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Nikos C. Kyrpides
Researcher at Joint Genome Institute
Publications - 735
Citations - 73233
Nikos C. Kyrpides is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 96, co-authored 711 publications receiving 62360 citations. Previous affiliations of Nikos C. Kyrpides include University of Crete & Oak Ridge National Laboratory.
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Journal ArticleDOI
Gene context analysis in the Integrated Microbial Genomes (IMG) data management system.
Konstantinos Mavromatis,Ken Chu,Natalia Ivanova,Sean D. Hooper,Victor M. Markowitz,Nikos C. Kyrpides +5 more
TL;DR: The data management system of the Integrated Microbial Genomes (IMG) is used as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations.
Journal ArticleDOI
Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers
Wayne Reeve,Graham O’Hara,Patrick S. G. Chain,Patrick S. G. Chain,Julie Ardley,Lambert Bräu,Kemanthi Nandesena,Ravi Tiwari,Alex Copeland,Matt Nolan,Cliff Han,Cliff Han,Thomas Brettin,Miriam Land,Miriam Land,Galina Ovchinikova,Natalia Ivanova,Konstantinos Mavromatis,Victor Markowitz,Nikos C. Kyrpides,Vanessa Melino,Matthew D. Denton,Ron Yates,John Howieson +23 more
TL;DR: This is the first completed genome sequence for a microsymbiont of annual clovers, and it is revealed that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes.
Journal ArticleDOI
COVID-19 pandemic reveals the peril of ignoring metadata standards.
Lynn M. Schriml,Maria Chuvochina,Neil M Davies,Emiley A. Eloe-Fadrosh,Robert D. Finn,Philip Hugenholtz,Christopher I. Hunter,Bonnie L. Hurwitz,Nikos C. Kyrpides,Folker Meyer,Ilene Karsch Mizrachi,Susanna-Assunta Sansone,Granger G. Sutton,Scott Tighe,Ramona Walls +14 more
TL;DR: The Genomic Standards Consortium board highlights the essential need for contextual genomic data FAIRness, for empowering key data-driven biological questions in response to the pandemic.
Posted ContentDOI
Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +64 more
TL;DR: Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups.
Journal ArticleDOI
A synthesis of bacterial and archaeal phenotypic trait data
Joshua S. Madin,Daniel A. Nielsen,Maria Brbic,Ross Corkrey,David Danko,Kyle F. Edwards,Martin K. M. Engqvist,Noah Fierer,Jemma L. Geoghegan,Michael R. Gillings,Nikos C. Kyrpides,Nikos C. Kyrpides,Elena Litchman,Christopher E. Mason,Lisa R. Moore,Søren Laurentius Nielsen,Ian T. Paulsen,Nathan D. Price,T. B. K. Reddy,T. B. K. Reddy,Matthew A. Richards,Eduardo P. C. Rocha,Thomas M. Schmidt,Heba Shaaban,Maulik Shukla,Fran Supek,Sasha G. Tetu,Sara Vieira-Silva,Alice R. Wattam,David A. Westfall,Mark Westoby +30 more
TL;DR: A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources.