Benli Chai

• James M. Tiedje17
• James R. Cole16
• Qiong Wang7
• Syed A. Hashsham7
• Robert D. Stedtfeld6
• Donna M. McGarrell5
• Fang Wang4
• George M. Garrity4
• Ryan J. Farris4
• Tiffany M. Stedtfeld4
• Hongjie Sheng3
• Santosh Gunturu3
• Tong Zhang3
• Woo Jun Sul3
• A. S. Kulam-Syed-Mohideen2
• Alex Bateman2
• Andrea Porras-Alfaro2
• Anton I. Petrov2
• C. Titus Brown2
• Christian Zwieb2
• E. Cardenas2
• Elspeth A. Bruford2
• Guy Cochrane2
• Hui Li2

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

   Authors: James R. Cole, Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun, C. Titus Brown, Andrea Porras-Alfaro, Cheryl R. Kuske, James M. Tiedje - Nucleic Acids Research, Nucleic Acids Res. 2013 cited by 4,596

2. 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

   Authors: Xiaole Yin, Xiaotao Jiang, Benli Chai, Liguan Li, Ying Yang, James R. Cole, James M. Tiedje, Tong Zhang - Bioinformatics, Bioinform. 2018 cited by 711

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

   Authors: James R. Cole, Qiong Wang, E. Cardenas, Jordan A. Fish, Benli Chai, Ryan J. Farris, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, Terry L. Marsh, George M. Garrity, James M. Tiedje - Nucleic Acids Research, Nucleic Acids Res. 2008 cited by 4,860

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

   Authors: Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, Tong Zhang - Bioinformatics, Bioinform. 2016 cited by 396

5. In-feed antibiotic effects on the swine intestinal microbiome

   Authors: Torey Looft, Timothy A. Johnson, Heather K. Allen, Darrell O. Bayles, David P. Alt, Robert D. Stedtfeld, Woo Jun Sul, Tiffany M. Stedtfeld, Benli Chai, James R. Cole, Syed A. Hashsham, James M. Tiedje, Thad B. Stanton - National Academy of Sciences, Proceedings of the National Academy of Sciences 2012 cited by 1,089

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

   Authors: Xun Qian, Santosh Gunturu, Jiarong Guo, Benli Chai, James R. Cole, Jie Gu, James M. Tiedje - Microbiome 2021 cited by 134

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

   Authors: Anton I. Petrov, Simon Kay, Ioanna Kalvari, Kevin Howe, Kristian Gray, Elspeth A. Bruford, Paul Kersey, Guy Cochrane, ROBERT FINN, Alex Bateman, Ana Kozomara, Sam Griffiths‐Jones, Adam Frankish, Christian Zwieb, Britney Y. Lau, Kelly P. Williams, Patricia P. Chan, Todd M. Lowe, Jamie J. Cannone, Robin R. Gutell, Magdalena A. Machnicka, Janusz M. Bujnicki, Maki Yoshihama, Naoya Kenmochi, Benli Chai, James R. Cole, M. Szymański, Wojciech M. Karłowski, Valerie Wood, Eva Huala, Tanya Berardini, Yi Zhao, Runsheng Chen, Weimin Zhu, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Joern Puetz, Peter F. Stadler, Daniel McDonald, Siddhartha Basu, Petra Fey, Stacia R. Engel, J. Michael Cherry, Pieter‐Jan Volders, Pieter Mestdagh, Jacek Wower, Michael B. Clark, Xiu Cheng Quek, Marcel E. Dinger - Nucleic Acids Research, Nucleic Acids Res. 2016 cited by 274

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

   Authors: Robert D. Stedtfeld, Xueping Guo, Tiffany M. Stedtfeld, Hongjie Sheng, Maggie R. Williams, Kristin Hauschild, Santosh Gunturu, Leo Tift, Fang Wang, Adina Howe, Benli Chai, Daqiang Yin, James R. Cole, James M. Tiedje, Syed A. Hashsham - FEMS Microbiology Ecology 2018 cited by 187

9. Sequence-based classification and identification of Fungi.

   Authors: David S. Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James R. Cole, Qiong Wang, P.W. Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul M. Kirk, Shiloh R. Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad L. Schoch, Christopher W. Smyth, Donald M. Walker, Andrea Porras‐Alfaro, John W. Taylor, David M. Geiser - 2018 cited by 215

10. Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome

    Authors: Fang Wang, Min Xu, Robert D. Stedtfeld, Hongjie Sheng, Jianbo Fan, Ming Liu, Benli Chai, Teotônio Soares de Carvalho, Hui Li, Zhongpei Li, Syed A. Hashsham, James M. Tiedje - Environmental Science & Technology 2018 cited by 144

11. Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes

    Authors: Yuhao Fu, Qingyuan Dou, Kornelia Smalla, Yu Wang, Timothy A. Johnson, Kristian K. Brandt, Zhi Mei, Maoyuan Liao, Syed A. Hashsham, Andreas Schäffer, Hauke Smidt, Tong Zhang, Hui Li, Robert D. Stedtfeld, Hongjie Sheng, Benli Chai, Marko Virta, Xin Jiang, Fang Wang, Yong‐Guan Zhu, James M. Tiedje - mLife 2023 cited by 55

12. FunGene: the functional gene pipeline and repository

    Authors: Jordan Fish, Benli Chai, Qiong Wang, Yanni Sun, C. Titus Brown, James M. Tiedje, James R. Cole - Frontiers in Microbiology 2013 cited by 663

13. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils

    Authors: Fang Wang, Robert D. Stedtfeld, Ok-Sun Kim, Benli Chai, Luxi Yang, Tiffany M. Stedtfeld, Soon Gyu Hong, Dockyu Kim, Hyoun Soo Lim, Syed A. Hashsham, James M. Tiedje, Woo Jun Sul - Environmental Science & Technology 2016 cited by 150

14. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

    Authors: James R. Cole, Benli Chai, Terry L. Marsh, Ryan J. Farris, Qiong Wang, S. A. Kulam, S. Chandra, Donna M. McGarrell, Thomas M. Schmidt, George M. Garrity, James M. Tiedje - Nucleic Acids Research, Nucleic Acids Res. 2003 cited by 1,428

15. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

    Authors: James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, S. A. Kulam, Donna M. McGarrell, George M. Garrity, James M. Tiedje - Nucleic Acids Research, Nucleic Acids Res. 2004 cited by 1,482

16. RNAcentral: an international database of ncRNA sequences

    Authors: Anton I. Petrov, Simon Kay, Richard Gibson, Eugene Kulesha, D. Staines, Elspeth A. Bruford, Matt W. Wright, Sarah Burge, ROBERT FINN, Paul Kersey, Guy Cochrane, Alex Bateman, Elspeth A. Bruford, Sam Griffiths‐Jones, Jennifer Harrow, Patricia P. Chan, Todd M. Lowe, Christian Zwieb, Jacek Wower, Kelly P. Williams, Corey Hudson, Robin R. Gutell, Michael B. Clark, Marcel E. Dinger, Xiu Cheng Quek, Janusz M. Bujnicki, Nam‐Hai Chua, Jun Liu, Huan Wang, Geir Skogerbø, Yi Zhao, Runsheng Chen, Weimin Zhu, James R. Cole, Benli Chai, Hsien‐Da Huang, His-Yuan Huang, J. Michael Cherry, Artemis G. Hatzigeorgiou, Kim D. Pruitt - Nucleic Acids Research, Nucleic Acids Res. 2014 cited by 128

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

    Authors: James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity, James M. Tiedje - Nucleic Acids Research, Nucleic Acids Res. 2006 cited by 1,169

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

    Authors: Ruonan Wu, Benli Chai, James R. Cole, Santosh Gunturu, Xue Guo, Renmao Tian, Ji-Dong Gu, Jizhong Zhou, James M. Tiedje - The ISME Journal 2020 cited by 18

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

    Authors: Shoko Iwai, Benli Chai, Woo Jun Sul, James R. Cole, Syed A. Hashsham, James M. Tiedje - The ISME Journal 2009 cited by 132

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

    Authors: Hassan Waseem, Maggie R. Williams, Tiffany M. Stedtfeld, Benli Chai, Robert D. Stedtfeld, James R. Cole, James M. Tiedje, Syed A. Hashsham - Environmental Science Processes & Impacts 2017 cited by 29

21. Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa

    Authors: Do Thi Xuan, Võ Thị Gương, Anna Rosling, Sadhna Alström, Benli Chai, Nils Högberg - Biology and Fertility of Soils 2011 cited by 166

All 21 papers shown.