Publications by authors named "Matthew R Henn"

57Publications

A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis.

Authors:
Matthew R Henn Edward J O'Brien Liyang Diao Brian G Feagan William J Sandborn Curtis Huttenhower Jennifer R Wortman Barbara H McGovern Sherry Wang-Weigand David I Lichter Meghan Chafee Christopher B Ford Patricia Bernardo Peng Zhao Sheri Simmons Amelia D Tomlinson David N Cook Roger J Pomerantz Bharat K Misra John G Auninš Michele Trucksis

Gastroenterology 2021 Jan 4;160(1):115-127.e30. Epub 2020 Aug 4.

Seres Therapeutics, Cambridge, Massachusetts.

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January 2021

SER-109, an Investigational Microbiome Drug to Reduce Recurrence after Clostridioides difficile infection: Lessons Learned from a Phase 2 Trial.

Authors:
Barbara H McGovern Christopher B Ford Matthew R Henn Darrell S Pardi Sahil Khanna Elizabeth L Hohmann Edward J O'Brien Christopher A Desjardins Patricia Bernardo Jennifer R Wortman Mary-Jane Lombardo Kevin D Litcofsky Jonathan A Winkler Christopher W J McChalicher Sunny S Li Amelia D Tomlinson Madhumitha Nandakumar David N Cook Roger J Pomerantz John G Auninš Michele Trucksis

Clin Infect Dis 2020 Apr 7. Epub 2020 Apr 7.

Seres Therapeutics, Cambridge, MA USA.

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April 2020

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial.

Authors:
Elaine W Yu Liu Gao Petr Stastka Michael C Cheney Jasmin Mahabamunuge Mariam Torres Soto Christopher B Ford Jessica A Bryant Matthew R Henn Elizabeth L Hohmann

PLoS Med 2020 03 9;17(3):e1003051. Epub 2020 Mar 9.

Harvard Medical School, Boston, Massachusetts, United States of America.

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March 2020

Reply to Lagier et al.

Authors:
Sahil Khanna Julie E Button Mary-Jane Lombardo Marin Vulic Matthew R Henn David N Cook Roger J Pomerantz Elizabeth L Hohmann

J Infect Dis 2017 01 20;215(1):162-164. Epub 2016 Oct 20.

Massachusetts General Hospital, Boston.

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January 2017

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Authors:
Damien C Tully Colin B Ogilvie Rebecca E Batorsky David J Bean Karen A Power Musie Ghebremichael Hunter E Bedard Adrianne D Gladden Aaron M Seese Molly A Amero Kimberly Lane Graham McGrath Suzane B Bazner Jake Tinsley Niall J Lennon Matthew R Henn Zabrina L Brumme Philip J Norris Eric S Rosenberg Kenneth H Mayer Heiko Jessen Sergei L Kosakovsky Pond Bruce D Walker Marcus Altfeld Jonathan M Carlson Todd M Allen

PLoS Pathog 2016 05 10;12(5):e1005619. Epub 2016 May 10.

Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America.

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May 2016

A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection.

Authors:
Sahil Khanna Darrell S Pardi Colleen R Kelly Colleen S Kraft Tanvi Dhere Matthew R Henn Mary-Jane Lombardo Marin Vulic Toshiro Ohsumi Jonathan Winkler Christina Pindar Barbara H McGovern Roger J Pomerantz John G Aunins David N Cook Elizabeth L Hohmann

J Infect Dis 2016 07 8;214(2):173-81. Epub 2016 Feb 8.

Massachusetts General Hospital, Boston, Massachusetts.

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July 2016

Standardized metadata for human pathogen/vector genomic sequences.

Authors:
Vivien G Dugan Scott J Emrich Gloria I Giraldo-Calderón Omar S Harb Ruchi M Newman Brett E Pickett Lynn M Schriml Timothy B Stockwell Christian J Stoeckert Dan E Sullivan Indresh Singh Doyle V Ward Alison Yao Jie Zheng Tanya Barrett Bruce Birren Lauren Brinkac Vincent M Bruno Elizabet Caler Sinéad Chapman Frank H Collins Christina A Cuomo Valentina Di Francesco Scott Durkin Mark Eppinger Michael Feldgarden Claire Fraser W Florian Fricke Maria Giovanni Matthew R Henn Erin Hine Julie Dunning Hotopp Ilene Karsch-Mizrachi Jessica C Kissinger Eun Mi Lee Punam Mathur Emmanuel F Mongodin Cheryl I Murphy Garry Myers Daniel E Neafsey Karen E Nelson William C Nierman Julia Puzak David Rasko David S Roos Lisa Sadzewicz Joana C Silva Bruno Sobral R Burke Squires Rick L Stevens Luke Tallon Herve Tettelin David Wentworth Owen White Rebecca Will Jennifer Wortman Yun Zhang Richard H Scheuermann

PLoS One 2014 17;9(6):e99979. Epub 2014 Jun 17.

J. Craig Venter Institute, Rockville, Maryland, and La Jolla, California, United States of America; Department of Pathology, University of California San Diego, San Diego, California, United States of America.

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February 2015

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

Authors:
Jonathan Z Li Brad Chapman Patrick Charlebois Oliver Hofmann Brian Weiner Alyssa J Porter Reshmi Samuel Saran Vardhanabhuti Lu Zheng Joseph Eron Babafemi Taiwo Michael C Zody Matthew R Henn Daniel R Kuritzkes Winston Hide Cara C Wilson Baiba I Berzins Edward P Acosta Barbara Bastow Peter S Kim Sarah W Read Jennifer Janik Debra S Meres Michael M Lederman Lori Mong-Kryspin Karl E Shaw Louis G Zimmerman Randi Leavitt Guy De La Rosa Amy Jennings

PLoS One 2014 6;9(3):e90485. Epub 2014 Mar 6.

ACTG Operations Center.

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January 2015

V-Phaser 2: variant inference for viral populations.

Authors:
Xiao Yang Patrick Charlebois Alex Macalalad Matthew R Henn Michael C Zody

BMC Genomics 2013 Oct 3;14:674. Epub 2013 Oct 3.

Broad Institute of MIT & Harvard, 7 Cambridge Center, Cambridge, MA 02142 USA.

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October 2013

Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing.

Authors:
Huda Makhluf Michael D Buck Kevin King Stuart T Perry Matthew R Henn Sujan Shresta

PLoS One 2013 14;8(1):e54220. Epub 2013 Jan 14.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.

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August 2013

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.

Authors:
Ruchi M Newman Thomas Kuntzen Brian Weiner Andrew Berical Patrick Charlebois Carla Kuiken Donald G Murphy Peter Simmonds Phil Bennett Niall J Lennon Bruce W Birren Michael C Zody Todd M Allen Matthew R Henn

J Infect Dis 2013 Jul 6;208(1):17-31. Epub 2012 Nov 6.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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July 2013

De novo assembly of highly diverse viral populations.

Authors:
Xiao Yang Patrick Charlebois Sante Gnerre Matthew G Coole Niall J Lennon Joshua Z Levin James Qu Elizabeth M Ryan Michael C Zody Matthew R Henn

BMC Genomics 2012 Sep 13;13:475. Epub 2012 Sep 13.

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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September 2012

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.

Authors:
Christine M Malboeuf Xiao Yang Patrick Charlebois James Qu Aaron M Berlin Monica Casali Kendra N Pesko Christian L Boutwell John P DeVincenzo Gregory D Ebel Todd M Allen Michael C Zody Matthew R Henn Joshua Z Levin

Nucleic Acids Res 2013 Jan 8;41(1):e13. Epub 2012 Sep 8.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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January 2013

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.

Authors:
Rex R Malmstrom Sébastien Rodrigue Katherine H Huang Libusha Kelly Suzanne E Kern Anne Thompson Sara Roggensack Paul M Berube Matthew R Henn Sallie W Chisholm

ISME J 2013 Jan 16;7(1):184-98. Epub 2012 Aug 16.

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

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January 2013

Characterization of a model of lethal dengue virus 2 infection in C57BL/6 mice deficient in the alpha/beta interferon receptor.

Authors:
Susana Orozco Michael A Schmid Poornima Parameswaran Ruben Lachica Matthew R Henn Robert Beatty Eva Harris

J Gen Virol 2012 Oct 18;93(Pt 10):2152-2157. Epub 2012 Jul 18.

Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.

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October 2012

Reemergence and decline of dengue virus serotype 3 in Puerto Rico.

Authors:
Gilberto A Santiago Kate McElroy-Horne Niall J Lennon Luis M Santiago Bruce W Birren Matthew R Henn Jorge L Muñoz-Jordán

J Infect Dis 2012 Sep 27;206(6):893-901. Epub 2012 Jun 27.

Division of Vector-borne Infectious Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico.

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September 2012

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Authors:
Veasna Duong Matthew R Henn Cameron Simmons Chantha Ngan Bunthin Y Laurent Gavotte Alain Viari Sivuth Ong Rekol Huy Niall J Lennon Sowath Ly Sirenda Vong Bruce W Birren Jeremy J Farrar Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 5;15:77-86. Epub 2012 Jun 5.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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April 2013

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Authors:
Poornima Parameswaran Patrick Charlebois Yolanda Tellez Andrea Nunez Elizabeth M Ryan Christine M Malboeuf Joshua Z Levin Niall J Lennon Angel Balmaseda Eva Harris Matthew R Henn

J Virol 2012 Aug 30;86(16):8546-58. Epub 2012 May 30.

Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.

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August 2012

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Authors:
Alexander R Macalalad Michael C Zody Patrick Charlebois Niall J Lennon Ruchi M Newman Christine M Malboeuf Elizabeth M Ryan Christian L Boutwell Karen A Power Doug E Brackney Kendra N Pesko Joshua Z Levin Gregory D Ebel Todd M Allen Bruce W Birren Matthew R Henn

PLoS Comput Biol 2012 15;8(3):e1002417. Epub 2012 Mar 15.

Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA.

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June 2012

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Authors:
Matthew R Henn Christian L Boutwell Patrick Charlebois Niall J Lennon Karen A Power Alexander R Macalalad Aaron M Berlin Christine M Malboeuf Elizabeth M Ryan Sante Gnerre Michael C Zody Rachel L Erlich Lisa M Green Andrew Berical Yaoyu Wang Monica Casali Hendrik Streeck Allyson K Bloom Tim Dudek Damien Tully Ruchi Newman Karen L Axten Adrianne D Gladden Laura Battis Michael Kemper Qiandong Zeng Terrance P Shea Sharvari Gujja Carmen Zedlack Olivier Gasser Christian Brander Christoph Hess Huldrych F Günthard Zabrina L Brumme Chanson J Brumme Suzane Bazner Jenna Rychert Jake P Tinsley Ken H Mayer Eric Rosenberg Florencia Pereyra Joshua Z Levin Sarah K Young Heiko Jessen Marcus Altfeld Bruce W Birren Bruce D Walker Todd M Allen

PLoS Pathog 2012 8;8(3):e1002529. Epub 2012 Mar 8.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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July 2012

Rapid diversification of coevolving marine Synechococcus and a virus.

Authors:
Marcia F Marston Francis J Pierciey Alicia Shepard Gary Gearin Ji Qi Chandri Yandava Stephan C Schuster Matthew R Henn Jennifer B H Martiny

Proc Natl Acad Sci U S A 2012 Mar 2;109(12):4544-9. Epub 2012 Mar 2.

Department of Biology and Marine Biology, Roger Williams University, Bristol, RI 02809, USA.

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March 2012

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice.

Authors:
Kendra N Pesko Kelly A Fitzpatrick Elizabeth M Ryan Pei-Yong Shi Bo Zhang Niall J Lennon Ruchi M Newman Matthew R Henn Gregory D Ebel

Virology 2012 May 23;427(1):10-7. Epub 2012 Feb 23.

Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA.

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May 2012

Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208.

Authors:
Jozef I Nissimov Charlotte A Worthy Paul Rooks Johnathan A Napier Susan A Kimmance Matthew R Henn Hiroyuki Ogata Michael J Allen

J Virol 2012 Mar;86(5):2896-7

Plymouth Marine Laboratory, Plymouth, United Kingdom.

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March 2012

Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202.

Authors:
Jozef I Nissimov Charlotte A Worthy Paul Rooks Johnathan A Napier Susan A Kimmance Matthew R Henn Hiroyuki Ogata Michael J Allen

J Virol 2012 Feb;86(4):2380-1

Plymouth Marine Laboratory, Plymouth, United Kingdom.

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February 2012

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.

Authors:
Molly OhAinle Angel Balmaseda Alexander R Macalalad Yolanda Tellez Michael C Zody Saira Saborío Andrea Nuñez Niall J Lennon Bruce W Birren Aubree Gordon Matthew R Henn Eva Harris

Sci Transl Med 2011 Dec;3(114):114ra128

Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-7354, USA.

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December 2011

Draft genome sequence of the coccolithovirus EhV-84.

Authors:
Jozef I Nissimov Charlotte A Worthy Paul Rooks Johnathan A Napier Susan A Kimmance Matthew R Henn Hiroyuki Ogata Michael J Allen

Stand Genomic Sci 2011 Oct 23;5(1):1-11. Epub 2011 Sep 23.

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October 2011

Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203.

Authors:
Jozef I Nissimov Charlotte A Worthy Paul Rooks Johnathan A Napier Susan A Kimmance Matthew R Henn Hiroyuki Ogata Michael J Allen

J Virol 2011 Dec;85(24):13468-9

Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3DH, United Kingdom.

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December 2011

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.

Authors:
Khoa T D Thai Matthew R Henn Michael C Zody Vianney Tricou Nguyen Minh Nguyet Patrick Charlebois Niall J Lennon Lisa Green Peter J de Vries Tran Tinh Hien Jeremy Farrar H Rogier van Doorn Menno D de Jong Bruce W Birren Edward C Holmes Cameron P Simmons

J Virol 2012 Jan 16;86(2):835-43. Epub 2011 Nov 16.

Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.

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January 2012

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.

Authors:
Christopher A Desjardins Mia D Champion Jason W Holder Anna Muszewska Jonathan Goldberg Alexandre M Bailão Marcelo Macedo Brigido Márcia Eliana da Silva Ferreira Ana Maria Garcia Marcin Grynberg Sharvari Gujja David I Heiman Matthew R Henn Chinnappa D Kodira Henry León-Narváez Larissa V G Longo Li-Jun Ma Iran Malavazi Alisson L Matsuo Flavia V Morais Maristela Pereira Sabrina Rodríguez-Brito Sharadha Sakthikumar Silvia M Salem-Izacc Sean M Sykes Marcus Melo Teixeira Milene C Vallejo Maria Emília Machado Telles Walter Chandri Yandava Sarah Young Qiandong Zeng Jeremy Zucker Maria Sueli Felipe Gustavo H Goldman Brian J Haas Juan G McEwen Gustavo Nino-Vega Rosana Puccia Gioconda San-Blas Celia Maria de Almeida Soares Bruce W Birren Christina A Cuomo

PLoS Genet 2011 Oct 27;7(10):e1002345. Epub 2011 Oct 27.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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October 2011

Human leukocyte antigen B27 selects for rare escape mutations that significantly impair hepatitis C virus replication and require compensatory mutations.

Authors:
Christoph Neumann-Haefelin Cesar Oniangue-Ndza Thomas Kuntzen Julia Schmidt Katja Nitschke John Sidney Célia Caillet-Saguy Marco Binder Nadine Kersting Michael W Kemper Karen A Power Susan Ingber Laura L Reyor Kelsey Hills-Evans Arthur Y Kim Georg M Lauer Volker Lohmann Alessandro Sette Matthew R Henn Stéphane Bressanelli Robert Thimme Todd M Allen

Hepatology 2011 Oct;54(4):1157-66

Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA.

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October 2011

Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase.

Authors:
Cesar Oniangue-Ndza Thomas Kuntzen Michael Kemper Andrew Berical Yaoyu E Wang Christoph Neumann-Haefelin Peter Kristian Foote Kelsey Hills-Evans Laura L Reyor Katherine Kane Adrianne D Gladden Allyson K Bloom Karen A Power Robert Thimme Georg M Lauer Matthew R Henn Arthur Y Kim Todd M Allen

J Virol 2011 Nov 31;85(22):11883-90. Epub 2011 Aug 31.

Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA.

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November 2011

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Authors:
Veasna Duong Cameron Simmons Laurent Gavotte Alain Viari Sivuth Ong Ngan Chantha Niall J Lennon Bruce W Birren Sirenda Vong Jeremy J Farrar Matthew R Henn Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 2;15:59-68. Epub 2011 Jul 2.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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April 2013

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Authors:
Jayna Raghwani Andrew Rambaut Edward C Holmes Vu Ty Hang Tran Tinh Hien Jeremy Farrar Bridget Wills Niall J Lennon Bruce W Birren Matthew R Henn Cameron P Simmons

PLoS Pathog 2011 Jun 2;7(6):e1002064. Epub 2011 Jun 2.

University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, United Kingdom.

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June 2011

Next-generation sequencing for HLA typing of class I loci.

Authors:
Rachel L Erlich Xiaoming Jia Scott Anderson Eric Banks Xiaojiang Gao Mary Carrington Namrata Gupta Mark A DePristo Matthew R Henn Niall J Lennon Paul I W de Bakker

BMC Genomics 2011 Jan 18;12:42. Epub 2011 Jan 18.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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January 2011

Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007.

Authors:
Kate L McElroy Gilberto A Santiago Niall J Lennon Bruce W Birren Matthew R Henn Jorge L Muñoz-Jordán

Emerg Infect Dis 2011 Jan;17(1):64-71

Dengue Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico.

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January 2011

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Authors:
Qing Yu Elizabeth M Ryan Todd M Allen Bruce W Birren Matthew R Henn Niall J Lennon

Bioinformatics 2011 Jan 9;27(2):266-7. Epub 2010 Nov 9.

Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA.

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January 2011

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

Authors:
Florencia Pereyra Xiaoming Jia Paul J McLaren Amalio Telenti Paul I W de Bakker Bruce D Walker Stephan Ripke Chanson J Brumme Sara L Pulit Mary Carrington Carl M Kadie Jonathan M Carlson David Heckerman Robert R Graham Robert M Plenge Steven G Deeks Lauren Gianniny Gabriel Crawford Jordan Sullivan Elena Gonzalez Leela Davies Amy Camargo Jamie M Moore Nicole Beattie Supriya Gupta Andrew Crenshaw Noël P Burtt Candace Guiducci Namrata Gupta Xiaojiang Gao Ying Qi Yuko Yuki Alicja Piechocka-Trocha Emily Cutrell Rachel Rosenberg Kristin L Moss Paul Lemay Jessica O'Leary Todd Schaefer Pranshu Verma Ildiko Toth Brian Block Brett Baker Alissa Rothchild Jeffrey Lian Jacqueline Proudfoot Donna Marie L Alvino Seanna Vine Marylyn M Addo Todd M Allen Marcus Altfeld Matthew R Henn Sylvie Le Gall Hendrik Streeck David W Haas Daniel R Kuritzkes Gregory K Robbins Robert W Shafer Roy M Gulick Cecilia M Shikuma Richard Haubrich Sharon Riddler Paul E Sax Eric S Daar Heather J Ribaudo Brian Agan Shanu Agarwal Richard L Ahern Brady L Allen Sherly Altidor Eric L Altschuler Sujata Ambardar Kathryn Anastos Ben Anderson Val Anderson Ushan Andrady Diana Antoniskis David Bangsberg Daniel Barbaro William Barrie J Bartczak Simon Barton Patricia Basden Nesli Basgoz Suzane Bazner Nicholaos C Bellos Anne M Benson Judith Berger Nicole F Bernard Annette M Bernard Christopher Birch Stanley J Bodner Robert K Bolan Emilie T Boudreaux Meg Bradley James F Braun Jon E Brndjar Stephen J Brown Katherine Brown Sheldon T Brown Jedidiah Burack Larry M Bush Virginia Cafaro Omobolaji Campbell John Campbell Robert H Carlson J Kevin Carmichael Kathleen K Casey Chris Cavacuiti Gregory Celestin Steven T Chambers Nancy Chez Lisa M Chirch Paul J Cimoch Daniel Cohen Lillian E Cohn Brian Conway David A Cooper Brian Cornelson David T Cox Michael V Cristofano George Cuchural Julie L Czartoski Joseph M Dahman Jennifer S Daly Benjamin T Davis Kristine Davis Sheila M Davod Edwin DeJesus Craig A Dietz Eleanor Dunham Michael E Dunn Todd B Ellerin Joseph J Eron John J W Fangman Claire E Farel Helen Ferlazzo Sarah Fidler Anita Fleenor-Ford Renee Frankel Kenneth A Freedberg Neel K French Jonathan D Fuchs Jon D Fuller Jonna Gaberman Joel E Gallant Rajesh T Gandhi Efrain Garcia Donald Garmon Joseph C Gathe Cyril R Gaultier Wondwoosen Gebre Frank D Gilman Ian Gilson Paul A Goepfert Michael S Gottlieb Claudia Goulston Richard K Groger T Douglas Gurley Stuart Haber Robin Hardwicke W David Hardy P Richard Harrigan Trevor N Hawkins Sonya Heath Frederick M Hecht W Keith Henry Melissa Hladek Robert P Hoffman James M Horton Ricky K Hsu Gregory D Huhn Peter Hunt Mark J Hupert Mark L Illeman Hans Jaeger Robert M Jellinger Mina John Jennifer A Johnson Kristin L Johnson Heather Johnson Kay Johnson Jennifer Joly Wilbert C Jordan Carol A Kauffman Homayoon Khanlou Robert K Killian Arthur Y Kim David D Kim Clifford A Kinder Jeffrey T Kirchner Laura Kogelman Erna Milunka Kojic P Todd Korthuis Wayne Kurisu Douglas S Kwon Melissa LaMar Harry Lampiris Massimiliano Lanzafame Michael M Lederman David M Lee Jean M L Lee Marah J Lee Edward T Y Lee Janice Lemoine Jay A Levy Josep M Llibre Michael A Liguori Susan J Little Anne Y Liu Alvaro J Lopez Mono R Loutfy Dawn Loy Debbie Y Mohammed Alan Man Michael K Mansour Vincent C Marconi Martin Markowitz Rui Marques Jeffrey N Martin Harold L Martin Kenneth Hugh Mayer M Juliana McElrath Theresa A McGhee Barbara H McGovern Katherine McGowan Dawn McIntyre Gavin X Mcleod Prema Menezes Greg Mesa Craig E Metroka Dirk Meyer-Olson Andy O Miller Kate Montgomery Karam C Mounzer Ellen H Nagami Iris Nagin Ronald G Nahass Margret O Nelson Craig Nielsen David L Norene David H O'Connor Bisola O Ojikutu Jason Okulicz Olakunle O Oladehin Edward C Oldfield Susan A Olender Mario Ostrowski William F Owen Eunice Pae Jeffrey Parsonnet Andrew M Pavlatos Aaron M Perlmutter Michael N Pierce Jonathan M Pincus Leandro Pisani Lawrence Jay Price Laurie Proia Richard C Prokesch Heather Calderon Pujet Moti Ramgopal Almas Rathod Michael Rausch J Ravishankar Frank S Rhame Constance Shamuyarira Richards Douglas D Richman Berta Rodes Milagros Rodriguez Richard C Rose Eric S Rosenberg Daniel Rosenthal Polly E Ross David S Rubin Elease Rumbaugh Luis Saenz Michelle R Salvaggio William C Sanchez Veeraf M Sanjana Steven Santiago Wolfgang Schmidt Hanneke Schuitemaker Philip M Sestak Peter Shalit William Shay Vivian N Shirvani Vanessa I Silebi James M Sizemore Paul R Skolnik Marcia Sokol-Anderson James M Sosman Paul Stabile Jack T Stapleton Sheree Starrett Francine Stein Hans-Jurgen Stellbrink F Lisa Sterman Valerie E Stone David R Stone Giuseppe Tambussi Randy A Taplitz Ellen M Tedaldi Amalio Telenti William Theisen Richard Torres Lorraine Tosiello Cecile Tremblay Marc A Tribble Phuong D Trinh Alice Tsao Peggy Ueda Anthony Vaccaro Emilia Valadas Thanes J Vanig Isabel Vecino Vilma M Vega Wenoah Veikley Barbara H Wade Charles Walworth Chingchai Wanidworanun Douglas J Ward Daniel A Warner Robert D Weber Duncan Webster Steve Weis David A Wheeler David J White Ed Wilkins Alan Winston Clifford G Wlodaver Angelique van't Wout David P Wright Otto O Yang David L Yurdin Brandon W Zabukovic Kimon C Zachary Beth Zeeman Meng Zhao

Science 2010 Dec 4;330(6010):1551-7. Epub 2010 Nov 4.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA.

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December 2010

Index cluster study of dengue virus infection in Nicaragua.

Authors:
Miguel Reyes Juan Carlos Mercado Katherine Standish Juan Carlos Matute Oscar Ortega Berman Moraga William Avilés Matthew R Henn Angel Balmaseda Guillermina Kuan Eva Harris

Am J Trop Med Hyg 2010 Sep;83(3):683-9

Socrates Flores Vivas Health Center, Ministry of Health, Managua, Nicaragua.

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September 2010

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Authors:
Matthew B Sullivan Katherine H Huang Julio C Ignacio-Espinoza Aaron M Berlin Libusha Kelly Peter R Weigele Alicia S DeFrancesco Suzanne E Kern Luke R Thompson Sarah Young Chandri Yandava Ross Fu Bryan Krastins Michael Chase David Sarracino Marcia S Osburne Matthew R Henn Sallie W Chisholm

Environ Microbiol 2010 Nov;12(11):3035-56

Massachusetts Institute of Technology, Cambridge, MA, USA.

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November 2010

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.

Authors:
Thi Ty Hang Vu Edward C Holmes Veasna Duong Thien Quy Nguyen Tinh Hien Tran Michael Quail Carol Churcher Julian Parkhill Jane Cardosa Jeremy Farrar Bridget Wills Niall J Lennon Bruce W Birren Philippe Buchy Matthew R Henn Cameron P Simmons

PLoS Negl Trop Dis 2010 Jul 20;4(7):e757. Epub 2010 Jul 20.

Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam.

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July 2010

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.

Authors:
Daniel E Neafsey Bridget M Barker Thomas J Sharpton Jason E Stajich Daniel J Park Emily Whiston Chiung-Yu Hung Cody McMahan Jared White Sean Sykes David Heiman Sarah Young Qiandong Zeng Amr Abouelleil Lynne Aftuck Daniel Bessette Adam Brown Michael FitzGerald Annie Lui J Pendexter Macdonald Margaret Priest Marc J Orbach John N Galgiani Theo N Kirkland Garry T Cole Bruce W Birren Matthew R Henn John W Taylor Steven D Rounsley

Genome Res 2010 Jul 1;20(7):938-46. Epub 2010 Jun 1.

Broad Institute, Cambridge, Massachusetts 02142, USA.

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July 2010

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Authors:
Matthew R Henn Matthew B Sullivan Nicole Stange-Thomann Marcia S Osburne Aaron M Berlin Libusha Kelly Chandri Yandava Chinnappa Kodira Qiandong Zeng Michael Weiand Todd Sparrow Sakina Saif Georgia Giannoukos Sarah K Young Chad Nusbaum Bruce W Birren Sallie W Chisholm

PLoS One 2010 Feb 5;5(2):e9083. Epub 2010 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

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February 2010

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

Authors:
Niall J Lennon Robert E Lintner Scott Anderson Pablo Alvarez Andrew Barry William Brockman Riza Daza Rachel L Erlich Georgia Giannoukos Lisa Green Andrew Hollinger Cindi A Hoover David B Jaffe Frank Juhn Danielle McCarthy Danielle Perrin Karen Ponchner Taryn L Powers Kamran Rizzolo Dana Robbins Elizabeth Ryan Carsten Russ Todd Sparrow John Stalker Scott Steelman Michael Weiand Andrew Zimmer Matthew R Henn Chad Nusbaum Robert Nicol

Genome Biol 2010 5;11(2):R15. Epub 2010 Feb 5.

Genome Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, MA 02141, USA.

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August 2010

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

Authors:
Florent E Angly Dana Willner Alejandra Prieto-Davó Robert A Edwards Robert Schmieder Rebecca Vega-Thurber Dionysios A Antonopoulos Katie Barott Matthew T Cottrell Christelle Desnues Elizabeth A Dinsdale Mike Furlan Matthew Haynes Matthew R Henn Yongfei Hu David L Kirchman Tracey McDole John D McPherson Folker Meyer R Michael Miller Egbert Mundt Robert K Naviaux Beltran Rodriguez-Mueller Rick Stevens Linda Wegley Lixin Zhang Baoli Zhu Forest Rohwer

PLoS Comput Biol 2009 Dec 11;5(12):e1000593. Epub 2009 Dec 11.

Biology Department, San Diego State University, San Diego, California, United States of America.

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December 2009

Trends in patterns of dengue transmission over 4 years in a pediatric cohort study in Nicaragua.

Authors:
Angel Balmaseda Katherine Standish Juan Carlos Mercado Juan Carlos Matute Yolanda Tellez Saira Saborío Samantha N Hammond Andrea Nuñez William Avilés Matthew R Henn Edward C Holmes Aubree Gordon Josefina Coloma Guillermina Kuan Eva Harris

J Infect Dis 2010 Jan;201(1):5-14

Departamento de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Nicaragua.

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January 2010

Whole genome amplification and de novo assembly of single bacterial cells.

Authors:
Sébastien Rodrigue Rex R Malmstrom Aaron M Berlin Bruce W Birren Matthew R Henn Sallie W Chisholm

PLoS One 2009 Sep 2;4(9):e6864. Epub 2009 Sep 2.

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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September 2009

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.

Authors:
Thomas J Sharpton Jason E Stajich Steven D Rounsley Malcolm J Gardner Jennifer R Wortman Vinita S Jordar Rama Maiti Chinnappa D Kodira Daniel E Neafsey Qiandong Zeng Chiung-Yu Hung Cody McMahan Anna Muszewska Marcin Grynberg M Alejandra Mandel Ellen M Kellner Bridget M Barker John N Galgiani Marc J Orbach Theo N Kirkland Garry T Cole Matthew R Henn Bruce W Birren John W Taylor

Genome Res 2009 Oct 28;19(10):1722-31. Epub 2009 Aug 28.

Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA.

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October 2009

Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients.

Authors:
Thomas Kuntzen Joerg Timm Andrew Berical Niall Lennon Aaron M Berlin Sarah K Young Bongshin Lee David Heckerman Jonathan Carlson Laura L Reyor Marianna Kleyman Cory M McMahon Christopher Birch Julian Schulze Zur Wiesch Timothy Ledlie Michael Koehrsen Chinnappa Kodira Andrew D Roberts Georg M Lauer Hugo R Rosen Florian Bihl Andreas Cerny Ulrich Spengler Zhimin Liu Arthur Y Kim Yanming Xing Arne Schneidewind Margaret A Madey Jaquelyn F Fleckenstein Vicki M Park James E Galagan Chad Nusbaum Bruce D Walker Gerond V Lake-Bakaar Eric S Daar Ira M Jacobson Edward D Gomperts Brian R Edlin Sharyne M Donfield Raymond T Chung Andrew H Talal Tony Marion Bruce W Birren Matthew R Henn Todd M Allen

Hepatology 2008 Dec;48(6):1769-78

Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

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December 2008

A high-density single nucleotide polymorphism map for Neurospora crassa.

Authors:
Randy Lambreghts Mi Shi William J Belden David Decaprio Danny Park Matthew R Henn James E Galagan Meray Bastürkmen Bruce W Birren Matthew S Sachs Jay C Dunlap Jennifer J Loros

Genetics 2009 Feb 17;181(2):767-81. Epub 2008 Nov 17.

Department of Environmental and Biomolecular Systems, Oregon Health & Science University, Beaverton, Oregon 97006, USA.

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February 2009

Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton.

Authors:
Achim Quaiser Purificación López-García Yvan Zivanovic Matthew R Henn Francisco Rodriguez-Valera David Moreira

Environ Microbiol 2008 Oct 8;10(10):2704-17. Epub 2008 Jul 8.

Unité d'Ecologie, Systématique et Evolution, CNRS UMR8079, Université Paris-Sud 11, 91405 Orsay, France.

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October 2008

A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame.

Authors:
Thomas Kuntzen Andrew Berical Jean Ndjomou Phil Bennett Arne Schneidewind Niall Lennon Bruce W Birren Carla Kuiken Matthew R Henn Peter Simmonds Todd M Allen

J Med Virol 2008 Aug;80(8):1370-8

Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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August 2008

Generating and testing molecular hypotheses in the dermatophytes.

Authors:
Theodore C White Brian G Oliver Yvonne Gräser Matthew R Henn

Eukaryot Cell 2008 Aug 6;7(8):1238-45. Epub 2008 Jun 6.

Seattle Biomedical Research Institute, 307 Westlake Ave. North, Suite 500, Seattle, WA 98109-5129, USA.

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August 2008

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.

Authors:
Ana-Belen Martin-Cuadrado Francisco Rodriguez-Valera David Moreira José C Alba Elena Ivars-Martínez Matthew R Henn Emmanuel Talla Purificación López-García

ISME J 2008 Aug 8;2(8):865-86. Epub 2008 May 8.

Division of Microbiology, Universidad Miguel Hernandez, Alicante, Spain.

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August 2008

Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

Authors:
Jay C Dunlap Katherine A Borkovich Matthew R Henn Gloria E Turner Matthew S Sachs N Louise Glass Kevin McCluskey Michael Plamann James E Galagan Bruce W Birren Richard L Weiss Jeffrey P Townsend Jennifer J Loros Mary Anne Nelson Randy Lambreghts Hildur V Colot Gyungsoon Park Patrick Collopy Carol Ringelberg Christopher Crew Liubov Litvinkova Dave DeCaprio Heather M Hood Susan Curilla Mi Shi Matthew Crawford Michael Koerhsen Phil Montgomery Lisa Larson Matthew Pearson Takao Kasuga Chaoguang Tian Meray Baştürkmen Lorena Altamirano Junhuan Xu

Adv Genet 2007 ;57:49-96

Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA.

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April 2007

Genomics of the fungal kingdom: insights into eukaryotic biology.

Authors:
James E Galagan Matthew R Henn Li-Jun Ma Christina A Cuomo Bruce Birren

Genome Res 2005 Dec;15(12):1620-31

The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA.

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December 2005

Growth-dependent stable carbon isotope fractionation by basidiomycete fungi: delta(13)C pattern and physiological process.

Authors:
Matthew R Henn Gerd Gleixner Ignacio H Chapela

Appl Environ Microbiol 2002 Oct;68(10):4956-64

Ecosystem Sciences Division, Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720-3110, USA.

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October 2002

Ecophysiology of C and N isotopic fractionation in forest fungi and the roots of the saprotrophic-mycorrhizal divide.

Authors:
Matthew R Henn Ignacio H Chapela

Oecologia 2001 Aug 1;128(4):480-487. Epub 2001 Aug 1.

Division of Ecosystem Sciences, Department of Environmental Science, Policy, and Management, University of California, Berkeley, 334 Hilgard Hall, 94720-3110, Berkeley, CA, USA.

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August 2001