Lista de obras -

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

artículo científico publicado en 2016

'Hygienic' lymphocytes convey increased cancer risk

artículo científico publicado en 2014

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

artículo científico publicado en 2016

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

artículo científico publicado en 2022

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

artículo científico publicado en 2019

A novel method for accurate operon predictions in all sequenced prokaryotes

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2019

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

artículo científico publicado en 2018

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

artículo científico publicado en 2007

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

artículo científico publicado en 2014

Biological networks

artículo científico publicado en 2003

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

artículo científico publicado en 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.

artículo científico publicado en 2008

Comparing patterns of natural selection across species using selective signatures

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

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

artículo científico publicado en 2003

Correcting for batch effects in case-control microbiome studies.

artículo científico publicado en 2018

Correction: The Life-Cycle of Operons.

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 2020

DNA phosphorothioation is widespread and quantized in bacterial genomes.

artículo científico publicado en 2011

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

artículo científico publicado en 2018

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

Dietary microbes modulate transgenerational cancer risk

artículo científico publicado en 2015

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

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

artículo científico publicado en 2005

Distribution-based clustering: using ecology to refine the operational taxonomic unit

artículo científico publicado en 2013

Dysbiosis is not an answer

artículo científico publicado en 2016

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

artículo científico publicado en 2021

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

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

Environmental genomics reveals a single-species ecosystem deep within Earth

artículo científico publicado en 2008

Erratum to: Host lifestyle affects human microbiota on daily timescales

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2020

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

artículo científico publicado en 2009

Global transcriptome analysis of the heat shock response of Shewanella oneidensis

artículo científico publicado en 2004

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

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2022

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

artículo científico publicado en 2013

Host lifestyle affects human microbiota on daily timescales

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

Inferring Correlation Networks from Genomic Survey Data ⬇️

artículo científico publicado el 20 de septiembre de 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2022

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

artículo científico publicado en 2017

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

artículo científico publicado en 2018

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

artículo científico publicado en 2010

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

artículo científico publicado en 2022

MicrobesOnline: an integrated portal for comparative and functional genomics

artículo científico publicado en 2009

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.

artículo científico publicado en 2018

Microbial Reprogramming Inhibits Western Diet-Associated Obesity

Microbial lysate upregulates host oxytocin

artículo científico publicado en 2016

Microbial reprogramming inhibits Western diet-associated obesity

artículo científico publicado en 2013

Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin

artículo científico publicado en 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

artículo científico publicado en 2022

Natural bacterial communities serve as quantitative geochemical biosensors

artículo científico publicado en 2015

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

artículo científico publicado en 2012

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities

artículo científico publicado en 2019

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

artículo científico publicado en 2006

OpenBiome remains open to serve the medical community

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2021

Policy: How to regulate faecal transplants

artículo científico publicado en 2014

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

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2018

Predicting human health from biofluid-based metabolomics using machine learning

artículo científico publicado en 2020

Probiotic bacteria induce a 'glow of health'

artículo científico publicado en 2013

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

artículo científico publicado en 2014

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations

artículo científico publicado en 2017

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

artículo científico publicado en 2020

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

Random sequences rapidly evolve into de novo promoters.

artículo científico publicado en 2018

Rapid evolutionary innovation during an Archaean genetic expansion.

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2004

Reply

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

artículo científico publicado en 2012

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

artículo científico publicado en 2019

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

artículo científico publicado en 2008

Response of Desulfovibrio vulgaris to alkaline stress

artículo científico publicado en 2007

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

artículo científico publicado en 2022

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach

artículo científico publicado en 2006

Salt-responsive gut commensal modulates TH17 axis and disease

artículo científico publicado en 2017

Searching for superstool: maximizing the therapeutic potential of FMT

artículo científico publicado en 2018

Shape and evolution of the fundamental niche in marine Vibrio

artículo científico publicado en 2012

Simple physical models connect theory and experiment in protein folding kinetics

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2016

Sympatric speciation: when is it possible in bacteria?

artículo científico publicado en 2013

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

artículo científico publicado en 2017

The MicrobesOnline Web site for comparative genomics

artículo científico publicado en 2005

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

artículo científico publicado en 2006

The histidine operon is ancient

artículo científico publicado en 2006

The life-cycle of operons

artículo científico publicado en 2006

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

artículo científico publicado en 2009

Tracking Strains in the Microbiome: Insights from Metagenomics and Models

artículo científico publicado en 2016

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

artículo científico publicado en 2005

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

artículo científico publicado en 2006

Transfer of noncoding DNA drives regulatory rewiring in bacteria

artículo científico publicado en 2014

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

artículo científico publicado en 2017

Unlocking short read sequencing for metagenomics

artículo científico publicado en 2010

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2020

dbOTU3: A new implementation of distribution-based OTU calling

artículo científico publicado en 2017

Lista de obras de

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

'Hygienic' lymphocytes convey increased cancer risk

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

A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

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

A novel method for accurate operon predictions in all sequenced prokaryotes

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

Adaptive Evolution within Gut Microbiomes of Healthy People

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

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

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

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

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

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

Biological networks

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

Cellular response of Shewanella oneidensis to strontium stress

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

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

Comparing patterns of natural selection across species using selective signatures

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

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

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

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

Correcting for batch effects in case-control microbiome studies.

Correction: The Life-Cycle of Operons.

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

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

DNA phosphorothioation is widespread and quantized in bacterial genomes.

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

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

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

Dietary microbes modulate transgenerational cancer risk

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

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

Distribution-based clustering: using ecology to refine the operational taxonomic unit

Dysbiosis is not an answer

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

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

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

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

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

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

Environmental genomics reveals a single-species ecosystem deep within Earth

Erratum to: Host lifestyle affects human microbiota on daily timescales

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

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

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

Framework for rational donor selection in fecal microbiota transplant clinical trials

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

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

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

Global transcriptome analysis of the heat shock response of Shewanella oneidensis

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

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

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

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

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

Host lifestyle affects human microbiota on daily timescales

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

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

Inferring Correlation Networks from Genomic Survey Data ⬇️

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

Interactions in self-assembled microbial communities saturate with diversity

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

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

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

Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites

Looking for Darwin's footprints in the microbial world

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

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

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

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

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

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

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