1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C
Published in Nature biotechnology (01.07.2017)
Published in Nature biotechnology (01.07.2017)
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Journal Article
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
Hadjithomas, Michalis, Chen, I-Min A, Chu, Ken, Huang, Jinghua, Ratner, Anna, Palaniappan, Krishna, Andersen, Evan, Markowitz, Victor, Kyrpides, Nikos C, Ivanova, Natalia N
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
Kloosterman, Alexander M, Cimermancic, Peter, Elsayed, Somayah S, Du, Chao, Hadjithomas, Michalis, Donia, Mohamed S, Fischbach, Michael A, van Wezel, Gilles P, Medema, Marnix H
Published in PLoS biology (01.12.2020)
Published in PLoS biology (01.12.2020)
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Hidden genomic evolution in a morphospecies-The landscape of rapidly evolving genes in Tetrahymena
Xiong, Jie, Yang, Wentao, Chen, Kai, Jiang, Chuanqi, Ma, Yang, Chai, Xiaocui, Yan, Guanxiong, Wang, Guangying, Yuan, Dongxia, Liu, Yifan, Bidwell, Shelby L, Zafar, Nikhat, Hadjithomas, Michalis, Krishnakumar, Vivek, Coyne, Robert S, Orias, Eduardo, Miao, Wei
Published in PLoS biology (03.06.2019)
Published in PLoS biology (03.06.2019)
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Journal Article
Selecting one of several mating types through gene segment joining and deletion in Tetrahymena thermophila
Cervantes, Marcella D, Hamilton, Eileen P, Xiong, Jie, Lawson, Michael J, Yuan, Dongxia, Hadjithomas, Michalis, Miao, Wei, Orias, Eduardo
Published in PLoS biology (01.03.2013)
Published in PLoS biology (01.03.2013)
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Journal Article
IMG/M: integrated genome and metagenome comparative data analysis system
Chen, I-Min A., Markowitz, Victor M., Chu, Ken, Palaniappan, Krishna, Szeto, Ernest, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Andersen, Evan, Huntemann, Marcel, Varghese, Neha, Hadjithomas, Michalis, Tennessen, Kristin, Nielsen, Torben, Ivanova, Natalia N., Kyrpides, Nikos C.
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites
Hadjithomas, Michalis, Chen, I-Min Amy, Chu, Ken, Ratner, Anna, Palaniappan, Krishna, Szeto, Ernest, Huang, Jinghua, Reddy, T B K, Cimermančič, Peter, Fischbach, Michael A, Ivanova, Natalia N, Markowitz, Victor M, Kyrpides, Nikos C, Pati, Amrita
Published in mBio (14.07.2015)
Published in mBio (14.07.2015)
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Journal Article
Correction: Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila
Cervantes, Marcella D, Hamilton, Eileen P, Xiong, Jie, Lawson, Michael J, Yuan, Dongxia, Hadjithomas, Michalis, Miao, Wei, Orias, Eduardo
Published in PLoS biology (01.10.2015)
Published in PLoS biology (01.10.2015)
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Journal Article
IMG/M: integrated genome and metagenome comparative data analysis system
Chen, I-Min A, Markowitz, Victor M, Chu, Ken, Palaniappan, Krishna, Szeto, Ernest, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Andersen, Evan, Huntemann, Marcel, Varghese, Neha, Hadjithomas, Michalis, Tennessen, Kristin, Nielsen, Torben, Ivanova, Natalia N, Kyrpides, Nikos C
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes
Lorenzi, Hernan, Khan, Asis, Behnke, Michael S, Namasivayam, Sivaranjani, Swapna, Lakshmipuram S, Hadjithomas, Michalis, Karamycheva, Svetlana, Pinney, Deborah, Brunk, Brian P, Ajioka, James W, Ajzenberg, Daniel, Boothroyd, John C, Boyle, Jon P, Dardé, Marie L, Diaz-Miranda, Maria A, Dubey, Jitender P, Fritz, Heather M, Gennari, Solange M, Gregory, Brian D, Kim, Kami, Saeij, Jeroen P J, Su, Chunlei, White, Michael W, Zhu, Xing-Quan, Howe, Daniel K, Rosenthal, Benjamin M, Grigg, Michael E, Parkinson, John, Liu, Liang, Kissinger, Jessica C, Roos, David S, Sibley, L David
Published in Nature communications (07.01.2016)
Published in Nature communications (07.01.2016)
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Journal Article
Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE
Ke, Jing, Zhao, Zhiying, Coates, Cameron R., Hadjithomas, Michalis, Kuftin, Andrea, Louie, Katherine, Weller, David, Thomashow, Linda, Mouncey, Nigel J., Northen, Trent R., Yoshikuni, Yasuo
Published in Metabolic engineering (08.12.2021)
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Published in Metabolic engineering (08.12.2021)
Journal Article
Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE
Ke, Jing, Zhao, Zhiying, Coates, Cameron R., Hadjithomas, Michalis, Kuftin, Andrea, Louie, Katherine, Weller, David, Thomashow, Linda, Mouncey, Nigel J., Northen, Trent R., Yoshikuni, Yasuo
Published in Metabolic engineering (01.01.2022)
Published in Metabolic engineering (01.01.2022)
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Journal Article
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
Chen, I-Min A, Markowitz, Victor M, Palaniappan, Krishna, Szeto, Ernest, Chu, Ken, Huang, Jinghua, Ratner, Anna, Pillay, Manoj, Hadjithomas, Michalis, Huntemann, Marcel, Mikhailova, Natalia, Ovchinnikova, Galina, Ivanova, Natalia N, Kyrpides, Nikos C
Published in BMC genomics (26.04.2016)
Published in BMC genomics (26.04.2016)
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Journal Article
Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols
Forry, Samuel P, Servetas, Stephanie L, Kralj, Jason G, Soh, Keng, Hadjithomas, Michalis, Cano, Raul, Carlin, Martha, Amorim, Maria G de, Auch, Benjamin, Bakker, Matthew G, Bartelli, Thais F, Bustamante, Juan P, Cassol, Ignacio, Chalita, Mauricio, Dias-Neto, Emmanuel, Duca, Aaron Del, Gohl, Daryl M, Kazantseva, Jekaterina, Haruna, Muyideen T, Menzel, Peter, Moda, Bruno S, Neuberger-Castillo, Lorieza, Nunes, Diana N, Patel, Isha R, Peralta, Rodrigo D, Saliou, Adrien, Schwarzer, Rolf, Sevilla, Samantha, Takenaka, Isabella K T M, Wang, Jeremy R, Knight, Rob, Gevers, Dirk, Jackson, Scott A
Published in Scientific reports (29.04.2024)
Published in Scientific reports (29.04.2024)
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Journal Article
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
Hadjithomas, Michalis, Chen, I-Min A., Chu, Ken, Huang, Jinghua, Ratner, Anna, Palaniappan, Krishna, Andersen, Evan, Markowitz, Victor, Kyrpides, Nikos C., Ivanova, Natalia N.
Published in Nucleic acids research (29.11.2016)
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Published in Nucleic acids research (29.11.2016)
Journal Article
IMG/M: integrated genome and metagenome comparative data analysis system
Chen, I-Min A., Markowitz, Victor M., Chu, Ken, Palaniappan, Krishna, Szeto, Ernest, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Andersen, Evan, Huntemann, Marcel, Varghese, Neha, Hadjithomas, Michalis, Tennessen, Kristin, Nielsen, Torben, Ivanova, Natalia N., Kyrpides, Nikos C.
Published in Nucleic acids research (13.10.2016)
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Published in Nucleic acids research (13.10.2016)
Journal Article
An integrated workflow for phenazine-modifying enzyme characterization
Coates, R. Cameron, Bowen, Benjamin P., Oberortner, Ernst, Thomashow, Linda, Hadjithomas, Michalis, Zhao, Zhiying, Ke, Jing, Silva, Leslie, Louie, Katherine, Wang, Gaoyan, Robinson, David, Tarver, Angela, Hamilton, Matthew, Lubbe, Andrea, Feltcher, Meghan, Dangl, Jeffery L., Pati, Amrita, Weller, David, Northen, Trent R., Cheng, Jan-Fang, Mouncey, Nigel J., Deutsch, Samuel, Yoshikuni, Yasuo
Published in Journal of industrial microbiology & biotechnology (01.07.2018)
Published in Journal of industrial microbiology & biotechnology (01.07.2018)
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Journal Article
Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C
Published in Nature biotechnology (01.04.2018)
Published in Nature biotechnology (01.04.2018)
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