Works by Henn, Matthew R.

Results: 38

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

Published in:

2020

By:

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

Publication type:

journal article

Dynamics of Dengue Disease Severity Determined by the Interplay Between Viral Genetics and Serotype-Specific Immunity.

Published in:

Science Translational Medicine, 2011, v. 3, n. 114, p. 1, doi. 10.1126/scitranslmed.3003084

By:

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

Publication type:

Article

Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986-2007.

Published in:

Emerging Infectious Diseases, 2011, v. 17, n. 1, p. 64, doi. 10.3201/eid1701.100961

By:

McElroy, Kate L.;
Santiago, Gilberto A.;
Lennon, Niall J.;
Birren, Bruce W.;
Henn, Matthew R.;
Muñoz-Jordán, Jorge L.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2013, v. 41, n. 1, p. e13, doi. 10.1093/nar/gks794

By:

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

Publication type:

Article

Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection.

Published in:

Clinical Infectious Diseases, 2024, v. 78, n. 4, p. 833, doi. 10.1093/cid/ciad636

By:

Straub, Timothy J;
Lombardo, Mary-Jane;
Bryant, Jessica A;
Diao, Liyang;
Lodise, Thomas P;
Freedberg, Daniel E;
Wortman, Jennifer R;
Litcofsky, Kevin D;
Hasson, Brooke R;
McGovern, Barbara H;
Ford, Christopher B;
Henn, Matthew R

Publication type:

Article

SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial.

Published in:

Clinical Infectious Diseases, 2021, v. 72, n. 12, p. 2132, doi. 10.1093/cid/ciaa387

By:

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

Publication type:

Article

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis.

Published in:

PLoS Genetics, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pgen.1002345

By:

Desjardins, Christopher A.;
Champion, Mia D.;
Holder, Jason W.;
Muszewska, Anna;
Goldberg, Jonathan;
Bailão, Alexandre M.;
Brigido, Marcelo Macedo;
Ferreira, Márcia Eliana da Silva;
Garcia, Ana Maria;
Grynberg, Marcin;
Gujja, Sharvari;
Heiman, David I.;
Henn, Matthew R.;
Kodira, Chinnappa D.;
León-Narváez, Henry;
Longo, Larissa V. G.;
Ma, Li-Jun;
Malavazi, Iran;
Matsuo, Alisson L.;
Morais, Flavia V.

Publication type:

Article

SER-109: An Oral Investigational Microbiome Therapeutic for Patients with Recurrent Clostridioides difficile Infection (rCDI).

Published in:

Antibiotics (2079-6382), 2022, v. 11, n. 9, p. 1234, doi. 10.3390/antibiotics11091234

By:

Khanna, Sahil;
Sims, Matthew;
Louie, Thomas J.;
Fischer, Monika;
LaPlante, Kerry;
Allegretti, Jessica;
Hasson, Brooke R.;
Fonte, Allyson T.;
McChalicher, Christopher;
Ege, David S.;
Bryant, Jessica A.;
Straub, Timothy J.;
Ford, Christopher B.;
Henn, Matthew R.;
Wang, Elaine E. L.;
von Moltke, Lisa;
Wilcox, Mark H.

Publication type:

Article

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments M. B. Sullivan et al. Comparative genomics of T4-like myoviruses.

Published in:

Environmental Microbiology, 2010, v. 12, n. 11, p. 3035, doi. 10.1111/j.1462-2920.2010.02280.x

By:

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

Publication type:

Article

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

Published in:

Environmental Microbiology, 2008, v. 10, n. 10, p. 2704, doi. 10.1111/j.1462-2920.2008.01691.x

By:

Quaiser, Achim;
López-García, Purificación;
Zivanovic, Yvan;
Henn, Matthew R.;
Rodriguez-Valera, Francisco;
Moreira, David

Publication type:

Article

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

Published in:

Journal of Medical Virology, 2008, v. 80, n. 8, p. 1370, doi. 10.1002/jmv.21240

By:

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

Publication type:

Article

Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection.

Published in:

NPJ Biofilms & Microbiomes, 2021, v. 7, n. 1, p. 1, doi. 10.1038/s41522-021-00184-w

By:

Normington, Charmaine;
Moura, Ines B.;
Bryant, Jessica A.;
Ewin, Duncan J.;
Clark, Emma V.;
Kettle, Morgan J.;
Harris, Hannah C.;
Spittal, William;
Davis, Georgina;
Henn, Matthew R.;
Ford, Christopher B.;
Wilcox, Mark H.;
Buckley, Anthony M.

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 2, p. 266, doi. 10.1093/bioinformatics/btq624

By:

Yu, Qing;
Ryan, Elizabeth M.;
Allen, Todd M.;
Birren, Bruce W.;
Henn, Matthew R.;
Lennon, Niall J.

Publication type:

Article

Isotopic fractionation during ammonium assimilation by basidiomycete fungi and its implications for natural nitrogen isotope patterns.

Published in:

New Phytologist, 2004, v. 162, n. 3, p. 771, doi. 10.1111/j.1469-8137.2004.01068.x

By:

Henn, Matthew R.;
Chapela, Ignacio H.

Publication type:

Article

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.

Published in:

PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757

By:

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

Publication type:

Article

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.

Published in:

PLoS Neglected Tropical Diseases, 2010, v. 4, n. 7, p. 1, doi. 10.1371/journal.pntd.0000757

By:

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

Publication type:

Article

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

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 1, p. 184, doi. 10.1038/ismej.2012.89

By:

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

Publication type:

Article

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.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2008, v. 2, n. 8, p. 865, doi. 10.1038/ismej.2008.40

By:

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

Publication type:

Article

V-Phaser 2: variant inference for viral populations.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-674

By:

Yang, Xiao;
Charlebois, Patrick;
Macalalad, Alex;
Henn, Matthew R.;
Zody, Michael C.

Publication type:

Article

De novo assembly of highly diverse viral populations.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 475, doi. 10.1186/1471-2164-13-475

By:

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

Publication type:

Article

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection.

Published in:

PLoS Pathogens, 2012, v. 8, n. 3, p. 1, doi. 10.1371/journal.ppat.1002529

By:

Henn, Matthew R.;
Boutwell, Christian L.;
Charlebois, Patrick;
Lennon, Niall J.;
Power, Karen A.;
Macalalad, Alexander R.;
Berlin, Aaron M.;
Malboeuf, Christine M.;
Ryan, Elizabeth M.;
Gnerre, Sante;
Zody, Michael C.;
Erlich, Rachel L.;
Green, Lisa M.;
Berical, Andrew;
Wang, Yaoyu;
Casali, Monica;
Streeck, Hendrik;
Bloom, Allyson K.;
Dudek, Tim;
Tully, Damien

Publication type:

Article

Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density- Dependent Transmission.

Published in:

PLoS Pathogens, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.ppat.1002064

By:

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

Publication type:

Article

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002417

By:

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

Publication type:

Article

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 12, p. 1, doi. 10.1371/journal.pcbi.1000593

By:

Angly, Florent E.;
Willner, Dana;
Prieto-Davó, Alejandra;
Edwards, Robert A.;
Schmieder, Robert;
Vega-Thurber, Rebecca;
Antonopoulos, Dionysios A.;
Barott, Katie;
Cottrell, Matthew T.;
Desnues, Christelle;
Dinsdale, Elizabeth A.;
Furlan, Mike;
Haynes, Matthew;
Henn, Matthew R.;
Yongfei Hu;
Kirchman, David L.;
McDole, Tracey;
McPherson, John D.;
Meyer, Folker;
Miller, R. Michael

Publication type:

Article

Reply to Lagier et al.

Published in:

2017

By:

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

Publication type:

Letter

Critical Microbiological View of SER-109.

Published in:

2017

By:

Lagier, Jean-Christophe;
Cadoret, Frédéric;
Raoult, Didier;
Khanna, Sahil;
Button, Julie E.;
Lombardo, Mary-Jane;
Vulic, Marin;
Henn, Matthew R.;
Cook, David N.;
Pomerantz, Roger J.;
Hohmann, Elizabeth L.

Publication type:

Letter

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

Published in:

Journal of Infectious Diseases, 2016, v. 214, n. 2, p. 173, doi. 10.1093/infdis/jiv766

By:

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

Publication type:

Article

Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy.

Published in:

PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0090485

By:

Li, Jonathan Z.;
Chapman, Brad;
Charlebois, Patrick;
Hofmann, Oliver;
Weiner, Brian;
Porter, Alyssa J.;
Samuel, Reshmi;
Vardhanabhuti, Saran;
Zheng, Lu;
Eron, Joseph;
Taiwo, Babafemi;
Zody, Michael C.;
Henn, Matthew R.;
Kuritzkes, Daniel R.;
Hide, Winston;
Wilson, Cara C.;
Berzins, Baiba I.;
Acosta, Edward P.;
Bastow, Barbara;
Kim, Peter S.

Publication type:

Article

Tracking the Evolution of Dengue Virus Strains D2S10 and D2S20 by 454 Pyrosequencing.

Published in:

PLoS ONE, 2013, v. 8, n. 1, p. 1, doi. 10.1371/journal.pone.0054220

By:

Makhluf, Huda;
Buck, Michael D.;
King, Kevin;
Perry, Stuart T.;
Henn, Matthew R.;
Shresta, Sujan

Publication type:

Article

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes.

Published in:

PLoS ONE, 2010, v. 5, n. 2, p. 1, doi. 10.1371/journal.pone.0009083

By:

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

Publication type:

Article

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells.

Published in:

PLoS ONE, 2009, v. 4, n. 9, p. 1, doi. 10.1371/journal.pone.0006864

By:

Rodrigue, Sébastien;
Malmstrom, Rex R.;
Berlin, Aaron M.;
Birren, Bruce W.;
Henn, Matthew R.;
Chisholm, Sallie W.

Publication type:

Article

A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa.

Published in:

2009

By:

Lambreghts, Randy;
Mi Shi;
Belden, William J.;
deCaprio, David;
Park, Danny;
Henn, Matthew R.;
Galagan, James E.;
Baştürkmen, Meray;
Birren, Bruce W.;
Sachs, Matthew S.;
Dunlap, Jay C.;
Loros, Jennifer J.

Publication type:

Abstract

Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants.

Published in:

Journal of Infectious Diseases, 2013, v. 208, n. 1, p. 17, doi. 10.1093/infdis/jis679

By:

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

Publication type:

Article

Reemergence and Decline of Dengue Virus Serotype 3 in Puerto Rico.

Published in:

Journal of Infectious Diseases, 2012, v. 206, n. 6, p. 893, doi. 10.1093/infdis/jis426

By:

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

Publication type:

Article

Trends in Patterns of Dengue Transmission over 4 Years in a Pediatric Cohort Study in Nicaragua.

Published in:

Journal of Infectious Diseases, 2010, v. 201, n. 1, p. 5, doi. 10.1086/648592

By:

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

Publication type:

Article

Ecophysiology of <sup>13</sup>C and <sup>15</sup>N isotopic fractionation in forest fungi and the roots of the saprotrophic-mycorrhizal divide.

Published in:

Oecologia, 2001, v. 128, n. 4, p. 480, doi. 10.1007/s004420100680

By:

Henn, Matthew R.;
Chapela, Ignacio H.

Publication type:

Article

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

Published in:

BMC Genomics, 2011, v. 12, n. 1, p. 42, doi. 10.1186/1471-2164-12-42

By:

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

Publication type:

Article

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

Published in:

PLoS Pathogens, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.ppat.1005619

By:

Tully, Damien C.;
Ogilvie, Colin B.;
Batorsky, Rebecca E.;
Bean, David J.;
Power, Karen A.;
Ghebremichael, Musie;
Bedard, Hunter E.;
Gladden, Adrianne D.;
Seese, Aaron M.;
Amero, Molly A.;
Lane, Kimberly;
McGrath, Graham;
Bazner, Suzane B.;
Tinsley, Jake;
Lennon, Niall J.;
Henn, Matthew R.;
Brumme, Zabrina L.;
Norris, Philip J.;
Rosenberg, Eric S.;
Mayer, Kenneth H.

Publication type:

Article