Eric A Franzosa

Eric A Franzosa

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Eric A Franzosa

Eric A Franzosa

Publications by authors named "Eric A Franzosa"

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Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.

Cell Host Microbe 2019 05;25(5):668-680.e7

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19313128193020
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http://dx.doi.org/10.1016/j.chom.2019.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544385PMC
May 2019

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.

Cell Host Microbe 2018 10;24(4):600-610.e4

The Broad Institute of MIT and Harvard, Infectious Disease and Microbiome, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2018.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277984PMC
October 2018

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools.

J Allergy Clin Immunol 2018 06 5;141(6):2311-2313. Epub 2018 Mar 5.

Harvard Medical School, Boston, Mass; Broad Institute of MIT and Harvard University, Cambridge, Mass. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2018.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994187PMC
June 2018

bioBakery: a meta'omic analysis environment.

Bioinformatics 2018 04;34(7):1235-1237

Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030947PMC
April 2018

Host genetic variation and its microbiome interactions within the Human Microbiome Project.

Genome Med 2018 01 29;10(1). Epub 2018 Jan 29.

Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s13073-018-0515-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789541PMC
January 2018

Experimental design and quantitative analysis of microbial community multiomics.

Genome Biol 2017 11 30;18(1):228. Epub 2017 Nov 30.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s13059-017-1359-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708111PMC
November 2017

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.

Cell Host Microbe 2017 Jul;22(1):25-37.e6

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2017.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672633PMC
July 2017

A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development.

Elife 2016 12 13;5. Epub 2016 Dec 13.

Institute of Molecular Biology, University of Oregon, Eugene, United States.

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http://dx.doi.org/10.7554/eLife.20145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5154760PMC
December 2016

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Cell 2016 11;167(4):1125-1136.e8

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.10.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131922PMC
November 2016

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Sci Transl Med 2016 06;8(343):343ra81

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/scitranslmed.aad0917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032909PMC
June 2016

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Cell 2016 May 28;165(4):842-53. Epub 2016 Apr 28.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950857PMC
May 2016

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

PLoS Comput Biol 2015 Dec 18;11(12):e1004557. Epub 2015 Dec 18.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684307PMC
December 2015

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Nat Methods 2015 Oct;12(10):902-3

Centre for Integrative Biology, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1038/nmeth.3589DOI Listing
October 2015

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Nat Rev Microbiol 2015 Jun 27;13(6):360-72. Epub 2015 Apr 27.

1] Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA. [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nrmicro3451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4800835PMC
June 2015

Identifying personal microbiomes using metagenomic codes.

Proc Natl Acad Sci U S A 2015 Jun 11;112(22):E2930-8. Epub 2015 May 11.

Biostatistics Department, Harvard School of Public Health, Boston, MA 02115; Microbial Systems and Communities, Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142;

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http://dx.doi.org/10.1073/pnas.1423854112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460507PMC
June 2015

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.

Cell Host Microbe 2015 Mar 26;17(3):385-391. Epub 2015 Feb 26.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2015.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369771PMC
March 2015

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Cell Host Microbe 2015 Feb 5;17(2):260-73. Epub 2015 Feb 5.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2015.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689191PMC
February 2015

Advancing the microbiome research community.

Cell 2014 Oct;159(2):227-30

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Health-Related Informatics and Bioimaging, University of Maryland School of Medicine, Baltimore, MD 21201, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.09.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221798PMC
October 2014

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

PLoS Pathog 2013 5;9(12):e1003778. Epub 2013 Dec 5.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855575PMC
September 2014

Functional profiling of the gut microbiome in disease-associated inflammation.

Genome Med 2013 31;5(7):65. Epub 2013 Jul 31.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA ; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/gm469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978847PMC
June 2014

Structural models for host-pathogen protein-protein interactions: assessing coverage and bias.

Pac Symp Biocomput 2012 :287-98

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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December 2013

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.

Genome Biol Evol 2013 ;5(4):734-44

Bioinformatics Program, Boston University, USA.

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http://dx.doi.org/10.1093/gbe/evt039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641637PMC
September 2013

Construction of functional linkage gene networks by data integration.

Methods Mol Biol 2013 ;939:215-32

Translational Sciences Department, Novartis Institutes for BioMedical Research, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-62703-107-3_14DOI Listing
June 2013

Independent effects of protein core size and expression on residue-level structure-evolution relationships.

PLoS One 2012 3;7(10):e46602. Epub 2012 Oct 3.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046602PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463513PMC
May 2013

Toward a three-dimensional view of protein networks between species.

Front Microbiol 2012 21;3:428. Epub 2012 Dec 21.

Bioinformatics Program, Boston University Boston, MA, USA.

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http://dx.doi.org/10.3389/fmicb.2012.00428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528071PMC
December 2012

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90.

PLoS One 2011 30;6(11):e28211. Epub 2011 Nov 30.

Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028211PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227642PMC
April 2012

Structural principles within the human-virus protein-protein interaction network.

Proc Natl Acad Sci U S A 2011 Jun 16;108(26):10538-43. Epub 2011 Jun 16.

Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.1101440108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127880PMC
June 2011

Protein evolution in yeast transcription factor subnetworks.

Nucleic Acids Res 2010 Oct 13;38(18):5959-69. Epub 2010 May 13.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkq353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952844PMC
October 2010

Structural determinants of protein evolution are context-sensitive at the residue level.

Mol Biol Evol 2009 Oct 13;26(10):2387-95. Epub 2009 Jul 13.

Boston University, Boston, USA.

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http://dx.doi.org/10.1093/molbev/msp146DOI Listing
October 2009

Integrated assessment of genomic correlates of protein evolutionary rate.

PLoS Comput Biol 2009 Jun 12;5(6):e1000413. Epub 2009 Jun 12.

Bioinformatics Program, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688033PMC
June 2009