D
Daniel Weaver
Researcher at SRI International
Publications - 28
Citations - 4733
Daniel Weaver is an academic researcher from SRI International. The author has contributed to research in topics: EcoCyc & Flux balance analysis. The author has an hindex of 17, co-authored 28 publications receiving 4199 citations. Previous affiliations of Daniel Weaver include Joint BioEnergy Institute & Artificial Intelligence Center.
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Journal ArticleDOI
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi,Richard Billington,Luciana Ferrer,Hartmut Foerster,Carol A. Fulcher,Ingrid M. Keseler,Anamika Kothari,Markus Krummenacker,Mario Latendresse,Lukas A. Mueller,Quang Ong,Suzanne M. Paley,Pallavi Subhraveti,Daniel Weaver,Peter D. Karp +14 more
TL;DR: The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.
Journal ArticleDOI
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Ingrid M. Keseler,Amanda Mackie,Alberto Santos-Zavaleta,Richard Billington,César Bonavides-Martínez,Ron Caspi,Carol A. Fulcher,Socorro Gama-Castro,Anamika Kothari,Markus Krummenacker,Mario Latendresse,Luis Muñiz-Rascado,Quang Ong,Suzanne M. Paley,Martín Peralta-Gil,Pallavi Subhraveti,David A. Velázquez-Ramírez,Daniel Weaver,Julio Collado-Vides,Ian T. Paulsen,Peter D. Karp +20 more
TL;DR: EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website, and new SmartTable tools allow users to browse collections of related Eco Cyc content.
Journal ArticleDOI
Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, Apis mellifera
Charles W. Whitfield,Susanta K. Behura,Stewart H. Berlocher,Andrew G. Clark,J. Spencer Johnston,Walter S. Sheppard,Deborah R. Smith,Andrew V. Suarez,Daniel Weaver,Neil D. Tsutsui +9 more
TL;DR: The results indicate that A. mellifera originated in Africa and expanded into Eurasia at least twice, resulting in populations in eastern and western Europe that are geographically close but genetically distant.
Journal ArticleDOI
The EcoCyc Database.
Peter D. Karp,Daniel Weaver,Suzanne M. Paley,Carol A. Fulcher,Aya Kubo,Anamika Kothari,Markus Krummenacker,Pallavi Subhraveti,Deepika Weerasinghe,Socorro Gama-Castro,Araceli M. Huerta,Luis Muñiz-Rascado,César Bonavides-Martínez,Verena Weiss,Martín Peralta-Gil,Alberto Santos-Zavaleta,Imke Schröder,Amanda Mackie,Robert P. Gunsalus,Julio Collado-Vides,Ingrid M. Keseler,Ian T. Paulsen +21 more
TL;DR: A detailed description of the data content of EcoCyc is provided and of the procedures by which this content is generated, to facilitate a system-level understanding of E. coli.
Journal ArticleDOI
HipA-Triggered Growth Arrest and β-Lactam Tolerance in Escherichia coli Are Mediated by RelA-Dependent ppGpp Synthesis
Gregory Bokinsky,Gregory Bokinsky,Edward E. K. Baidoo,Edward E. K. Baidoo,Swetha Akella,Swetha Akella,Helcio Burd,Helcio Burd,Daniel Weaver,Daniel Weaver,Jorge Alonso-Gutierrez,Jorge Alonso-Gutierrez,Hector Garcia-Martin,Hector Garcia-Martin,Taek Soon Lee,Taek Soon Lee,Jay D. Keasling,Jay D. Keasling,Jay D. Keasling +18 more
TL;DR: The active metabolism of HipA-arrested cells are harnessed to provide a bacteriophage-resistant platform for the production of biotechnologically relevant compounds, which may represent an innovative solution to the costly problem of phage contamination in industrial fermentations.