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Emily M. Dietrich
Researcher at Argonne National Laboratory
Publications - 7
Citations - 2703
Emily M. Dietrich is an academic researcher from Argonne National Laboratory. The author has contributed to research in topics: Gene & Computer science. The author has an hindex of 5, co-authored 6 publications receiving 1646 citations. Previous affiliations of Emily M. Dietrich include University of Chicago.
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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.
Journal ArticleDOI
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
James J. Davis,James J. Davis,Alice R. Wattam,Alice R. Wattam,Ramy K. Aziz,Thomas Brettin,Thomas Brettin,Ralph Butler,Ralph Butler,Rory Butler,Philippe Chlenski,Neal Conrad,Neal Conrad,Allan Dickerman,Emily M. Dietrich,Emily M. Dietrich,Joseph L. Gabbard,Svetlana Gerdes,Andrew Guard,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Daniel E. Murphy-Olson,Daniel E. Murphy-Olson,Marcus Nguyen,Marcus Nguyen,Eric K. Nordberg,Gary J. Olsen,Robert Olson,Robert Olson,Jamie C. Overbeek,Jamie C. Overbeek,Ross Overbeek,Bruce Parrello,Bruce Parrello,Gordon D. Pusch,Maulik Shukla,Maulik Shukla,Chris Thomas,Margo VanOeffelen,Veronika Vonstein,Andrew S. Warren,Fangfang Xia,Fangfang Xia,Dawen Xie,Hyunseung Yoo,Hyunseung Yoo,Rick Stevens,Rick Stevens +48 more
TL;DR: The recent updates to the PATRIC resource are reported, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.
Journal ArticleDOI
PATRIC as a unique resource for studying antimicrobial resistance
Dionysios A. Antonopoulos,Rida Assaf,Ramy K. Aziz,Thomas Brettin,Christopher Bun,Neal Conrad,James J. Davis,Emily M. Dietrich,Terry Disz,Svetlana Gerdes,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Daniel E. Murphy-Olson,Eric K. Nordberg,Gary J. Olsen,Robert Olson,Ross Overbeek,Bruce Parrello,Gordon D. Pusch,John Santerre,Maulik Shukla,Rick Stevens,Margo VanOeffelen,Veronika Vonstein,Andrew S. Warren,Alice R. Wattam,Fangfang Xia,Hyunseung Yoo +28 more
TL;DR: This work has undertaken a large AMR protein annotation effort, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST and has been manually curated so that it projects stably across genomes.
Posted ContentDOI
The DOE Systems Biology Knowledgebase (KBase)
Adam P. Arkin,Rick Stevens,Robert W. Cottingham,Sergei Maslov,Christopher S. Henry,Paramvir S. Dehal,Doreen Ware,Fernando Perez,Nomi L. Harris,Shane Canon,Michael W. Sneddon,Matthew L. Henderson,William J. Riehl,Dan Gunter,Dan Murphy-Olson,Stephen Y. Chan,Roy T. Kamimura,Thomas Brettin,Folker Meyer,Dylan Chivian,David J. Weston,Elizabeth M. Glass,Brian H. Davison,Sunita Kumari,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,Matthew DeJongh,Scott Devoid,Emily M. Dietrich,Meghan M Drake,Inna Dubchak,Janaka N. Edirisinghe,Gang Fang,José P. Faria,Paul M. Frybarger,Wolfgang Gerlach,Mark Gerstein,James Gurtowski,Holly L. Haun,Fei He,Rashmi Jain,Marcin P. Joachimiak,Kevin P. Keegan,Shinnosuke Kondo,Kumar,Miriam Land,Mark Mills,Pavel S. Novichkov,Taeyun Oh,Gary J. Olsen,Olson B,Bruce Parrello,Shiran Pasternak,Erik Pearson,Sarah S. Poon,Gavin Price,Srividya Ramakrishnan,Priya Ranjan,Pamela C. Ronald,Michael C. Schatz,Seaver Smd,Maulik Shukla,Roman A. Sutormin,Mustafa H Syed,James Thomason,Nathan L. Tintle,Daifeng Wang,Fangfang Xia,Hyunseung Yoo,Shinjae Yoo +78 more
TL;DR: The KBase platform has extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling, and a software development kit allowing the community to add functionality to the system.