Crystallogr Sect E Struct Rep Online. 2006 Jun;62(6):m1219-m1220.


The dental education environment.

Haden NK, Andrieu SC, Chadwick DG, Chmar JE, Cole JR, George MC, Glickman GN, Glover JF, Goldberg JS, Hendricson WD, Meyerowitz C, Neumann L, Pyle M, Tedesco LA, Valachovic RW, Weaver RG, Winder RL, Young SK, Kalkwarf KL; ADEA Commission on Change and Innovation in Dental Education.

J Dent Educ. 2006 Dec;70(12):1265-70.


Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.

Stedtfeld RD, Wick LM, Baushke SW, Tourlousse DM, Herzog AB, Xia Y, Rouillard JM, Klappenbach JA, Cole JR, Gulari E, Tiedje JM, Hashsham SA.

Appl Environ Microbiol. 2007 Jan;73(2):380-9. Epub 2006 Nov 17.


The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.

Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D169-72. Epub 2006 Nov 7.

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