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List of works by Eric J. Alm

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

scientific article

'Hygienic' lymphocytes convey increased cancer risk

scientific article

16S rRNA sequencing analysis: the devil is in the details

scientific article published on 24 April 2020

A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio

scientific article published on 07 February 2017

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments

scientific article

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

scientific article published on 5 August 2022

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

scientific article published on 02 September 2019

A novel method for accurate operon predictions in all sequenced prokaryotes

scientific article

A practical guide to methods controlling false discoveries in computational biology.

scientific article published on 4 June 2019

Adaptive Evolution within Gut Microbiomes of Healthy People

scientific article published on 23 April 2019

Adaptive evolution within the gut microbiome of individual people

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

scientific article

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function.

scientific article published on 20 May 2019

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

scientific article published on 29 October 2018

Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough

scientific article

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Beneficial bacteria stimulate host immune cells to counteract dietary and genetic predisposition to mammary cancer in mice

scientific article

Biological networks

scientific article

Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria: Supplementary

scholarly article published 13 January 2019

Cellular response of Shewanella oneidensis to strontium stress

scientific article published in January 2006

Co-evolution and Co-speciation of Host-Gut Bacteria Systems

scientific article published on 01 July 2020

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

scientific article published on 26 September 2008

Comparing patterns of natural selection across species using selective signatures

scientific article

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

scientific article published on 12 December 2019

Computational methods for high-throughput comparative analyses of natural microbial communities

scientific article

Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress

Contact order revisited: influence of protein size on the folding rate

scientific article published on September 2003

Correcting for batch effects in case-control microbiome studies.

scientific article

Correction: The Life-Cycle of Operons.

scientific article published on 28 July 2006

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

scientific article

Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

scientific article published on 17 December 2020

DNA phosphorothioation is widespread and quantized in bacterial genomes.

scientific article

Defining the gut microbiota in individuals with periodontal diseases: an exploratory study.

scientific article published on 3 July 2018

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy

scientific article published on January 2017

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

scientific article published on 14 September 2015

Dietary microbes modulate transgenerational cancer risk

scientific article

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks

scientific article

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit ⬇️

scientific article published on August 23, 2013

Dysbiosis is not an answer

scientific article published on 25 November 2016

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

scientific article published on 29 June 2021

Ecology drives a global network of gene exchange connecting the human microbiome

scientific article published on 30 October 2011

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

scientific article

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

article by Sean M Kearney et al published 13 June 2018 in The ISME Journal

Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis

scientific article

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

scientific article published on 05 March 2009

Environmental genomics reveals a single-species ecosystem deep within Earth

scientific article

Erratum to: Host lifestyle affects human microbiota on daily timescales

scientific article published on 31 May 2016

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

scientific article published on 10 July 2018

Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial

scientific article published on 06 June 2017

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study

scientific article

Framework for rational donor selection in fecal microbiota transplant clinical trials

scientific article published on 10 October 2019

Frozen encapsulated stool in recurrent Clostridium difficile: exploring the role of pills in the treatment hierarchy of fecal microbiota transplant nonresponders

scientific article

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria

scientific article published on 08 June 2020

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

scientific article

Global transcriptome analysis of the heat shock response of Shewanella oneidensis

scientific article

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea

scientific article published on 16 December 2021

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

scientific article published on 01 December 2018

High resolution time series reveals cohesive but short-lived communities in coastal plankton

scientific article

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

scientific article published on 3 June 2022

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

scientific article

Host lifestyle affects human microbiota on daily timescales

scientific article

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment

scientific article

Improved gene tree error correction in the presence of horizontal gene transfer

scientific article

Inferring Correlation Networks from Genomic Survey Data ⬇️

scientific article published on September 20, 2012

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

scientific article

Interactions in self-assembled microbial communities saturate with diversity

scientific article published on 26 February 2019

Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication

scientific article

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

scientific article published on 01 January 2019

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors

scientific article published on 21 June 2019

Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites

scientific article published on 29 June 2020

Looking for Darwin's footprints in the microbial world

scientific article published on 15 April 2009

Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management

scientific article published on 13 July 2020

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

scientific article published on 22 September 2015

Maternal Microbiota Modulate a Fragile X-like Syndrome in Offspring Mice

scientific article published in 2022

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

scientific article

Metagenomic mining of regulatory elements enables programmable species-selective gene expression.

scientific article

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

scientific article published on September 2010

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

scientific article published in April 2022

MicrobesOnline: an integrated portal for comparative and functional genomics

scientific article

Microbial Emulsion Matrices: A Novel Method to Produce Stable, Orally Available Capsules for Fecal Microbiota Transplantation to Treat Clostridium difficile

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

scientific article published on 20 February 2018

Microbial Reprogramming Inhibits Western Diet-Associated Obesity

Microbial lysate upregulates host oxytocin

scientific article published on 5 November 2016

Microbial reprogramming inhibits Western diet-associated obesity

scientific article

Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin

scientific article published in 2013

NMR characterization of residual structure in the denatured state of protein L

Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States

scientific article published on 3 May 2022

Natural bacterial communities serve as quantitative geochemical biosensors

scientific article published on 12 May 2015

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease

scientific article

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities

scientific article published on 09 May 2019

OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments

scientific article

OpenBiome remains open to serve the medical community

scientific article

Operon formation is driven by co-regulation and not by horizontal gene transfer

scientific article published on June 2005

Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal

scientific article published on 01 August 2018

Persistence of Dengue (Serotypes 2 and 3), Zika, Yellow Fever, and Murine Hepatitis Virus RNA in Untreated Wastewater

scientific article

Policy: How to regulate faecal transplants

scientific article

Population genomics of early events in the ecological differentiation of bacteria.

scientific article published on April 2012

Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota

scientific article published on 08 September 2020

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

scientific article published in Scientific Reports

Predicting human health from biofluid-based metabolomics using machine learning

scientific article published on 19 October 2020

Probiotic bacteria induce a 'glow of health'

scientific article

Probiotic microbes sustain youthful serum testosterone levels and testicular size in aging mice

scientific article

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations

scientific article

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort

scientific article published on 01 January 2020

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Random sequences rapidly evolve into de novo promoters.

scientific article published on 18 April 2018

Rapid evolutionary innovation during an Archaean genetic expansion.

scientific article

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss

scientific article published on 14 September 2013

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria

scientific article

Reply

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

scientific article published on 22 November 2012

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

scientific article published in May 2008

Response of Desulfovibrio vulgaris to alkaline stress

scientific article

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

scientific article published in January 2022

SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases

scientific article published on 21 July 2020

SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases

scientific article published on 07 April 2020

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

scientific article published on 23 June 2020

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach

scientific article

Salt-responsive gut commensal modulates TH17 axis and disease

scientific article published on 15 November 2017

Searching for superstool: maximizing the therapeutic potential of FMT

scientific article published on 01 July 2018

Shape and evolution of the fundamental niche in marine Vibrio

scientific article

Simple physical models connect theory and experiment in protein folding kinetics

scientific article published in September 2002

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

scientific article published on 06 April 2020

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

scientific article published in February 2018

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem.

scientific article

Sympatric speciation: when is it possible in bacteria?

scientific article

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

scientific article published on 23 January 2017

The MicrobesOnline Web site for comparative genomics

scientific article

The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study

scientific article published on 06 January 2020

The evolution of two-component systems in bacteria reveals different strategies for niche adaptation

scientific article published on 3 November 2006

The histidine operon is ancient

scientific article published on 11 April 2006

The life-cycle of operons

scientific article published on 23 June 2006

The slow:fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes

scientific article

Tracking Strains in the Microbiome: Insights from Metagenomics and Models

scientific article

Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions

scientific article

Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH.

scientific article

Transfer of noncoding DNA drives regulatory rewiring in bacteria

scientific article

Transmission of human-associated microbiota along family and social networks

scientific article published on 25 March 2019

Two dynamic regimes in the human gut microbiome

scientific article

Unlocking short read sequencing for metagenomics

scientific article

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

scientific article published on 23 February 2017

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

scientific article published on 07 May 2019

Virtual microfluidics for digital quantification and single-cell sequencing

scientific article published on August 2016

Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020

scientific article published in September 2021

Wastewater-Based Epidemiology: Global Collaborative to Maximize Contributions in the Fight Against COVID-19

scientific article published on 12 June 2020

dbOTU3: A new implementation of distribution-based OTU calling

scientific article

epicPCR (Emulsion, Paired Isolation, and Concatenation PCR)

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