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Eric A. Franzosa
Researcher at Harvard University
Publications - 91
Citations - 18400
Eric A. Franzosa is an academic researcher from Harvard University. The author has contributed to research in topics: Microbiome & Metagenomics. The author has an hindex of 40, co-authored 75 publications receiving 11531 citations. Previous affiliations of Eric A. Franzosa include McGill University & Broad Institute.
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Journal ArticleDOI
MetaPhlAn2 for enhanced metagenomic taxonomic profiling.
Duy Tin Truong,Eric A. Franzosa,Timothy L. Tickle,Timothy L. Tickle,Matthias Scholz,George Weingart,Edoardo Pasolli,Adrian Tett,Curtis Huttenhower,Curtis Huttenhower,Nicola Segata +10 more
TL;DR: Improvements in the underlying pipeline for identifying marker genes and the profiling procedure resulted in much improved quantitative performances (higher correlation with true abundances, lower false positive and false negative rates).
Journal ArticleDOI
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Jason Lloyd-Price,Jason Lloyd-Price,Cesar Arze,Ashwin N. Ananthakrishnan,Melanie Schirmer,Melanie Schirmer,Julian Avila-Pacheco,Tiffany W. Poon,Elizabeth Andrews,Nadim J. Ajami,Kevin S. Bonham,Kevin S. Bonham,Colin J. Brislawn,David Casero,Holly Courtney,Antonio Gonzalez,Thomas G. Graeber,A. Brantley Hall,Kathleen Lake,Carol J. Landers,Himel Mallick,Himel Mallick,Damian R. Plichta,Mahadev Prasad,Gholamali Rahnavard,Gholamali Rahnavard,Jenny S. Sauk,Dmitry Shungin,Dmitry Shungin,Yoshiki Vázquez-Baeza,Richard A. White,Jonathan Braun,Lee A. Denson,Lee A. Denson,Janet K. Jansson,Rob Knight,Subra Kugathasan,Dermot P.B. McGovern,Joseph F. Petrosino,Thaddeus S. Stappenbeck,Harland S. Winter,Clary B. Clish,Eric A. Franzosa,Hera Vlamakis,Ramnik J. Xavier,Ramnik J. Xavier,Ramnik J. Xavier,Curtis Huttenhower,Curtis Huttenhower +48 more
TL;DR: It is demonstrated that periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts, and integrative analysis identified microbial, biochemical, and host factors central to this dysregulation.
Journal ArticleDOI
A proteome-scale map of the human interactome network
Thomas Rolland,Murat Tasan,Benoit Charloteaux,Samuel J. Pevzner,Quan Zhong,Quan Zhong,Nidhi Sahni,Song Yi,Irma Lemmens,Celia Fontanillo,Roberto Mosca,Atanas Kamburov,Susan Dina Ghiassian,Susan Dina Ghiassian,Xinping Yang,Lila Ghamsari,Dawit Balcha,Bridget E. Begg,Pascal Braun,Marc Brehme,Martin P. Broly,Anne-Ruxandra Carvunis,Dan Convery-Zupan,Roser Corominas,Jasmin Coulombe-Huntington,Jasmin Coulombe-Huntington,Elizabeth Dann,Matija Dreze,Amélie Dricot,Changyu Fan,Eric A. Franzosa,Eric A. Franzosa,Fana Gebreab,Bryan J. Gutierrez,Madeleine F. Hardy,Mike Jin,Shuli Kang,Ruth Kiros,Guan Ning Lin,Katja Luck,Andrew MacWilliams,Jörg Menche,Jörg Menche,Ryan R. Murray,Alexandre Palagi,Matthew M. Poulin,Xavier Rambout,Xavier Rambout,John Rasla,Patrick Reichert,Viviana Romero,Elien Ruyssinck,Julie M. Sahalie,Annemarie Scholz,Akash A. Shah,Amitabh Sharma,Amitabh Sharma,Yun Shen,Kerstin Spirohn,Stanley Tam,Alexander O. Tejeda,Shelly A. Trigg,Jean-Claude Twizere,Jean-Claude Twizere,Kerwin Vega,Jennifer M. Walsh,Michael E. Cusick,Yu Xia,Yu Xia,Albert-László Barabási,Albert-László Barabási,Albert-László Barabási,Lilia M. Iakoucheva,Patrick Aloy,Javier De Las Rivas,Jan Tavernier,Michael A. Calderwood,David E. Hill,Tong Hao,Frederick P. Roth,Marc Vidal +80 more
TL;DR: The map uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help "connect the dots" of the genomic revolution.
Journal ArticleDOI
Species-level functional profiling of metagenomes and metatranscriptomes.
Eric A. Franzosa,Eric A. Franzosa,Lauren J. McIver,Lauren J. McIver,Gholamali Rahnavard,Gholamali Rahnavard,Luke R. Thompson,Melanie Schirmer,Melanie Schirmer,George Weingart,Karen Schwarzberg Lipson,Rob Knight,J. Gregory Caporaso,Nicola Segata,Curtis Huttenhower,Curtis Huttenhower +15 more
TL;DR: HUMAnN2 is developed, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities and introduces ‘contributional diversity’ to explain patterns of ecological assembly across different microbial community types.
Journal ArticleDOI
Gut microbiome structure and metabolic activity in inflammatory bowel disease
Eric A. Franzosa,Eric A. Franzosa,Alexandra Sirota-Madi,Julian Avila-Pacheco,Nadine Fornelos,Henry J. Haiser,Stefan Reinker,Tommi Vatanen,A. Brantley Hall,Himel Mallick,Himel Mallick,Lauren J. McIver,Lauren J. McIver,Jenny Sauk,Robin G. Wilson,Betsy W. Stevens,Justin M. Scott,Kerry A. Pierce,Amy Deik,Kevin Bullock,Floris Imhann,Jeffrey A. Porter,Alexandra Zhernakova,Jingyuan Fu,Rinse K. Weersma,Cisca Wijmenga,Cisca Wijmenga,Clary B. Clish,Hera Vlamakis,Curtis Huttenhower,Curtis Huttenhower,Ramnik J. Xavier +31 more
TL;DR: Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort, providing an improved understanding of perturbations of the microbiome–metabolome interface in IBD.