Works by Cole, James R.

Results: 44

Interprofessional Collaborative Practice: How Could Dentistry Participate?

Published in:

2018

By:

Cole II, James R.;
Dodge, William W.;
Findley, John S.;
Horn, Bruce D.;
Kalkwarf, Kenneth L.;
Martin Jr., Max M.;
Valachovic, Richard W.;
Winder, Ronald L.;
Young, Stephen K.;
Cole, James R 2nd;
Martin, Max M Jr

Publication type:

journal article

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

Published in:

Bioinformatics, 2016, v. 32, n. 15, p. 2346, doi. 10.1093/bioinformatics/btw136

By:

Ying Yang;
Xiaotao Jiang;
Benli Chai;
Liping Ma;
Bing Li;
Anni Zhang;
Cole, James R.;
Tiedje, James M.;
Tong Zhang

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 17, p. 2103, doi. 10.1093/bioinformatics/btt357

By:

Zhang, Yuan;
Sun, Yanni;
Cole, James R.

Publication type:

Article

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming.

Published in:

Nature Climate Change, 2016, v. 6, n. 6, p. 595, doi. 10.1038/nclimate2940

By:

Xue, Kai;
M. Yuan, Mengting;
J. Shi, Zhou;
Qin, Yujia;
Deng, Ye;
Cheng, Lei;
Wu, Liyou;
He, Zhili;
Van Nostrand, Joy D.;
Bracho, Rosvel;
Natali, Susan;
Schuur, Edward. A. G.;
Luo, Chengwei;
Konstantinidis, Konstantinos T.;
Wang, Qiong;
Cole, James R.;
Tiedje, James M.;
Luo, Yiqi;
Zhou, Jizhong

Publication type:

Article

Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms.

Published in:

PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0032491

By:

Yemin Lan;
Qiong Wang;
Cole, James R.;
Rosen, Gail L.

Publication type:

Article

Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils.

Published in:

Molecular Ecology, 2022, v. 31, n. 5, p. 1403, doi. 10.1111/mec.16319

By:

Wu, Linwei;
Yang, Felix;
Feng, Jiajie;
Tao, Xuanyu;
Qi, Qi;
Wang, Cong;
Schuur, Edward A. G.;
Bracho, Rosvel;
Huang, Yi;
Cole, James R.;
Tiedje, James M.;
Zhou, Jizhong

Publication type:

Article

Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.

Published in:

Molecular Ecology, 2021, v. 30, n. 4, p. 926, doi. 10.1111/mec.15773

By:

Cheng, Jingmin;
Yang, Yunfeng;
Yuan, Mengting M.;
Gao, Qun;
Wu, Liyou;
Qin, Ziyan;
Shi, Zhou J.;
Schuur, Edward A. G.;
Cole, James R.;
Tiedje, James M.;
Zhou, Jizhong

Publication type:

Article

Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2020, v. 14, n. 7, p. 1651, doi. 10.1038/s41396-020-0635-1

By:

Wu, Ruonan;
Chai, Benli;
Cole, James R.;
Gunturu, Santosh K.;
Guo, Xue;
Tian, Renmao;
Gu, Ji-Dong;
Zhou, Jizhong;
Tiedje, James M.

Publication type:

Article

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

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05667-7

By:

Liang, Junyi;
Zhou, Zhenghu;
Huo, Changfu;
Shi, Zheng;
Cole, James R.;
Huang, Lei;
Konstantinidis, Konstantinos T.;
Li, Xiaoming;
Liu, Bo;
Luo, Zhongkui;
Penton, C. Ryan;
Schuur, Edward A. G.;
Tiedje, James M.;
Wang, Ying-Ping;
Wu, Liyou;
Xia, Jianyang;
Zhou, Jizhong;
Luo, Yiqi

Publication type:

Article

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

Published in:

2011

By:

Yilmaz, Pelin;
Kottmann, Renzo;
Field, Dawn;
Knight, Rob;
Cole, James R.;
Amaral-Zettler, Linda;
Gilbert, Jack A.;
Karsch-Mizrachi, Ilene;
Johnston, Anjanette;
Cochrane, Guy;
Vaughan, Robert;
Hunter, Christopher;
Park, Joonhong;
Morrison, Norman;
Rocca-Serra, Philippe;
Sterk, Peter;
Arumugam, Manimozhiyan;
Bailey, Mark;
Baumgartner, Laura;
Birren, Bruce W.

Publication type:

Opinion

The Genomic Standards Consortium.

Published in:

PLoS Biology, 2011, v. 9, n. 6, p. 1, doi. 10.1371/journal.pbio.1001088

By:

Field, Dawn;
Amaral-Zettler, Linda;
Cochrane, Guy;
Cole, James R.;
Dawyndt, Peter;
Garrity, George M.;
Gilbert, Jack;
Glöckner, Frank Oliver;
Hirschman, Lynette;
Karsch-Mizrachi, Ilene;
Klenk, Hans-Peter;
Knight, Rob;
Kottmann, Renzo;
Kyrpides, Nikos;
Meyer, Folker;
Gil, Inigo San;
Sansone, Susanna-Assunta;
Schriml, Lynn M.;
Sterk, Peter;
Tatusova, Tatiana

Publication type:

Article

Computational aspects of systematic biology.

Published in:

Briefings in Bioinformatics, 2006, v. 7, n. 2, p. 186, doi. 10.1093/bib/bbl005

By:

Lilburn, Timothy G.;
Harrison, Scott H.;
Cole, James R.;
Garrity, George M.

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2015, p. 1, doi. 10.3389/fmicb.2015.00746

By:

Penton, Christopher R.;
Louis, Derek St.;
Pham, Amanda;
Cole, James R.;
Liyou Wu;
Yiqi Luo;
Schuur, E. A. G.;
Jizhong Zhou;
Tiedje, James M.;
Waldrop, Mark;
Comte, Jérôme

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2010, v. 4, n. 2, p. 279, doi. 10.1038/ismej.2009.104

By:

Shoko Iwai;
Benli Chai;
Woo Jun Sul;
Cole, James R.;
Hashsham, Syed A.;
Tiedje, James M.

Publication type:

Article

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pcbi.1003737

By:

Zhang, Yuan;
Sun, Yanni;
Cole, James R.

Publication type:

Article

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.

Published in:

Microbiome, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40168-021-01047-4

By:

Qian, Xun;
Gunturu, Santosh;
Guo, Jiarong;
Chai, Benli;
Cole, James R.;
Gu, Jie;
Tiedje, James M.

Publication type:

Article

DOES IT HAVE A NECESSARY ROIE iN DENTiSTRY?

Published in:

Journal of the American College of Dentists, 2012, v. 79, n. 3, p. 13

By:

Cole, James R.;
Findley, John S.;
Martin Jr., Max M.;
Cole, James S.;
Dodge, William W.;
Winder, Ronald L.;
Young, Stephen K.;
Glover, Joel F.;
Kalkwarf, Kenneth L.

Publication type:

Article

ITS HisTORy AND ROIE ¡N TIHE HEAITIH PROFESSIONS.

Published in:

Journal of the American College of Dentists, 2012, v. 79, n. 3, p. 5

By:

Dodge, William W.;
Winder, Ronald L.;
Young, Stephen K.;
Cole, James R.;
Findley, John S.;
Martin, Max M.;
Glover, Joel F.;
Kalkwarf, Kenneth L.

Publication type:

Article

COMMENTARY AFTER THIRTY YEARS OF PRIVATE PRACTIVE IN ORAL SURGERY.

Published in:

Journal of the American College of Dentists, 2004, v. 71, n. 3, p. 11

By:

Cole II, James R.

Publication type:

Article

FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf348

By:

Gerhardt, Kenji;
Ruiz-Perez, Carlos A;
Rodriguez-R, Luis M;
Jain, Chirag;
Tiedje, James M;
Cole, James R;
Konstantinidis, Konstantinos T

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. W1, p. W282, doi. 10.1093/nar/gky467

By:

Rodriguez-R, Luis M.;
Gunturu, Santosh;
Harvey, William T.;
Rosselló-Mora, Ramon;
Tiedje, James M.;
Cole, James R.;
Konstantinidis, Konstantinos T.

Publication type:

Article

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

Published in:

PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157008

By:

Chai, Benli;
Tsoi, Tamara V.;
Iwai, Shoko;
Liu, Cun;
Fish, Jordan A.;
Gu, Cheng;
Johnson, Timothy A.;
Zylstra, Gerben;
Teppen, Brian J.;
Li, Hui;
Hashsham, Syed A.;
Boyd, Stephen A.;
Cole, James R.;
Tiedje, James M.

Publication type:

Article

History and impact of RDP.

Published in:

RNA Biology, 2014, v. 11, n. 3, p. 1, doi. 10.4161/rna.28306

By:

Cole, James R.;
Tiedje, James M.

Publication type:

Article

Will Large DSO-Managed Group Practices Be the Predominant Setting for Oral Health Care by 2025? Two Viewpoints.

Published in:

2015

By:

Cole, James R.;
Dodge, William W.;
Findley, John S.;
Young, Stephen K.;
Horn, Bruce D.;
Kalkwarf, Kenneth L.;
Martin Jr., Max M.;
Winder, Ronald L.

Publication type:

Opinion

Does Faculty Development Enhance Teaching Effectiveness?

Published in:

Journal of Dental Education, 2007, v. 71, n. 12, p. 1513

By:

Hendricson, William D.;
Anderson, Eugene;
Andrieu, Sandra C.;
Chadwick, D. Gregory;
Cole, James R.;
George, Mary C.;
Glickman, Gerald N.;
Glover, Joel F.;
Goldberg, Jerold S.;
Haden, N. Karl;
Kalkwarf, Kenneth L.;
Meyerowitz, Cyril;
Neumann, Laura M.;
Pyle, Marsha;
Tedesco, Lisa A.;
Valachovic, Richard W.;
Weaver, Richard G.;
Winder, Ronald L.;
Young, Stephen K.

Publication type:

Article

The Dental Education Environment.

Published in:

Journal of Dental Education, 2006, v. 70, n. 12, p. 1265

By:

Haden, N. Karl;
Andrieu, Sandra C.;
Chadwick, Gregory;
Chmar, Jacqueline E.;
Cole, James R.;
George, Mary C.;
Glickman, Gerald N.;
Glover, Joel F.;
Goldberg, Jerold S.;
Hendricson, William D.;
Meyerowitz, Cyril;
Neumann, Laura;
Pyle, Marsha;
Tedesco, Lisa A.;
Valachovic, Richard W.;
Weaver, Richard G.;
Winder, Ronald L.;
Young, Stephen K.;
Kalkwarf, Kenneth L.

Publication type:

Article

Educational Strategies Associated with Development of Problem-Solving, Critical Thinking, and Self-Directed Learning.

Published in:

Journal of Dental Education, 2006, v. 70, n. 9, p. 925

By:

Hendricson, William D.;
Andrieu, Sandra C.;
Chadwick, Gregory;
Chmar, Jacqueline E.;
Cole, James R.;
George, Mary C.;
Glickman, Gerald N.;
Glover, Joel F.;
Goldberg, Jerold S.;
Haden, N. Karl;
Meyerowitz, Cyril;
Neumann, Laura;
Pyle, Marsha;
Tedesco, Lisa A.;
Valachovic, Richard W.;
Weaver, Richard G.;
Winder, Ronald L.;
Young, Stephen K.;
Kalkwarf, Kenneth L.

Publication type:

Article

The Case for Change in Dental Education.

Published in:

Journal of Dental Education, 2006, v. 70, n. 9, p. 921

By:

Pyle, Marsha;
Andrieu, Sandra C.;
Chadwick, D. Gregory;
Chmar, Jacqueline E.;
Cole, James R.;
George, Mary C.;
Glickman, Gerald N.;
Glover, Joel F.;
Goldberg, Jerold S.;
Haden, N. Karl;
Hendricson, William D.;
Meyerowitz, Cyril;
Neumann, Laura;
Tedesco, Lisa A.;
Valachovic, Richard W.;
Weaver, Richard G.;
Winder, Ronald L.;
Young, Stephen K.;
Kalkwarf, Kenneth L.

Publication type:

Article

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

Published in:

Mycologia, 2016, v. 108, n. 1, p. 1, doi. 10.3852/14-293

By:

Deshpande, Vinita;
Qiong Wang;
Greenfield, Paul;
Charleston, Michael;
Porras-Alfaro, Andrea;
Kuske, Cheryl R.;
Cole, James R.;
Midgley, David J.;
Tran-Dinh, Nai

Publication type:

Article

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

Published in:

Microbiome, 2015, v. 3, n. 1, p. 1, doi. 10.1186/s40168-015-0093-6

By:

Qiong Wang;
Fish, Jordan A.;
Gilman, Mariah;
Yanni Sun;
Brown, C. Titus;
Tiedje, James M.;
Cole, James R.

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2017, p. 1, doi. 10.3389/fmicb.2017.01708

By:

Stedtfeld, Robert D.;
Chai, Benli;
Crawford, Robert B.;
Stedtfeld, Tiffany M.;
Williams, Maggie R.;
Shao Xiangwen;
Tomomi Kuwahara;
Cole, James R.;
Kaminski, Norbert E.;
Tiedje, James M.;
Hashsham, Syed A.

Publication type:

Article

rrndb: the Ribosomal RNA Operon Copy Number Database.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 181, doi. 10.1093/nar/29.1.181

By:

Klappenbach, Joel A.;
Saxman, Paul R.;
Cole, James R.;
Schmidt, Thomas M.

Publication type:

Article

The RDP-II (Ribosomal Database Project).

Published in:

Nucleic Acids Research, 2001, v. 29, n. 1, p. 173, doi. 10.1093/nar/29.1.173

By:

Maidak, Bonnie L.;
Cole, James R.;
Lilburn, Timothy G.;
Parker, Charles T.;
Saxman, Paul R.;
Farris, Ryan J.;
Garrity, George M.;
Olsen, Gary J.;
Schmidt, Thomas M.;
Tiedje, James M.

Publication type:

Article

The RDP (Ribosomal Database Project) continues.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 173, doi. 10.1093/nar/28.1.173

By:

Maidak, Bonnie L.;
Cole, James R.;
Lilburn, Timothy G.;
Parker Jr, Charles T.;
Saxman, Paul R.;
Stredwick, Jason M.;
Garrity, George M.;
Li, Bing;
Olsen, Gary J.;
Pramanik, Sakti;
Schmidt, Thomas M.;
Tiedje, James M.

Publication type:

Article

A new version of the RDP (Ribosomal Database Project).

Published in:

Nucleic Acids Research, 1999, v. 27, n. 1, p. 171, doi. 10.1093/nar/27.1.171

By:

Maidak, Bonnie L.;
Cole, James R.;
Parker, Jr, Charles T.;
Garrity, George M.;
Larsen, Niels;
Li, Bing;
Lilburn, Timothy G.;
McCaughey, Michael J.;
Olsen, Gary J.;
Overbeek, Ross;
Pramanik, Sakti;
Schmidt, Thomas M.;
Tiedje, James M.;
Woese, Carl R.

Publication type:

Article

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.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. 2263, doi. 10.1093/bioinformatics/bty053

By:

Yin, Xiaole;
Jiang, Xiao-Tao;
Chai, Benli;
Li, Liguan;
Yang, Ying;
Cole, James R;
Tiedje, James M;
Zhang, Tong

Publication type:

Article

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.

Published in:

Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00957

By:

Guo, Jiarong;
Quensen, John F.;
Sun, Yanni;
Wang, Qiong;
Brown, C. Titus;
Cole, James R.;
Tiedje, James M.

Publication type:

Article

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.

Published in:

Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00838-5

By:

Tao, Xuanyu;
Feng, Jiajie;
Yang, Yunfeng;
Wang, Gangsheng;
Tian, Renmao;
Fan, Fenliang;
Ning, Daliang;
Bates, Colin T.;
Hale, Lauren;
Yuan, Mengting M.;
Wu, Linwei;
Gao, Qun;
Lei, Jiesi;
Schuur, Edward A. G.;
Yu, Julian;
Bracho, Rosvel;
Luo, Yiqi;
Konstantinidis, Konstantinos T.;
Johnston, Eric R.;
Cole, James R.

Publication type:

Article

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.

Published in:

Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-019-0778-3

By:

Feng, Jiajie;
Wang, Cong;
Lei, Jiesi;
Yang, Yunfeng;
Yan, Qingyun;
Zhou, Xishu;
Tao, Xuanyu;
Ning, Daliang;
Yuan, Mengting M.;
Qin, Yujia;
Shi, Zhou J.;
Guo, Xue;
He, Zhili;
Van Nostrand, Joy D.;
Wu, Liyou;
Bracho-Garillo, Rosvel G.;
Penton, C. Ryan;
Cole, James R.;
Konstantinidis, Konstantinos T.;
Luo, Yiqi

Publication type:

Article

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

Published in:

Global Change Biology, 2018, v. 24, n. 10, p. 4946, doi. 10.1111/gcb.14325

By:

Liang, Junyi;
Xia, Jiangyang;
Shi, Zheng;
Jiang, Lifen;
Ma, Shuang;
Lu, Xingjie;
Mauritz, Marguerite;
Natali, Susan M.;
Pegoraro, Elaine;
Penton, Christopher Ryan;
Plaza, César;
Salmon, Verity G.;
Celis, Gerardo;
Cole, James R.;
Konstantinidis, Konstantinos T.;
Tiedje, James M.;
Zhou, Jizhong;
Schuur, Edward A. G.;
Luo, Yiqi

Publication type:

Article

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

Published in:

Global Change Biology, 2018, v. 24, n. 1, p. 297, doi. 10.1111/gcb.13820

By:

Yuan, Mengting M.;
Zhang, Jin;
Xue, Kai;
Wu, Liyou;
Deng, Ye;
Deng, Jie;
Hale, Lauren;
Zhou, Xishu;
He, Zhili;
Yang, Yunfeng;
Van Nostrand, Joy D.;
Schuur, Edward A. G.;
Konstantinidis, Konstantinos T.;
Penton, Christopher R.;
Cole, James R.;
Tiedje, James M.;
Luo, Yiqi;
Zhou, Jizhong

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D633, doi. 10.1093/nar/gkt1244

By:

Cole, James R.;
Wang, Qiong;
Fish, Jordan A.;
Chai, Benli;
McGarrell, Donna M.;
Sun, Yanni;
Brown, C. Titus;
Porras-Alfaro, Andrea;
Kuske, Cheryl R.;
Tiedje, James M.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2010, v. 38, n. 22, p. e200, doi. 10.1093/nar/gkq873

By:

Claesson, Marcus J.;
Wang, Qiong;
O'Sullivan, Orla;
Greene-Diniz, Rachel;
Cole, James R.;
Ross, R. Paul;
O'Toole, Paul W.

Publication type:

Article

Multiplex Approach for Screening Genetic Markers of Microbial Indicators.

Published in:

Water Environment Research (10614303), 2007, v. 79, n. 3, p. 260, doi. 10.2175/106143007X181378

By:

Stedtfeld, Robert D.;
Baushke, Sam;
Tourlousse, Dieter;
Chai, Benli;
Cole, James R.;
Hashsham, Syed A.

Publication type:

Article