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Bruce Parrello
Researcher at Argonne National Laboratory
Publications - 19
Citations - 17501
Bruce Parrello is an academic researcher from Argonne National Laboratory. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 11, co-authored 15 publications receiving 13873 citations. Previous affiliations of Bruce Parrello include University of Chicago & 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
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
Ross Overbeek,Robert Olson,Gordon D. Pusch,Gary J. Olsen,James J. Davis,Terry Disz,Robert Edwards,Svetlana Gerdes,Bruce Parrello,Maulik Shukla,Veronika Vonstein,Alice R. Wattam,Fangfang Xia,Rick Stevens +13 more
TL;DR: The interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources are described.
Journal ArticleDOI
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
Thomas Brettin,Thomas Brettin,James J. Davis,James J. Davis,Terry Disz,Robert Edwards,Robert Edwards,Svetlana Gerdes,Gary J. Olsen,Robert Olson,Robert Olson,Ross Overbeek,Bruce Parrello,Gordon D. Pusch,Maulik Shukla,James Thomason,Rick Stevens,Rick Stevens,Veronika Vonstein,Alice R. Wattam,Fangfang Xia,Fangfang Xia +21 more
TL;DR: The RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines and offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job.
Journal ArticleDOI
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
Alice R. Wattam,James J. Davis,James J. Davis,Rida Assaf,Sébastien Boisvert,Thomas Brettin,Thomas Brettin,Christopher Bun,Neal Conrad,Neal Conrad,Emily M. Dietrich,Emily M. Dietrich,Terry Disz,Joseph L. Gabbard,Svetlana Gerdes,Christopher S. Henry,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Eric K. Nordberg,Gary J. Olsen,Daniel E. Murphy-Olson,Robert Olson,Robert Olson,Ross Overbeek,Bruce Parrello,Gordon D. Pusch,Maulik Shukla,Maulik Shukla,Veronika Vonstein,Andrew S. Warren,Fangfang Xia,Fangfang Xia,Hyunseung Yoo,Hyunseung Yoo,Rick Stevens,Rick Stevens +36 more
TL;DR: The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center, which provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace.
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.