John-Marc Chandonia
Lawrence Berkeley National Laboratory
63 Papers
545 Citations
John-Marc Chandonia is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Structural genomics & Biology. The author has an hindex of 23, co-authored 56 publications. Previous affiliations of John-Marc Chandonia include Laboratory of Molecular Biology & University of California, San Francisco.
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Papers
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
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.
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
Shibu Yooseph,Granger G. Sutton,Douglas B. Rusch,Aaron L. Halpern,Shannon J. Williamson,Karin A. Remington,Jonathan A. Eisen,Jonathan A. Eisen,Karla B. Heidelberg,Gerard Manning,Weizhong Li,Lukasz Jaroszewski,Piotr Cieplak,Christopher S. Miller,Huiying Li,Susan T. Mashiyama,Marcin P. Joachimiak,Christopher van Belle,John-Marc Chandonia,John-Marc Chandonia,David A W Soergel,Yufeng Zhai,Kannan Natarajan,Shaun W. Lee,Benjamin J. Raphael,Vineet Bafna,Robert Friedman,Steven E. Brenner,Adam Godzik,David Eisenberg,Jack E. Dixon,Susan S. Taylor,Robert L. Strausberg,Marvin Frazier,J. Craig Venter +34 more
TL;DR: This work used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling sequences to add a great deal of diversity to known protein families and shed light on their evolution.
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
TL;DR: The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.
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The impact of structural genomics: expectations and outcomes.
TL;DR: The novelty, cost, and impact of structures solved by SG centers are quantitatively analyzed, and traditional structural biology papers are cited significantly more often, suggesting greater current impact.