Eric John Alm (Eric J Alm, E J Alm)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 25

Top Topics

Irritable Bowel Syndrome

Microbial Community

Induced Pluripotent Stem Cells

Top Venues

Science (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric John Alm, Mathilde Poyet, Ândrea Kely Campos Ribeiro Dos Santos
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems 9 (3) (2024)
Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric John Alm, Mathilde Poyet, Ândrea Kely Campos Ribeiro Dos Santos
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems 9 (3) (2024)
Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric John Alm, Mathilde Poyet, Ândrea Kely Campos Ribeiro Dos Santos
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems 9 (3) (2024)
Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric John Alm, Mathilde Poyet, Ândrea Kely Campos Ribeiro Dos Santos
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems (2024)
Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric John Alm, Mathilde Poyet, Ândrea Kely Campos Ribeiro Dos Santos
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems 9 (3) (2024)
Robert Lyle McPherson, Christine R Isabella, Rebecca L Walker, Dallis Sergio, Sunhee Bae, Tony Gaca, Smrithi Raman, Le Thanh Tu Nguyen, Darryl A Wesener, Melanie Halim, Michael G Wuo, Amanda Dugan, Robert Kerby, Soumi Ghosh, Federico E Rey, Catherine Dhennezel, Gleb Pishchany, Valerie Lensch, Hera Vlamakis, Eric John Alm, Ramnik J Xavier, Laura L Kiessling
Lectin-Seq: A method to profile lectin-microbe interactions in native communities. Science advances 9 (30) (2023)
Prashant Singh, Eric John Alm, John M Kelley, Vivian Cheng, Mark Smith, Zain Kassam, Judy Nee, Johanna Iturrino, Anthony Lembo
Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D. Gut microbes 14 (1) (2022)
Djenet Bousbaine, Laura I Fisch, Mariya London, Preksha Bhagchandani, Tiago Rezende de Castro, Mark Mimee, Scott W Olesen, Bernardo Sgarbi Reis, Libusha Kelly, Juliana Bortolatto, Mathilde Poyet, Ross W Cheloha, John Sidney, Jingjing Ling, Aaron Gupta, Timothy K Lu, Alessandro Sette, Eric John Alm, James J Moon, Gabriel D Victora, Daniel Mucida, Hidde L Ploegh, Angelina M Bilate
A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. Science (New York, N.Y.) 377 (6606) (2022)
Wenshan Zheng, Shijie Zhao, Yehang Yin, Huidan Zhang, David M Needham, Ethan D Evans, Chengzhen L Dai, Peter J Lu, Eric John Alm, David A Weitz
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science (New York, N.Y.) 376 (6597) (2022)
Thomas Gurry, Le Thanh Tu Nguyen, Xiaoqian Yu, Eric John Alm
Functional heterogeneity in the fermentation capabilities of the healthy human gut microbiota. PloS one 16 (7) (2021)
Amy M Tsou, Scott W Olesen, Eric John Alm, Scott B Snapper
16S rRNA sequencing analysis: the devil is in the details. Gut microbes 11 (5) (2020)
Fuqing Wu, Jianbo Zhang, Amy Xiao, Xiaoqiong Gu, Wei Lin Lee, Federica Armas, Kathryn Kauffman, William Hanage, Mariana Matus, Newsha Ghaeli, Noriko Endo, Claire Duvallet, Mathilde Poyet, Katya Moniz, Alex D Washburne, Timothy B Erickson, Peter R Chai, Janelle Thompson, Eric John Alm
SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 5 (4) (2020)
Ethan D Evans, Chengzhen L Dai, Siavash Isazadeh, Shinkyu Park, Carlo Ratti, Eric John Alm
Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites. PLoS computational biology 16 (6) (2020)
Xiaoqian Yu, Thomas Gurry, Le Thanh Tu Nguyen, Hunter S Richardson, Eric John Alm
Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota. mBio 11 (5) (2020)
Antonio L C Gomes, Nathan I Johns, Anthony Yang, Florencia Velez-Cortes, Christopher S Smillie, Mark B Smith, Eric John Alm, Harris H Wang
Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. The ISME journal 14 (9) (2020)
Xiaofang Jiang, A Brantley Hall, Timothy D Arthur, Damian Rafal Plichta, Christian T Covington, Mathilde Poyet, Jessica Crothers, Peter L Moses, Andrew C Tolonen, Hera Vlamakis, Eric John Alm, Ramnik J Xavier
Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science (New York, N.Y.) 363 (6423) (2019)
Ilana L Brito, Thomas Gurry, Shijie Zhao, Katherine Huang, Sarah K Young, Terrence P Shea, Waisea Naisilisili, Aaron P Jenkins, Stacy D Jupiter, Dirk Gevers, Eric John Alm
Transmission of human-associated microbiota along family and social networks. Nature microbiology 4 (6) (2019)
Arnau Vich Vila, Floris Imhann, Valerie Collij, Soesma A Jankipersadsing, Thomas Gurry, Zlatan Mujagic, Alexander Kurilshikov, Marc Jan Bonder, Xiaofang Jiang, Ettje F Tigchelaar, Jackie Dekens, Vera Peters, Michiel D Voskuil, Marijn C Visschedijk, Hendrik M van Dullemen, Daniel Keszthelyi, Morris A Swertz, Lude Franke, Rudi Alberts, Eleonora A M Festen, Gerard Dijkstra, Adrian A M Masclee, Marten H Hofker, Ramnik J Xavier, Eric John Alm, Jingyuan Fu, Cisca Wijmenga, Daisy M A E Jonkers, Alexandra Zhernakova, Rinse K Weersma
Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Science translational medicine 10 (472) (2019)
M Poyet, M Groussin, Sean M Gibbons, J Avila-Pacheco, X Jiang, S M Kearney, A R Perrotta, Brittany Berdy, S Zhao, T D Lieberman, P K Swanson, M Smith, S Roesemann, J E Alexander, S A Rich, J Livny, H Vlamakis, Andrew T Chan, K Bullock, A Deik, J Scott, K A Pierce, R J Xavier, Eric John Alm
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nature medicine 25 (9) (2019)
Xiaofang Jiang, Andrew Brantley Hall, Ramnik J Xavier, Eric John Alm
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PloS one 14 (12) (2019)
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric John 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-Rodriguez, 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 P 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 A Lozupone, Massoud Maher, Clarisse A 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 R Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam R Rivers, Michael Scott 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 Johan Jozias 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
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37 (8) (2019)
Claire Duvallet, Caroline Zellmer, Pratik Panchal, Shrish Budree, Majdi Osman, Eric John Alm
Framework for rational donor selection in fecal microbiota transplant clinical trials. PloS one 14 (10) (2019)
Talita Gomes Baeta Lourenςo, Sarah J Spencer, Eric John Alm, Ana Paula Vieira Colombo
Defining the gut microbiota in individuals with periodontal diseases: an exploratory study. Journal of oral microbiology 10 (1) (2018)
Sean M Gibbons, Claire Duvallet, Eric John Alm
Correcting for batch effects in case-control microbiome studies. PLoS computational biology 14 (4) (2018)
Trishla Sinha, Arnau Vich Vila, Sanzhima Garmaeva, Soesma A Jankipersadsing, Floris Imhann, Valerie Collij, Marc Jan Bonder, Xiaofang Jiang, Thomas Gurry, Eric John Alm, Mauro D'Amato, Rinse K Weersma, Sicco A Scherjon, Cisca Wijmenga, Jingyuan Fu, Alexander Kurilshikov, Alexandra Zhernakova
Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut microbes 10 (3) (2018)