A
Aaron A. Best
Researcher at Hope College
Publications - 46
Citations - 12935
Aaron A. Best is an academic researcher from Hope College. The author has contributed to research in topics: Genome & Comparative genomics. The author has an hindex of 17, co-authored 43 publications receiving 11018 citations. Previous affiliations of Aaron A. Best include University of Illinois at Urbana–Champaign.
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Journal ArticleDOI
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.
Journal ArticleDOI
High-throughput generation, optimization and analysis of genome-scale metabolic models
Christopher S. Henry,Matthew DeJongh,Aaron A. Best,Paul M. Frybarger,Ben Linsay,Rick Stevens,Rick Stevens +6 more
TL;DR: The Model SEED is introduced, a web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic models and introduces techniques to automate nearly every step of this process, taking ∼48 h to reconstruct a metabolic model from an assembled genome sequence.
Journal ArticleDOI
Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.
Hilary G. Morrison,Andrew G. McArthur,Frances D. Gillin,Stephen B. Aley,Rodney D. Adam,Gary J. Olsen,Aaron A. Best,W. Zacheus Cande,Feng Chen,Michael J. Cipriano,Barbara J. Davids,Scott C. Dawson,Heidi G. Elmendorf,Adrian B. Hehl,Michael Holder,Susan M. Huse,Ulandt Kim,Erica Lasek-Nesselquist,Gerard Manning,Anuranjini Nigam,Julie E. J. Nixon,Daniel Palm,Nora Q.E. Passamaneck,Anjali Prabhu,Claudia I. Reich,David S. Reiner,John Samuelson,Staffan G. Svärd,Mitchell L. Sogin +28 more
TL;DR: The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways.
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
Toward the automated generation of genome-scale metabolic networks in the SEED
Matthew DeJongh,Kevin Formsma,Paul Boillot,John Gould,Matthew Rycenga,Matthew Rycenga,Aaron A. Best +6 more
TL;DR: The method sets the stage for the automated generation of substantially complete metabolic networks for over 400 complete genome sequences currently in the SEED, an open-source software environment for comparative genome annotation and analysis.