Publications by authors named "Eric Alm"

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Host transcriptional responses to gut microbiome variation arising from urbanism.
Sabrina Arif, Shreya Nirmalan, Adnan Alazizi, Henriette Mair-Meijers, Adwoa Agyei, Eric J Alm

bioRxiv· October 2025

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Convergent genomic responses of human gut bacteria to variations in industrialization.
Malte Rühlemann, Lénárd L Szánthó, Silvio Waschina, Lucas Moitinho-Silva, Laura K Mews, Eric J Alm

bioRxiv· October 2025

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Industrialization drives convergent microbial and physiological shifts in the human metaorganism.
Mathilde Poyet, Malte Rühlemann, Ana P Schaan, Yue Ma, Lucas Moitinho-Silva, Eric J Alm

bioRxiv· October 2025

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Sulfated dietary fiber protects gut microbiota from antibiotics.
Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E Erdman, Eric J Alm

Microbiome· August 2025

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Sparse autoencoders uncover biologically interpretable features in protein language model representations.
Onkar Gujral, Mihir Bafna, Eric Alm, Bonnie Berger

Proc Natl Acad Sci U S A· August 2025

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Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.
Nurul Fauzani Jamaluddin, Olga Brovkina, Nurshamimi Nor Rashid, Anis Rageh Al-Maleki, Yvonne Ai-Lian Lim, Eric Alm

Sci Rep· July 2025

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Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.
Yupeng Fan, Dongyu Wang, Joy X Yang, Daliang Ning, Zhili He, Eric J Alm

Microbiome· April 2025

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Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.
Shane R Byrne, Michael S DeMott, Yifeng Yuan, Farzan Ghanegolmohammadi, Stefanie Kaiser, Eric J Alm

Microbiome· March 2025

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CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.
An-Ni Zhang, Jeffry M Gaston, Pablo Cárdenas, Shijie Zhao, Xiaoqiong Gu, Eric J Alm

Cell Genom· January 2025

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X-Mapper: fast and accurate sequence alignment via gapped x-mers.
Jeffry M Gaston, Eric J Alm, An-Ni Zhang

Genome Biol· January 2025

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Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers.
Jeffry M Gaston, Eric J Alm, An-Ni Zhang

Genome Biol· January 2025

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Longitudinal Microbiome Changes in Children Exposed to Proton Pump Inhibitors.
Yanjia Jason Zhang, Sarah Connearney, Lisa Hester, Maritha Du, Andrea Catacora, Eric J Alm

Clin Transl Gastroenterol· September 2024

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Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after fecal microbiota transplant in inflammatory bowel disease.
Yanjia Jason Zhang, Athos Bousvaros, Michael Docktor, Abby L Kaplan, Paul A Rufo, Eric J Alm

Sci Rep· August 2024

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Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome.
Yifeng Yuan, Michael S DeMott, Shane R Byrne, Katia Flores, Mathilde Poyet, Eric J Alm

bioRxiv· June 2024

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Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.
Shane R Byrne, Michael S DeMott, Yifeng Yuan, Farzan Ghanegolmohammadi, Stefanie Kaiser, Eric J Alm

bioRxiv· May 2024

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Fast and accurate variant identification tool for sequencing-based studies.
Jeffry M Gaston, Eric J Alm, An-Ni Zhang

BMC Biol· April 2024

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Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.
Ana Paula Schaan, Amanda Vidal, An-Ni Zhang, Mathilde Poyet, Eric J Alm

mSystems· March 2024

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An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii.
Jianbo Zhang, Yu-Ja Huang, Martin Trapecar, Charles Wright, Kirsten Schneider, Eric J Alm

NPJ Biofilms Microbiomes· March 2024

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Environmental stress mediates groundwater microbial community assembly.
Daliang Ning, Yajiao Wang, Yupeng Fan, Jianjun Wang, Joy D Van Nostrand, Eric J Alm

Nat Microbiol· February 2024

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Structured community transitions explain the switching capacity of microbial systems.
Chengyi Long, Jie Deng, Jen Nguyen, Yang-Yu Liu, Eric J Alm

Proc Natl Acad Sci U S A· February 2024

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Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.
Xiaoqian Annie Yu, Craig McLean, Jan-Hendrik Hehemann, David Angeles-Albores, Fuqing Wu, Eric J Alm

ISME J· January 2024

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An immune-competent human gut microphysiological system enables inflammation-modulation of .
Jianbo Zhang, Yu-Ja Huang, Martin Trapecar, Charles Wright, Kirsten Schneider, Eric J Alm

Res Sq· October 2023

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Lectin-Seq: A method to profile lectin-microbe interactions in native communities.
Robert L McPherson, Christine R Isabella, Rebecca L Walker, Dallis Sergio, Sunhee Bae, Eric J Alm

Sci Adv· July 2023

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Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by Community and University Campus wastewater surveillance.
Feng Jun Desmond Chua, Se Yeon Kim, Eric Hill, Jia Wei Cai, Wei Lin Lee, Eric J Alm

Sci Total Environ· June 2023

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Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after Fecal Microbiota Transplant in Inflammatory Bowel Disease.
Yanjia Jason Zhang, Athos Bousvaros, Michael Docktor, Abby Kaplan, Paul A Rufo, Eric J Alm

medRxiv· February 2023

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