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Nikos C. Kyrpides

lawrence berkeley national laboratory

116H-index
943Paper Count
8.7WCitation Count
Published Papers 175
Publication Date
Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments
err2026-07-16
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errZihao Gao; Jun Wu; Alexander G. Lucaci; Jian Ouyang; Lan Wang; Krista A. Ryon; Eran Elhaik; Alexander J. Probst; Xavier Rodó; Thirumalaisamy P. Velavan; Anastasia Chasapi; Christos A. Ouzounis; Manuela Oliveira; Emmanuel Dias-Neto; Olayinka Osuolale; Michael Poulsen; Dmitry Meleshko; Malay Bhattacharyya; Juan A. Ugalde; Alba Tull; Kathleen H. Rubins; Maria A. Sierra; Braden T. Tierney; Bharath Prithiviraj; Nitesh Kumar Sharma; Viorel Munteanu; Serghei Mangul; Kubra Can Kurt; Masayuki Ushio; Natalia Mazur-Panasiuk; Katarzyna Kopera; Kamila Marszałek; Michał Kowalski; Rodolfo Brizola Toscan; Wojciech Branicki; Krzysztof Pyrć; Paweł P. Łabaj; Balakrishnan Subramanian; Alina Frolova; Joshua G. Burkhart; Youping Deng; Klas I. Udekwu; Lynn M. Schriml; Nur Hazlin Hazrin-Chong; Haruo Suzuki; Patrick K. H. Lee; Antonio Pedro Camargo; Nikos C. Kyrpides; Di Liu; Lin-Fa Wang; Christopher E. Mason; Tieliu Shi
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Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome
err2026-05-28
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errG. Ghiotto; G. Zampieri; E. Orellana; A. Chatzis; P. G. Kougias; A. Camargo; S. Roux; S. Campanaro; N. C. Kyrpides; L. Treu
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Author Correction: A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes
err2026-04-21
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errMateus B. Fiamenghi; Antonio Pedro Camargo; Natalia N. Ivanova; Emily B. Graham; Ruonan Wu; Kirsten S. Hofmockel; Nikos C. Kyrpides
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A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes
err2025-11-18
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errMateus B. Fiamenghi; Antonio Pedro Camargo; Natalia N. Ivanova; Emily B. Graham; Ruonan Wu; Kirsten S. Hofmockel; Nikos C. Kyrpides
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Draft genome sequence of Muricoccus roseus DSM 14916T, isolated from a children's care center in Finland
err2025-11-01
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PREAI
errValenzuela, Alejandra; Cortez, Jair; Mande, Janelle; Fondse, Cody; Thiel, Vera; Labutti, Kurt; Kyrpides, Nikos; Seshadri, Rekha; Van Laar, Tricia A.
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metagRoot: a comprehensive database of protein families associated with plant root microbiomes
err2025-09-01
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PREAI
errChasapi, Maria N.; Chasapi, Iro N.; Aplakidou, Eleni; Baltoumas, Fotis A.; Karatzas, Evangelos; Iliopoulos, Ioannis; Stravopodis, Dimitrios J.; Emiris, Ioannis Z.; Buluc, Aydin; Georgakopoulos-Soares, Ilias; Kyrpides, Nikos C.; Pavlopoulos, Georgios A.
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Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg
err2025-03-05
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errOAAI
errKioukis, Antonios; Camargo, Antonio Pedro; Pavlidis, Pavlos; Iliopoulos, Ioannis; Kyrpides, Nikos C.; Lagkouvardos, Ilias
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Genomes OnLine Database (GOLD) v.10: new features and updates
err2024-11-05
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errMukherjee, Supratim; Stamatis, Dimitri; Li, Cindy Tianqing; Ovchinnikova, Galina; Kandimalla, Mahathi; Handke, Van; Reddy, Anuha; Ivanova, Natalia; Woyke, Tanja; Eloe-Fardosh, Emiley A.; Chen, I-Min A.; Kyrpides, Nikos C.; Reddy, T. B. K.
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Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.
errMBIO
IF4.7
err2024-04-10
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errMiliotis, Georgios; Sengupta, Pratyay; Hameed, Asif; Chuvochina, Maria; McDonagh, Francesca; Simpson, Anna C.; Parker, Ceth W.; Singh, Nitin K.; Rekha, Punchappady D.; Morris, Dearbhaile; Raman, Karthik; Kyrpides, Nikos C.; Hugenholtz, Philip; Venkateswaran, Kasthuri
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Genomes OnLine Database (GOLD) v.8: overview and updates (vol 49,Pg D723-D733,2021)
err2024-02-28
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errMukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon; Ovchinnikova, Galina; Sundaramurthi, Jagadish Chandrabose; Lee, Janey; Kandimalla, Mahathi; Woyke, Tanja; Eloe-Fardosh, Emiley A.; Kyrpides, Nikos C.; Reddy, T. B. K.
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IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
err2023-11-01
err16
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errCamargo, Antonio Pedro; Call, Lee; Roux, Simon; Nayfach, Stephen; Huntemann, Marcel; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Mukherjeep, Supratim; Reddy, T. B. K.; Chen, I-Min A.; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Woyke, Tanja; Baltrus, David A.; Castaneda-Barba, Salvador; de la Cruz, Fernando; Funnell, Barbara E.; Hall, James P. J.; Mukhopadhyay, Aindrila; Rocha, Eduardo P. C.; Stalder, Thibault; Top, Eva; Kyrpides, Nikos C.
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NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes
err2023-10-09
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errBaltoumas, Fotis A.; Karatzas, Evangelos; Liu, Sirui; Ovchinnikov, Sergey; Sofianatos, Yorgos; Chen, I-Min; Kyrpides, Nikos C.; Pavlopoulos, Georgios A.
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Identification of mobile genetic elements with geNomad
err2023-09-21
err116
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errCamargo, Antonio Pedro; Roux, Simon; Schulz, Frederik; Babinski, Michal; Xu, Yan; Hu, Bin; Chain, Patrick S. G.; Nayfach, Stephen; Kyrpides, Nikos C.
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Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018
err2023-02-28
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errKlonowska, Agnieszka; Ardley, Julie; Moulin, Lionel; Zandberg, Jaco; Patrel, Delphine; Gollagher, Margaret; Marinova, Dora; Reddy, T. B. K.; Varghese, Neha; Huntemann, Marcel; Woyke, Tanja; Seshadri, Rekha; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne
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Standardized naming of microbiome samples in Genomes OnLine Database
err2023-02-16
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errMukherjee, Supratim; Ovchinnikova, Galina; Stamatis, Dimitri; Li, Cindy Tianqing; Chen, I-Min A.; Kyrpides, Nikos C.; Reddy, T. B. K.
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Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot
err2022-12-20
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errCamargo, Antonio P.; de Souza, Rafael S. C.; Jose, Juliana; Gerhardt, Isabel R.; Dante, Ricardo A.; Mukherjee, Supratim; Huntemann, Marcel; Kyrpides, Nikos C.; Carazzolle, Marcelo F.; Arruda, Paulo
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Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes
err2022-12-01
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errSeshadri, Rekha; Roux, Simon; Huber, Katharina J.; Wu, Dongying; Yu, Sora; Udwary, Dan; Call, Lee; Nayfach, Stephen; Hahnke, Richard L.; Pukall, Rudiger; White, James R.; Varghese, Neha J.; Webb, Cody; Palaniappan, Krishnaveni; Reimer, Lorenz C.; Sarda, Joaquim; Bertsch, Jonathon; Mukherjee, Supratim; Reddy, T. B. K.; Hajek, Patrick P.; Huntemann, Marcel; Chen, I-Min A.; Spunde, Alex; Clum, Alicia; Shapiro, Nicole; Wu, Zong-Yen; Zhao, Zhiying; Zhou, Yuguang; Evtushenko, Lyudmila; Thijs, Sofie; Stevens, Vincent; Eloe-Fadrosh, Emiley A.; Mouncey, Nigel J.; Yoshikuni, Yasuo; Whitman, William B.; Klenk, Hans-Peter; Woyke, Tanja; Goeker, Markus; Kyrpides, Nikos C.; Ivanova, Natalia N.
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IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
err2022-11-18
err119
errOAAI
errCamargo, Antonio Pedro; Nayfach, Stephen; Chen, I-Min A.; Palaniappan, Krishnaveni; Ratner, Anna; Chu, Ken; Ritter, Stephan J.; Reddy, T. B. K.; Mukherjee, Supratim; Schulz, Frederik; Call, Lee; Neches, Russell Y.; Woyke, Tanja; Ivanova, Natalia N.; Eloe-Fadrosh, Emiley A.; Kyrpides, Nikos C.; Roux, Simon
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The IMG/M data management and analysis system v.7: content updates and new features
err2022-11-16
err129
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errChen, I-Min A.; Chu, Ken; Palaniappan, Krishnaveni; Ratner, Anna; Huang, Jinghua; Huntemann, Marcel; Hajek, Patrick; Ritter, Stephan J.; Webb, Cody; Wu, Dongying; Varghese, Neha J.; Reddy, T. B. K.; Mukherjee, Supratim; Ovchinnikova, Galina; Nolan, Matt; Seshadri, Rekha; Roux, Simon; Visel, Axel; Woyke, Tanja; Eloe-Fadrosh, Emiley A.; Kyrpides, Nikos C.; Ivanova, Natalia N.
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Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9
err2022-11-01
err49
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errMukherjee, Supratim; Stamatis, Dimitri; Li, Cindy Tianqing; Ovchinnikova, Galina; Bertsch, Jon; Sundaramurthi, Jagadish Chandrabose; Kandimalla, Mahathi; Nicolopoulos, Paul A.; Favognano, Alessandro; Chen, I-Min A.; Kyrpides, Nikos C.; Reddy, T. B. K.
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