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（^# = 共同第一作者，* = 通讯作者）

2024

LinXing Chen *, Jillian F Banfield *. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nature Microbiology 9, 737–750 (2024). https://doi.org/10.1038/s41564-023-01598-2.

Ling-Dong Shi, Jacob West-Roberts, Marie C. Schoelmerich, Petar I. Penev, LinXing Chen, Yuki Amano, Shufei Lei, Rohan Sachdeva, and Jillian F. Banfield. "Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements." Nature Microbiology (2024). https://doi.org/10.1038/s41564-024-01740-8. 

Dan Huang, Rong Xia, Chengyi Chen, Jingqiu Liao, Linxing Chen, Dongsheng Wang, Pedro JJ Alvarez, and Pingfeng Yu. "Adaptive strategies and ecological roles of phages in habitats under physicochemical stress." Trends in Microbiology (2024). https://doi.org/10.1016/j.tim.2024.02.002.

Lou, Yue Clare, LinXing Chen, Adair L. Borges, Jacob A. West-Roberts, Brian A. Firek, Michael Morowitz, and Jill Banfield. "Infant gut bacteriophage strain persistence during the first three years of life. Cell Host & Microbe (2024) 32, 1-13. https://doi.org/10.1016/j.chom.2023.11.015.  

Benjamin A Adler^#, Marena I Trinidad^#, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M Karp, Petr Skopintsev, Brittney Thornton, Rachel F Weissman, Peter H Yoon, Linxing Chen, Tomas Hessler, Amy R Eggers, David A Colognori, Ron Boger, Erin E Doherty, Connor A Tsuchida, Ryan V Tran, Laura Hofman, Honglue Shi, Kevin M Wasko, Zehan Zhou, Chenglong Xia, Muntathar Al-Shimary, Jaymin Patel, Vienna Thomas, Rithu Pattali, Matthew J Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F Maxwell, Andrew Murdock, Glenn Ramit, Hope R Henderson, Roland W Calvert, Rebecca S Bamert, Audrone Lapinaite, Patrick Pausch, Joshua C Cofsky, Erik J Sontheimer, Blake Wiedenheft, Peter C Fineran, Stan Brouns, Dipali Sashital, Brian C Thomas, Christopher T Brown, Daniela S Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F Banfield, David F Savage, Jennifer A Doudna. CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes. Nucleic Acids Research (2024), 52 (D1), D590-D596, https://doi.org/10.1093/nar/gkad890.

 

2023

Kelly J Whaley-Martin ^#, Lin-Xing Chen ^#, Tara Colebrander Nelson, Jay Gordon, Rose Kantor, Lauren E Twible, Stephanie Marshall, Laura Rossi, Benoit Bessette, Christian Baron, Simon Apte, Jill Banfield, Lesley A Warren. O₂ partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters. Nature Communications (2023), 14(1), p.2006. https://www.nature.com/articles/s41467-023-37426-8 

Peter H. Yoon^#, Petr Skopintsev^#, Honglue Shi^#, LinXing Chen, Benjamin A. Adler, Muntathar Al-Shimary, Rory J. Craig, Kenneth J. Loi, Evan C. DeTurk, Zheng Li, Jasmine Amerasekera, Marena Trinidad, Hunter Nisonoff, Kai Chen, Arushi Lahiri, Ron Boger, Steve Jacobsen, Jillian F. Banfield, Jennifer A. Doudna. Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes. Nucleic Acids Research, Volume 51, Issue 22, 11 December 2023, Pages 12414–12427, https://doi.org/10.1093/nar/gkad1053.

Albert K. Liu^#, Benjamin Kaeser^#, LinXing Chen, Jacob West-Roberts, Leah J. Taylor-Kearney, Adi Lavy, Damian Günzing, Wen-Jun Li, Michal Hammel, Eva Nogales, Jillian F. Banfield, Patrick M. Shih. Deep-branching evolutionary intermediates reveal structural origins of form I rubisco. Current Biology (2023) 33,1–10. https://doi.org/10.1016/j.cub.2023.10.053.

Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li WJ, Hua ZS, Chen LX, et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature (2023), Jun 14:1-8. https://www.nature.com/articles/s41586-023-06186-2 

Jett Liu, Alexander L. Jaffe, LinXing Chen, Batbileg Bor, Jillian F. Banfield. Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria. mBio (2023). https://doi.org/10.1128/mbio.01766-23.  

 

2022

Lin-Xing Chen, Alexander L Jaffe, Adair L Borges, Petar Penev, Tara Colenbrander Nelson, Lesley A Warren, Jill Banfield. Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication. ISME Communications 2, no. 1 (2022): 1-10. https://www.nature.com/articles/s43705-022-00111-w 

Jessen, Gerdhard L., Lin-Xing Chen, Jiro F. Mori, Tara E. Colenbrander Nelson, Gregory F. Slater, Matthew BJ Lindsay, Jillian F. Banfield, and Lesley A. Warren. Alum Addition Triggers Hypoxia in an Engineered Pit Lake. Microorganisms 10, no. 3 (2022): 510. https://www.mdpi.com/2076-2607/10/3/510 

 Crisci, Marco A., Paula M. Corsini, Nicola Bordin, Lin-Xing Chen, Jillian F. Banfield, and Joanne M. Santini. Detection and enumeration of Lak megaphages in microbiome samples by endpoint and quantitative PCR. STAR protocols 3, no. 1 (2022): 101029. https://doi.org/10.1016/j.xpro.2021.101029 

Jaffe, Alexander L., Maxime Fuster, Marie C. Schoelmerich, Lin-Xing Chen, Jonathan Colombet, Hermine Billard, Télesphore Sime-Ngando, and Jill Banfield. Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria. mSystems (2022), DOI:https://doi.org/10.1128/msystems.00223-22. 

 

2021

Marco Alberto Crisci ^#, Lin-Xing Chen ^#, Audra E Devoto, Adair L Borges, Nicola Bordin, Rohan Sachdeva, Adrian Tett, Allison M Sharrar, Nicola Segata, Francesco Debenedetti, Mick Bailey, Rachel Burt, Rhiannon M Wood, Lewis J Rowden, Paula M Corsini, Mark A Holmes, Shufei Lei, Jillian F Banfield, Joanne M Santini. Closely related Lak megaphages replicate in the microbiomes of diverse animals. IScience (2021) 24: 102875. https://www.sciencedirect.com/science/article/pii/S2589004221008439 

Valerie De Anda, Lin-Xing Chen, Nina Dombrowski, Zhengshuang Hua, Hong-Chen Jiang, Jillian Banfield, Wen-Jun Li, Brett Baker. Brockarchaeota, a novel archaeal lineage capable of methylotrophy. Nature Communications (2021). https://www.nature.com/articles/s41467-021-22736-6 

 

2020

Lin-Xing Chen, Raphael Meheust, Alexander Crits-Christoph, Katherine D McMahon, Tara Colenbrander Nelson, Lesley A Warren, Jill Banfield. Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation. Nature Microbiology 5 (2020): 1504-1515. https://www.nature.com/articles/s41564-020-0779-9 

Lin-Xing Chen, Karthik Anantharaman, Alon Shaiber, A. Murat Eren, and Jillian F. Banfield. Accurate and Complete Genomes from Metagenomes. Genome Research (2020). https://genome.cshlp.org/content/30/3/315 

Al-Shayeb B ^#, Sachdeva R ^#, Lin-Xing Chen, et al. and Jillian F. Banfield. Clades of huge phage from across Earth’s ecosystems. Nature 578 (2020): 425-431. https://www.nature.com/articles/s41586-020-2007-4 

Raphaël Méheust, Cindy J Castelle, Paula B Matheus Carnevali, Ibrahim F Farag, Christine He, Lin-Xing Chen, Yuki Amano, Laura A Hug, Jillian F Banfield. Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. The ISME Journal (2020) 14: 2907-2922. https://www.nature.com/articles/s41396-020-0716-1 

Caitlin M Gionfriddo, Matthew B Stott, Jean F Power, Jacob M Ogorek, David P Krabbenhoft, Ryan Wick, Kathryn Holt, Lin-Xing Chen, Brian C Thomas, Jillian F Banfield, John W Moreau. Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs. Applied and Environmental Microbiology (2020). https://journals.asm.org/doi/10.1128/aem.00176-20 

Alon Shaiber, Amy D Willis, Tom O Delmont, Simon Roux, Lin-Xing Chen, Abigail C Schmid, Mahmoud Yousef, Andrea R Watson, Karen Lolans, Ozcan C Esen, Sonny TM Lee, Nora Downey, Hilary G Morrison, Floyd Dewhirst, Jessica L Mark Welch, A Murat Eren. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biology (2020). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02195-w 

 

Before 2020

Lin-Xing Chen, Yanlin Zhao, Katherine D. McMahon, Jiro F. Mori, Gerdhard L. Jessen, Tara Colenbrander Nelson, Lesley A. Warren, and Jillian F. Banfield. Wide distribution of phage that infect freshwater SAR11 bacteria. mSystems 4, no. 5 (2019): e00410-19.

 Lin-Xing Chen, Al-Shayeb B, Méheust R, Li W-J, Doudna JA and Banfield JF. Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems. Front. Microbiol (2019). 10:928. doi: 10.3389/fmicb.2019.00928.

Jiro F Mori, Lin-Xing Chen, Gerdhard L Jessen, Sarah B Rudderham, Joyce M McBeth, Matthew BJ Lindsay, Gregory F Slater, Jillian F Banfield, Lesley A Warren. Putative mixotrophic nitrifying-denitrifying Gammaproteobacteria implicated in nitrogen cycling within the ammonia/oxygen transition zone of an oil sands pit lake. Front. Microbiol. 10:2435. doi: 10.3389/fmicb.2019.02435.

Guillaume Borrel, Panagiotis S Adam, Luke J McKay, Lin-Xing Chen, Isabel Natalia Sierra-García, Christian MK Sieber, Quentin Letourneur, Amine Ghozlane, Gary L Andersen, Wen-Jun Li, Steven J Hallam, Gerard Muyzer, Valéria Maia de Oliveira, William P Inskeep, Jillian F Banfield, Simonetta Gribaldo. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology (2019) 4: 603-613.

 Lin-Xing Chen, Celia Méndez-García, Nina Dombrowski, Luis E. Servín-Garcidueñas, Emiley A. Eloe-Fadrosh, Bao-Zhu Fang, Zhen-Hao Luo, Sha Tan, Xiao-Yang Zhi, Zheng- Shuang Hua, Esperanza Martinez-Romero, Tanja Woyke, Li-Nan Huang, Jesús Sánchez, Ana Isabel Peláez, Manuel Ferrer, Brett J. Baker, Wen-Sheng Shu. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. The ISME journal (2018) 12: 756-775.

Jia-Ling Li, Nimaichand Salam, Pan-Deng Wang, Lin-Xing Chen, Jian-Yu Jiao, Xin Li, Wen-Dong Xian, Ming-Xian Han, Bao-Zhu Fang, Xiao-Zhen Mou, Wen-Jun Li. Discordance between resident and active bacterioplankton in free-living and particle-associated communities in estuary ecosystem. Microbial ecology (2018) 76: 637-647.

Jia-Liang Kuang, Marc W Cadotte, Yongjian Chen, Haoyue Shu, Jun Liu, Lin-Xing Chen, Zhengshuang Hua, Wensheng Shu, Jizhong Zhou, Linan Huang. Conservation of species-and trait-based modeling network interactions in extremely acidic microbial community assembly. Front. Microbiol. (2017) 8: 1486.

 Lin-Xing Chen, Li-nan Huang, Celia Méndez-García, Jia-liang Kuang, Zheng-shuang Hua, Jun Liu, Wen-sheng Shu. Microbial communities, processes and functions in acid mine drainage ecosystems. Current opinion in biotechnology (2016) 38: 150-158.

Jia-Liang Kuang, Linan Huang, Zhili He, Lin-Xing Chen, Zhengshuang Hua, Pu Jia, Shengjin Li, Jun Liu, Jintian Li, Jizhong Zhou, Wensheng Shu. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. The ISME journal (2016) 10: 1527–1539.

Xiao-Min Li, Wei Zhang, Tongxu Liu, Lin-Xing Chen, Pengcheng Chen, Fangbai Li. Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe (II) oxidation at circumneutral pH in paddy soil. Soil Biology and Biochemistry (2016) 94: 70-79.

Rui-Li Fang ^#, Lin-Xing Chen ^#, Wen-Sheng Shu, Shu-Zhong Yao, Si-Wen Wang, Yu-Qing Chen. Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps. American journal of translational research (2016) 8: 1581-1592.

Lin-Xing Chen ^#, Min Hu ^#, Li-nan Huang, Zheng-shuang Hua, Jia-liang Kuang, Sheng-jin Li and Wen-sheng Shu. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. The ISME Journal (2015) 9: 1579-1592.

Zheng-Shuang Hua ^#, Yu-Jiao Han^#, Lin-Xing Chen ^#, Jun Liu, Min Hu, Sheng-Jin Li, Jia-Liang Kuang, Patrick SG Chain, Li-Nan Huang, and Wen-Sheng Shu. "Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics." The ISME journal (2015) 9: 1280-1294.

Sheng-Jin Li, Zheng-Shuang Hua, Li-Nan Huang, Jie Li, Su-Hua Shi, Lin-Xing Chen, Jia-Liang Kuang, Jun Liu, Min Hu, Wen-Sheng Shu. Microbial communities evolve faster in extreme environments. Scientific reports (2014) 4: 6205.

 Jun Liu, Zheng-Shuang Hua, Lin-Xing Chen, Jia-Liang Kuang, Sheng-Jin Li, Wen-Sheng Shu, Li-Nan Huang. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Applied and environmental microbiology (2014) 80: 3677-3686.

Ya-ting Chen, Jin-tian Li, Lin-Xing Chen, Zheng-shuang Hua, Li-nan Huang, Jun Liu, Bi-bo Xu, Bin Liao, Wen-sheng Shu. Biogeochemical processes governing natural pyrite oxidation and release of acid metalliferous drainage. Environmental science & technology (2014) 48: 5537-5545.

 Lin-Xing Chen ^#, Jin-Tian Li ^#, Ya-Ting Chen, Li-Nan Huang, Zheng-Shuang Hua, Min Hu et al. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environmental Microbiology (2013) 15: 2431-2344.

Jia-Liang Kuang, Li-Nan Huang, Lin-Xing Chen, Zheng-Shuang Hua, Sheng-Jin Li, Min Hu, Jin-Tian Li, Wen-Sheng Shu. Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. The ISME Journal (2013) 7: 1038-1050.