The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level von Rodriguez-R, Luis M, Gunturu, Santosh, Harvey, William T, Rosselló-Mora, Ramon, Tiedje, James M, Cole, James R, Konstantinidis, Konstantinos T

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FunGene: the functional gene pipeline and repository von Fish, Jordan A, Chai, Benli, Wang, Qiong, Sun, Yanni, Brown, C Titus, Tiedje, James M, Cole, James R

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

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Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy von Wang, Qiong, Garrity, George M, Tiedje, James M, Cole, James R

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Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems von Qian, Xun, Gunturu, Santosh, Guo, Jiarong, Chai, Benli, Cole, James R, Gu, Jie, Tiedje, James M

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In-feed antibiotic effects on the swine intestinal microbiome von Looft, Torey, Johnson, Timothy A., Allen, Heather K., Bayles, Darrell O., Alt, David P., Stedtfeld, Robert D., Sul, Woo Jun, Stedtfeld, Tiffany M., Chai, Benli, Cole, James R., Hashsham, Syed A., Tiedje, James M., Stanton, Thad B.

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Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture von Johnson, Timothy A, Stedtfeld, Robert D, Wang, Qiong, Cole, James R, Hashsham, Syed A, Looft, Torey, Zhu, Yong-Guan, Tiedje, James M

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Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements von Stedtfeld, Robert D, Guo, Xueping, Stedtfeld, Tiffany M, Sheng, Hongjie, Williams, Maggie R, Hauschild, Kristin, Gunturu, Santosh, Tift, Leo, Wang, Fang, Howe, Adina, Chai, Benli, Yin, Daqiang, Cole, James R, Tiedje, James M, Hashsham, Syed A

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

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Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming von Guo, Xue, Gao, Qun, Yuan, Mengting, Wang, Gangsheng, Zhou, Xishu, Feng, Jiajie, Shi, Zhou, Hale, Lauren, Wu, Linwei, Zhou, Aifen, Tian, Renmao, Liu, Feifei, Wu, Bo, Chen, Lijun, Jung, Chang Gyo, Niu, Shuli, Li, Dejun, Xu, Xia, Jiang, Lifen, Escalas, Arthur, Wu, Liyou, He, Zhili, Van Nostrand, Joy D., Ning, Daliang, Liu, Xueduan, Yang, Yunfeng, Schuur, Edward. A. G., Konstantinidis, Konstantinos T., Cole, James R., Penton, C. Ryan, Luo, Yiqi, Tiedje, James M., Zhou, Jizhong

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Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions von Claesson, Marcus J, Wang, Qiong, O'Sullivan, Orla, Greene-Diniz, Rachel, Cole, James R, Ross, R. Paul, O'Toole, Paul W

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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity von Rodriguez-R, Luis M, Gunturu, Santosh, Tiedje, James M, Cole, James R, Konstantinidis, Konstantinos T

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Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms von Lan, Yemin, Wang, Qiong, Cole, James R, Rosen, Gail L

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How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? von Rodriguez-R, Luis M, Castro, Juan C, Kyrpides, Nikos C, Cole, James R, Tiedje, James M, Konstantinidis, Konstantinos T

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Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences von Deshpande, Vinita, Wang, Qiong, Greenfield, Paul, Charleston, Michael, Porras-Alfaro, Andrea, Kuske, Cheryl R., Cole, James R., Midgley, David J, Tran-Dinh, Nai

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Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community von 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, Schuur, Edward A G, Tiedje, James M, Zhou, Jizhong

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The Genomic Standards Consortium von 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, San Gil, Inigo, Sansone, Susanna-Assunta, Schriml, Lynn M, Sterk, Peter, Tatusova, Tatiana, Ussery, David W, White, Owen, Wooley, John

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

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A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data von Zhang, Yuan, Sun, Yanni, Cole, James R

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

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