Curtis Huttenhower

Curtis Huttenhower

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Curtis Huttenhower

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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam 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 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 Walters Yunhu Wan Mingxun Wang Jonathan Warren 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

Nat Biotechnol 2019 Sep;37(9):1091

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0252-6DOI Listing
September 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Authors:
Evan Bolyen Jai Ram Rideout Matthew R Dillon Nicholas A Bokulich Christian C Abnet Gabriel A Al-Ghalith Harriet Alexander Eric J Alm Manimozhiyan Arumugam Francesco Asnicar Yang Bai Jordan E Bisanz Kyle Bittinger Asker Brejnrod Colin J Brislawn C Titus Brown Benjamin J Callahan Andrés Mauricio Caraballo-Rodríguez John Chase Emily K Cope Ricardo Da Silva Christian Diener Pieter C Dorrestein Gavin M Douglas Daniel M Durall Claire Duvallet Christian F Edwardson Madeleine Ernst Mehrbod Estaki Jennifer Fouquier Julia M Gauglitz Sean M Gibbons Deanna L Gibson Antonio Gonzalez Kestrel Gorlick Jiarong Guo Benjamin Hillmann Susan Holmes Hannes Holste Curtis Huttenhower Gavin A Huttley Stefan Janssen Alan K Jarmusch Lingjing Jiang Benjamin D Kaehler Kyo Bin Kang Christopher R Keefe Paul Keim Scott T Kelley Dan Knights Irina Koester Tomasz Kosciolek Jorden Kreps Morgan G I Langille Joslynn Lee Ruth Ley Yong-Xin Liu Erikka Loftfield Catherine Lozupone Massoud Maher Clarisse Marotz Bryan D Martin Daniel McDonald Lauren J McIver Alexey V Melnik Jessica L Metcalf Sydney C Morgan Jamie T Morton Ahmad Turan Naimey Jose A Navas-Molina Louis Felix Nothias Stephanie B Orchanian Talima Pearson Samuel L Peoples Daniel Petras Mary Lai Preuss Elmar Pruesse Lasse Buur Rasmussen Adam 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 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 Walters Yunhu Wan Mingxun Wang Jonathan Warren 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

Nat Biotechnol 2019 08;37(8):852-857

Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

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http://dx.doi.org/10.1038/s41587-019-0209-9DOI Listing
August 2019

The interleukin-33 receptor contributes to pulmonary responses to ozone in male mice: role of the microbiome.

Respir Res 2019 Aug 27;20(1):197. Epub 2019 Aug 27.

Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Av Bld1 room 319, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s12931-019-1168-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712741PMC
August 2019

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.

Am J Epidemiol 2019 Jun;188(6):1023-1026

Graduate School of Public Health and Health Policy, City University of New York, New York, New York.

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http://dx.doi.org/10.1093/aje/kwz006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545282PMC
June 2019

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

Microbiota contribute to obesity-related increases in the pulmonary response to ozone.

Am J Respir Cell Mol Biol 2019 May 30. Epub 2019 May 30.

Harvard University T H Chan School of Public Health, 1857, Department of Environmental Health, Boston, Massachusetts, United States ;

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http://dx.doi.org/10.1165/rcmb.2019-0144OCDOI Listing
May 2019

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome.

Am J Pathol 2018 12 20;188(12):2839-2852. Epub 2018 Sep 20.

Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2018.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284552PMC
December 2018

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

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Cell Host Microbe 2018 07;24(1):146-154.e4

The Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2018.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091882PMC
July 2018

Long-term use of antibiotics and risk of colorectal adenoma.

Gut 2018 04 4;67(4):672-678. Epub 2017 Apr 4.

Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1136/gutjnl-2016-313413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628103PMC
April 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

The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: A Prospective, Pilot Study.

Urology 2018 Jan 6;111:122-128. Epub 2017 Sep 6.

Department of Urology, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY.

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http://dx.doi.org/10.1016/j.urology.2017.08.039DOI Listing
January 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

A Bayesian method for detecting pairwise associations in compositional data.

PLoS Comput Biol 2017 Nov 15;13(11):e1005852. Epub 2017 Nov 15.

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.1005852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706738PMC
November 2017

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

Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue.

JAMA Oncol 2017 Jul;3(7):921-927

Division of MPE Molecular Pathological Epidemiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts4Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts9Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts13Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1001/jamaoncol.2016.6374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502000PMC
July 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

Microbial strain-level population structure and genetic diversity from metagenomes.

Genome Res 2017 04 6;27(4):626-638. Epub 2017 Feb 6.

Centre for Integrative Biology, University of Trento, 38123 Trento, Italy.

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http://dx.doi.org/10.1101/gr.216242.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378180PMC
April 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

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome.

Environ Sci Technol 2016 09 7;50(18):9807-15. Epub 2016 Sep 7.

Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.est.6b00262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032049PMC
September 2016

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.

Appl Environ Microbiol 2016 06 31;82(12):3572-81. Epub 2016 May 31.

GNS Science, Extremophiles Research Group, Wairakei Research Centre, Taupō, New Zealand Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA Broad Institute, Cambridge, Massachusetts, USA Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand

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http://dx.doi.org/10.1128/AEM.00139-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959169PMC
June 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

Fecal Microbiome in Epidemiologic Studies-Letter.

Cancer Epidemiol Biomarkers Prev 2016 05 9;25(5):869. Epub 2016 Mar 9.

Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1055-9965.EPI-16-0063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4898650PMC
May 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

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Nat Microbiol 2016 05 27;1(7):16070. Epub 2016 May 27.

Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy.

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http://dx.doi.org/10.1038/nmicrobiol.2016.70DOI Listing
May 2016

Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer.

PLoS Comput Biol 2016 Apr 14;12(4):e1004820. Epub 2016 Apr 14.

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

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http://dx.doi.org/10.1371/journal.pcbi.1004820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831844PMC
April 2016

The healthy human microbiome.

Genome Med 2016 04 27;8(1):51. Epub 2016 Apr 27.

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

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http://dx.doi.org/10.1186/s13073-016-0307-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848870PMC
April 2016

The microbiome quality control project: baseline study design and future directions.

Genome Biol 2015 Dec 9;16:276. Epub 2015 Dec 9.

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

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http://dx.doi.org/10.1186/s13059-015-0841-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674991PMC
December 2015

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

Cross-biome comparison of microbial association networks.

Front Microbiol 2015 27;6:1200. Epub 2015 Oct 27.

Center for the Biology of Disease, VIB Leuven, Belgium ; Department of Microbiology and Immunology, REGA Institute, KU Leuven Leuven, Belgium ; Department of Applied Biological Sciences, Vrije Universiteit Brussel Brussels, Belgium.

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http://dx.doi.org/10.3389/fmicb.2015.01200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621437PMC
November 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

Fusobacterium nucleatum and T Cells in Colorectal Carcinoma.

JAMA Oncol 2015 Aug;1(5):653-61

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts3Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts5Department of Pathology, Brigham and Women's Hospital.

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http://dx.doi.org/10.1001/jamaoncol.2015.1377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537376PMC
August 2015

Compact graphical representation of phylogenetic data and metadata with GraPhlAn.

PeerJ 2015 18;3:e1029. Epub 2015 Jun 18.

Centre for Integrative Biology (CIBIO), University of Trento , Italy.

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http://dx.doi.org/10.7717/peerj.1029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476132PMC
July 2015