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Patrick S. G. Chain
Researcher at Los Alamos National Laboratory
Publications - 321
Citations - 38829
Patrick S. G. Chain is an academic researcher from Los Alamos National Laboratory. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 65, co-authored 301 publications receiving 34601 citations. Previous affiliations of Patrick S. G. Chain include McMaster University & Joint Genome Institute.
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Journal ArticleDOI
Genome Project Standards in a New Era of Sequencing
Patrick S. G. Chain,Darren Grafham,Robert S. Fulton,Michael Fitzgerald,Jessica B. Hostetler,Donna M. Muzny,Johar Ali,Bruce W. Birren,D. C. Bruce,D. C. Bruce,Christian J. Buhay,James R. Cole,Yan Ding,Shannon Dugan,Dawn Field,George M. Garrity,Richard A. Gibbs,Tina GravesT. Graves,Cliff S. Han,Cliff S. Han,Scott H. Harrison,Sarah K. Highlander,Philip Hugenholtz,H. M. Khouri,Chinnappa D. Kodira,Eugene Kolker,Nikos C. Kyrpides,D. Lang,Alla Lapidus,S. A. Malfatti,Victor Markowitz,T. Metha,Karen E. Nelson,Julian Parkhill,Samuel Pitluck,Xiang Qin,Timothy D. Read,Jeremy Schmutz,Shanmuga Sozhamannan,Peter Sterk,Robert L. Strausberg,Granger G. Sutton,Nicholas R. Thomson,James M. Tiedje,George M. Weinstock,Aye Wollam,John C. Detter +46 more
TL;DR: In this article, the authors propose a method to distinguish good from poor data sets by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database.
Journal ArticleDOI
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
TL;DR: The recent technological advances in next generation sequencing have brought the field closer to the goal of reconstructing all genomes within a community by presenting high throughput sequencing at much lower costs by allowing a massive increase in available raw sequence data.
Journal ArticleDOI
The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans
Harry R. Beller,Patrick S. G. Chain,Patrick S. G. Chain,Tracy E. Letain,Anu Chakicherla,Frank W. Larimer,Frank W. Larimer,Paul G. Richardson,Matthew A. Coleman,Ann P. Wood,Donovan P. Kelly +10 more
TL;DR: The genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles and groundwater restoration.
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The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes
Mark W. J. van Passel,Ravi Kant,Erwin G. Zoetendal,Caroline M. Plugge,Muriel Derrien,Stephanie Malfatti,Stephanie Malfatti,Patrick S. G. Chain,Patrick S. G. Chain,Tanja Woyke,Airi Palva,Willem M. de Vos,Willem M. de Vos,Hauke Smidt +13 more
TL;DR: Large repositories of GI tract metagenomes allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.
Journal ArticleDOI
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility
Patrick S. G. Chain,Vincent J. Denef,Konstantinos T. Konstantinidis,Konstantinos T. Konstantinidis,Lisa M. Vergez,Lisa M. Vergez,Loreine Agulló,Valeria Latorre Reyes,Valeria Latorre Reyes,Loren Hauser,Macarena Córdova,Luis Gómez,Myriam González,Miriam Land,Victoria Lao,Frank W. Larimer,John J. LiPuma,Eshwar Mahenthiralingam,Stephanie Malfatti,Stephanie Malfatti,Christopher J. Marx,J. Jacob Parnell,Alban Ramette,Paul G. Richardson,Michael Seeger,Daryl J. Smith,Theodore Spilker,Woo Jun Sul,Tamara V. Tsoi,Luke E. Ulrich,Igor B. Zhulin,James M. Tiedje +31 more
TL;DR: The first nonpathogenic B. xenovorans LB400 (LB400) isolate has been sequenced in this article, where the authors find significant differences in functional specialization between the three replicons of LB400.