K
Kyle Bittinger
Researcher at Children's Hospital of Philadelphia
Publications - 161
Citations - 60220
Kyle Bittinger is an academic researcher from Children's Hospital of Philadelphia. The author has contributed to research in topics: Microbiome & Gut flora. The author has an hindex of 47, co-authored 124 publications receiving 44718 citations. Previous affiliations of Kyle Bittinger include University of Pennsylvania.
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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.
Journal ArticleDOI
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen,Jai Ram Rideout,Matthew R. Dillon,Nicholas A. Bokulich,Christian C. Abnet,Gabriel A. Al-Ghalith,Harriet Alexander,Harriet Alexander,Eric J. Alm,Manimozhiyan Arumugam,Francesco Asnicar,Yang Bai,Jordan E. Bisanz,Kyle Bittinger,Asker Daniel Brejnrod,Colin J. Brislawn,C. Titus Brown,Benjamin J. Callahan,Andrés Mauricio Caraballo-Rodríguez,John Chase,Emily K. Cope,Ricardo Silva,Christian Diener,Pieter C. Dorrestein,Gavin M. Douglas,Daniel M. Durall,Claire Duvallet,Christian F. Edwardson,Madeleine Ernst,Madeleine Ernst,Mehrbod Estaki,Jennifer Fouquier,Julia M. Gauglitz,Sean M. Gibbons,Sean M. Gibbons,Deanna L. Gibson,Antonio Gonzalez,Kestrel Gorlick,Jiarong Guo,Benjamin Hillmann,Susan Holmes,Hannes Holste,Curtis Huttenhower,Curtis Huttenhower,Gavin A. Huttley,Stefan Janssen,Alan K. Jarmusch,Lingjing Jiang,Benjamin D. Kaehler,Benjamin D. Kaehler,Kyo Bin Kang,Kyo Bin Kang,Christopher R. Keefe,Paul Keim,Scott T. Kelley,Dan Knights,Irina Koester,Tomasz Kosciolek,Jorden Kreps,Morgan G. I. Langille,Joslynn S. Lee,Ruth E. Ley,Ruth E. Ley,Yong-Xin Liu,Erikka Loftfield,Catherine A. Lozupone,Massoud Maher,Clarisse Marotz,Bryan D Martin,Daniel McDonald,Lauren J. McIver,Lauren J. McIver,Alexey V. Melnik,Jessica L. Metcalf,Sydney C. Morgan,Jamie Morton,Ahmad Turan Naimey,Jose A. Navas-Molina,Jose A. Navas-Molina,Louis-Félix Nothias,Stephanie B. Orchanian,Talima Pearson,Samuel L. Peoples,Samuel L. Peoples,Daniel Petras,Mary L. Preuss,Elmar Pruesse,Lasse Buur Rasmussen,Adam R. Rivers,Michael S. Robeson,Patrick Rosenthal,Nicola Segata,Michael Shaffer,Arron Shiffer,Rashmi Sinha,Se Jin Song,John R. Spear,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Pedro J. Torres,Pauline Trinh,Anupriya Tripathi,Peter J. Turnbaugh,Sabah Ul-Hasan,Justin J. J. van der Hooft,Fernando Vargas,Yoshiki Vázquez-Baeza,Emily Vogtmann,Max von Hippel,William A. Walters,Yunhu Wan,Mingxun Wang,Jonathan Warren,Kyle C. Weber,Kyle C. Weber,Charles H. D. Williamson,Amy D. Willis,Zhenjiang Zech Xu,Jesse R. Zaneveld,Yilong Zhang,Qiyun Zhu,Rob Knight,J. Gregory Caporaso +123 more
TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Journal ArticleDOI
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).
Journal ArticleDOI
Normalization and microbial differential abundance strategies depend upon data characteristics
Sophie Weiss,Zhenjiang Zech Xu,Shyamal D. Peddada,Amnon Amir,Kyle Bittinger,Antonio Gonzalez,Catherine A. Lozupone,Jesse R. Zaneveld,Yoshiki Vázquez-Baeza,Amanda Birmingham,Embriette R. Hyde,Rob Knight +11 more
TL;DR: These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.