D
Dustin Machi
Researcher at University of Virginia
Publications - 30
Citations - 3275
Dustin Machi is an academic researcher from University of Virginia. The author has contributed to research in topics: Medicine & Computer science. The author has an hindex of 8, co-authored 22 publications receiving 2261 citations. Previous affiliations of Dustin Machi include University of Maryland, Baltimore & Virginia Tech.
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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
PATRIC, the bacterial bioinformatics database and analysis resource
Alice R. Wattam,David Abraham,Oral Dalay,Terry Disz,Timothy P. Driscoll,Joseph L. Gabbard,Joseph J. Gillespie,Roger Gough,Deborah Hix,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Eric K. Nordberg,Robert Olson,Ross Overbeek,Gordon D. Pusch,Maulik Shukla,Julie R. Schulman,Rick Stevens,Daniel E. Sullivan,Veronika Vonstein,Andrew S. Warren,Rebecca Will,Meredith J. C. Wilson,Hyunseung Yoo,Chengdong Zhang,Yan Zhang,Bruno W. S. Sobral +27 more
TL;DR: The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) and describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
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.
Book ChapterDOI
Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center
Alice R. Wattam,Thomas Brettin,Thomas Brettin,James J. Davis,James J. Davis,Svetlana Gerdes,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Robert Olson,Robert Olson,Ross Overbeek,Gordon D. Pusch,Maulik Shukla,Maulik Shukla,Rick Stevens,Rick Stevens,Veronika Vonstein,Andrew S. Warren,Fangfang Xia,Fangfang Xia,Hyunseung Yoo,Hyunseung Yoo +22 more
TL;DR: The main focus of this chapter is on assembly, annotation, and the downstream comparative analysis functionality that is freely available in the PATRIC resource.