F
Frederic D. Bushman
Researcher at University of Pennsylvania
Publications - 480
Citations - 99758
Frederic D. Bushman is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Integrase & Microbiome. The author has an hindex of 119, co-authored 442 publications receiving 84206 citations. Previous affiliations of Frederic D. Bushman include Children's Hospital of Philadelphia & Cleveland Clinic.
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Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Gary D. Wu,Jun Chen,Christian Hoffmann,Christian Hoffmann,Kyle Bittinger,Ying-Yu Chen,Sue A. Keilbaugh,Meenakshi Bewtra,Dan Knights,William A. Walters,Rob Knight,Rohini Sinha,Erin Gilroy,Kernika Gupta,Robert N. Baldassano,Lisa Nessel,Hongzhe Li,Frederic D. Bushman,James D. Lewis +18 more
TL;DR: Alternative enterotype states are associated with long-term diet, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella) and other enterotypes distinguished primarily by levels of Bacteroide and Prevotella.
Journal ArticleDOI
PyNAST: a flexible tool for aligning sequences to a template alignment
J. Gregory Caporaso,Kyle Bittinger,Frederic D. Bushman,Todd Z. DeSantis,Gary L. Andersen,Rob Knight +5 more
TL;DR: PyNAST as discussed by the authors is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).
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Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis
Robert A. Koeth,Zeneng Wang,Bruce S. Levison,Jennifer A. Buffa,Elin Org,Brendan Sheehy,Earl B. Britt,Xiaoming Fu,Yuping Wu,Lin Li,Jonathan D. Smith,Joseph A. DiDonato,Jun Chen,Hongzhe Li,Gary D. Wu,James D. Lewis,Manya Warrier,J. Mark Brown,Ronald M. Krauss,W.H. Wilson Tang,Frederic D. Bushman,Aldons J. Lusis,Stanley L. Hazen +22 more
TL;DR: It is demonstrated that metabolism by intestinal microbiota of dietary l-carnitine, a trimethylamine abundant in red meat, also produces TMAO and accelerates atherosclerosis in mice, and intestinal microbiota may contribute to the well-established link between high levels of red meat consumption and CVD risk.
Journal ArticleDOI
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Astrid R. W Schroder,Paul Shinn,Huaming Chen,Charles C. Berry,Joseph R. Ecker,Frederic D. Bushman +5 more
TL;DR: Global analysis of cellular transcription indicated that active genes were preferential integration targets, particularly genes that were activated in cells after infection by HIV-1, and this data suggests how selective targeting promotes aggressive HIV replication.