Eric J. Alm

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• An integrated framework for early detection and transmissibility assessment of emerging variants in wastewater

  International Journal of Hygiene and Environmental Health · 2026-04-02

• <i>Blautia wexlerae</i> Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-14

• Mapping population immunity: How protease and antibody fragmentation shape wastewater findings

  Water Research · 2026-02-12

• Host transcriptional responses to gut microbiome variation arising from urbanismPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-26

• Industrialization drives convergent microbial and physiological shifts in the human metaorganismPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-20 · 2 citations

• Convergent genomic responses of human gut bacteria to variations in industrializationPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-20 · 2 citations

• Sparse autoencoders uncover biologically interpretable features in protein language model representations

  Proceedings of the National Academy of Sciences · 2025-08-19 · 25 citations

• Sulfated dietary fiber protects gut microbiota from antibiotics

  Microbiome · 2025-08-06 · 5 citations

• Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle

  Scientific Reports · 2025-07-05 · 6 citations

• <i>Bifidobacterium longum</i> subsp. <i>nexti</i> subsp. nov., a novel subspecies isolated from infant stoolPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-23 · 1 citations

• 33: COMMENSALS DEPLETED IN OBESITY ACTIVATE ENTEROENDOCRINE CELLS AND IMPROVE HOST METABOLISM

  Gastroenterology · 2025-05-01

• Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

  Microbiome · 2025-04-28 · 8 citations

• Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome

  Microbiome · 2025-03-24 · 1 citations

• An integrated framework for early detection and transmissibility assessment of emerging variants in wastewaterPreprint

  medRxiv · 2025-02-20

• Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers

  Genome biology · 2025-01-27

• X-Mapper: fast and accurate sequence alignment via gapped x-mers

  Genome biology · 2025-01-22 · 4 citations

• CRISPR-Cas spacer acquisition is a rare event in human gut microbiome

  Cell Genomics · 2024-12-24 · 8 citations

• Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquiferPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-02 · 1 citations

• Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Molecular and Computational Technologies for Environmental Microbiology (Final Scientific/Technical Report)

  2024-10-21

• Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after fecal microbiota transplant in inflammatory bowel disease

  Scientific Reports · 2024-08-06 · 18 citations