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Items: 1 to 50 of 191

1.

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.

Feng J, Penton CR, He Z, Van Nostrand JD, Yuan MM, Wu L, Wang C, Qin Y, Shi ZJ, Guo X, Schuur EAG, Luo Y, Bracho R, Konstantinidis KT, Cole JR, Tiedje JM, Yang Y, Zhou J.

MBio. 2019 Feb 26;10(1). pii: e02521-18. doi: 10.1128/mBio.02521-18.

2.

Assessment of Naming in Non-native English Speakers with Epilepsy.

Gooding A, Cole JR, Hamberger MJ.

J Int Neuropsychol Soc. 2018 Nov;24(10):1057-1063. doi: 10.1017/S1355617718000632. Epub 2018 Sep 4.

PMID:
30178735
3.

More replenishment than priming loss of soil organic carbon with additional carbon input.

Liang J, Zhou Z, Huo C, Shi Z, Cole JR, Huang L, Konstantinidis KT, Li X, Liu B, Luo Z, Penton CR, Schuur EAG, Tiedje JM, Wang YP, Wu L, Xia J, Zhou J, Luo Y.

Nat Commun. 2018 Aug 9;9(1):3175. doi: 10.1038/s41467-018-05667-7.

4.

Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.

Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2018 Sep 1;94(9). doi: 10.1093/femsec/fiy130.

PMID:
30052926
5.

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT.

Nucleic Acids Res. 2018 Jul 2;46(W1):W282-W288. doi: 10.1093/nar/gky467.

6.

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra.

Liang J, Xia J, Shi Z, Jiang L, Ma S, Lu X, Mauritz M, Natali SM, Pegoraro E, Penton CR, Plaza C, Salmon VG, Celis G, Cole JR, Konstantinidis KT, Tiedje JM, Zhou J, Schuur EAG, Luo Y.

Glob Chang Biol. 2018 Oct;24(10):4946-4959. doi: 10.1111/gcb.14325. Epub 2018 Jun 12.

PMID:
29802797
7.

Interprofessional Collaborative Practice: How Could Dentistry Participate?

Cole JR 2nd, Dodge WW, Findley JS, Horn BD, Kalkwarf KL, Martin MM Jr, Valachovic RW, Winder RL, Young SK.

J Dent Educ. 2018 May;82(5):441-445. doi: 10.21815/JDE.018.048.

8.

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT.

mSystems. 2018 Apr 10;3(3). pii: e00039-18. doi: 10.1128/mSystems.00039-18. eCollection 2018 May-Jun.

9.

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 Jul 1;34(13):2263-2270. doi: 10.1093/bioinformatics/bty053.

PMID:
29408954
10.

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.

11.

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.

12.

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.

PMID:
28715138
13.

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.

14.

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.

15.

RNAcentral: a comprehensive database of non-coding RNA sequences.

The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME.

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28.

16.

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.

17.

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.

PMID:
27153579
18.

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.

19.

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.

PMID:
26553774
20.

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.

21.

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.

22.

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.

23.

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.

PMID:
26115293
25.

RNAcentral: an international database of ncRNA sequences.

RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, Pruitt KD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991. Epub 2014 Oct 28.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

PMID:
23782615
36.

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.

PMID:
23189799
37.

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.

PMID:
23189798
38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

PMID:
19231823
50.

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.

PMID:
19215638

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