D
Dylan Chivian
Researcher at Lawrence Berkeley National Laboratory
Publications - 38
Citations - 6799
Dylan Chivian is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Protein structure prediction & Genome. The author has an hindex of 27, co-authored 36 publications receiving 5683 citations. Previous affiliations of Dylan Chivian include Joint BioEnergy Institute & Massachusetts Institute of Technology.
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Journal ArticleDOI
Protein structure prediction and analysis using the Robetta server
TL;DR: The Robetta server provides automated tools for protein structure prediction and analysis and current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning.
Journal ArticleDOI
KBase: The United States Department of Energy Systems Biology Knowledgebase.
Adam P. Arkin,Adam P. Arkin,Robert W. Cottingham,Christopher S. Henry,Nomi L. Harris,Rick Stevens,Sergei Maslov,Paramvir S. Dehal,Doreen Ware,Fernando Perez,Shane Canon,Michael W. Sneddon,Matthew L. Henderson,William J. Riehl,Dan Murphy-Olson,Stephen Y. Chan,Roy T. Kamimura,Sunita Kumari,Meghan M Drake,Thomas Brettin,Elizabeth M. Glass,Dylan Chivian,Dan Gunter,David J. Weston,Benjamin H. Allen,Jason K. Baumohl,Aaron A. Best,Benjamin P. Bowen,Steven E. Brenner,Christopher Bun,John-Marc Chandonia,Jer Ming Chia,R. L. Colasanti,Neal Conrad,James J. Davis,Brian H. Davison,Matthew DeJongh,Scott Devoid,Emily M. Dietrich,Inna Dubchak,Janaka N. Edirisinghe,Janaka N. Edirisinghe,Gang Fang,José P. Faria,Paul M. Frybarger,Wolfgang Gerlach,Mark Gerstein,Annette Greiner,James Gurtowski,Holly L. Haun,Fei He,Rashmi Jain,Rashmi Jain,Marcin P. Joachimiak,Kevin P. Keegan,Shinnosuke Kondo,Vivek Kumar,Miriam Land,Folker Meyer,Mark Mills,Pavel S. Novichkov,Taeyun Oh,Taeyun Oh,Gary J. Olsen,Robert Olson,Bruce Parrello,Shiran Pasternak,Erik Pearson,Sarah S. Poon,Gavin Price,Srividya Ramakrishnan,Priya Ranjan,Priya Ranjan,Pamela C. Ronald,Pamela C. Ronald,Michael C. Schatz,Samuel M. D. Seaver,Maulik Shukla,Roman A. Sutormin,Mustafa H Syed,James Thomason,Nathan L. Tintle,Daifeng Wang,Fangfang Xia,Hyunseung Yoo,Shinjae Yoo,Dantong Yu +86 more
TL;DR: Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Olson, Dan; Chan, Stephen Y; Kamimura, Roy T.
Journal ArticleDOI
Environmental genomics reveals a single-species ecosystem deep within Earth.
Dylan Chivian,Eoin L. Brodie,Eric J. Alm,David E. Culley,Paramvir S. Dehal,Todd Z. DeSantis,Thomas M. Gihring,Alla Lapidus,Li-Hung Lin,Stephen Lowry,Duane P. Moser,Paul G. Richardson,Gordon Southam,Greg Wanger,Lisa M. Pratt,Lisa M. Pratt,Gary L. Andersen,Terry C. Hazen,Terry C. Hazen,Fred J. Brockman,Adam P. Arkin,Adam P. Arkin,Tullis C. Onstott,Tullis C. Onstott +23 more
TL;DR: DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome that indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea.
Journal ArticleDOI
MicrobesOnline: an integrated portal for comparative and functional genomics
Paramvir S. Dehal,Marcin P. Joachimiak,Morgan N. Price,John T. Bates,Jason K. Baumohl,Dylan Chivian,Greg D. Friedland,Katherine H. Huang,Keith Keller,Pavel S. Novichkov,Inna Dubchak,Eric J. Alm,Adam P. Arkin +12 more
TL;DR: MicrobesOnline as mentioned in this paper is a community resource for comparative and functional genome analysis, including a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree.
Journal ArticleDOI
A genomic catalog of Earth’s microbiomes
Stephen Nayfach,Simon Roux,Rekha Seshadri,Daniel W. Udwary,Neha Varghese,Frederik Schulz,Dongying Wu,David Paez-Espino,I-Min Chen,Marcel Huntemann,Krishna Palaniappan,Joshua Ladau,Supratim Mukherjee,T. B. K. Reddy,Torben Nielsen,Edward Kirton,José P. Faria,Janaka N. Edirisinghe,Christopher S. Henry,Sean P. Jungbluth,Dylan Chivian,Paramvir S. Dehal,Elisha M. Wood-Charlson,Adam P. Arkin,Susannah G. Tringe,Axel Visel,Tanja Woyke,Nigel J Mouncey,Natalia Ivanova,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +30 more
TL;DR: The utility of this collection of >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans is demonstrated for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses.