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List of works by Jeroen Raes

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine

scientific article

A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies

scientific article

A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens).

scientific article

A framework for human microbiome research

scientific article

A global ocean atlas of eukaryotic genes.

scientific article published on 25 January 2018

A holistic approach to marine eco-systems biology

scientific article

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults

scientific article published in Nature Communications

A metagenome-wide association study of gut microbiota in type 2 diabetes

scientific article (publication date: 4 October 2012)

A metagenomic insight into our gut's microbiome

scientific article

A molecular study of microbe transfer between distant environments

scientific article

A nitrile hydratase in the eukaryote Monosiga brevicollis

scientific article published in 2008

A web application for sample size and power calculation in case-control microbiome studies.

scientific article published on 19 February 2016

A20 controls intestinal homeostasis through cell-specific activities

scientific article published on 30 September 2014

Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

article

An improved statistical method for detecting heterotachy in nucleotide sequences

scientific article published on 3 May 2006

Analysis of the draft genome of Pseudomonas fluorescens ATCC17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines

scientific article published on 23 April 2014

And then there were many: MADS goes genomic

scientific article published on October 2003

Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating

scientific article published on 10 August 2016

Assessment of metagenomic assembly using simulated next generation sequencing data

scientific article

Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 21 December 2020

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 01 December 2018

Bidirectional Interactions between Arboviruses and the Bacterial and Viral Microbiota in Aedes aegypti and Culex quinquefasciatus

scientific article published in 2022

Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis.

scientific article published on 7 July 2016

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of to Healthy Volunteers

CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies

scientific article

Caspase deficiency alters the murine gut microbiome

scientific article published on 20 October 2011

Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host

scientific article published on 29 October 2021

CoNet app: inference of biological association networks using Cytoscape.

scientific article published on 27 June 2016

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

scholarly article by Honggui Wang et al published February 2017 in Soil Biology and Biochemistry

Commensal microbiota influence systemic autoimmune responses.

scientific article

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

article

Comparisons of gut microbiota profiles in wild-type and gelatinase B/matrix metalloproteinase-9-deficient mice in acute DSS-induced colitis

Computational approaches to predict bacteriophage-host relationships.

scientific article

Correction: Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

scientific article published on 04 November 2019

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

scientific article

Cross-biome comparison of microbial association networks

scientific article

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

scientific article

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

scientific article

Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome

scientific article

Depression and suicidality: A link to premature T helper cell aging and increased Th17 cells

scientific article published on 14 February 2020

Design of synthetic microbial consortia for gut microbiota modulation

scientific article published on 17 August 2019

Discovering functional novelty in metagenomes: examples from light-mediated processes

scientific article published on 10 October 2008

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published on 2 December 2015

Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease

scientific article published on 29 October 2015

Duplication and divergence: the evolution of new genes and old ideas

scientific article

Early-Career Scientists Shaping the World

scientific article published on 07 May 2019

Editorial overview: It's the ecology, stupid: microbiome research in the post-stamp collecting age

scholarly article by Jeroen Raes published August 2018 in Current Opinion in Microbiology

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples

scientific article published on 30 May 2022

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Expanding the scope and scale of microbiome research

scientific article published on 05 September 2019

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

scientific article

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults

scientific article

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks

scientific article published on 21 November 2016

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

scientific article

Functional divergence of proteins through frameshift mutations

scientific article published in August 2005

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

publication published on 08 December 2021

Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.

scientific article published on January 2003

Genome-wide analysis of core cell cycle genes in Arabidopsis

scientific article

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

scientific article published on 22 June 2020

Genome-wide characterization of the lignification toolbox in Arabidopsis

scientific article published in November 2003

Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants

scientific article published in May 2003

Get the most out of your metagenome: computational analysis of environmental sequence data

scientific article

Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes

scholarly article by Geert Rb Huys et al published August 2018 in Current Opinion in Microbiology

Gut microbiome variation is associated to Multiple Sclerosis phenotypic subtypes

scientific article published on 12 March 2020

Gut microbiota affects sensitivity to acute DSS-induced colitis independently of host genotype

scientific article

Gut microbiota dynamics and uraemic toxins: one size does not fit all

scientific article published on 21 November 2018

Heritable components of the human fecal microbiome are associated with visceral fat.

scientific article published on 26 September 2016

Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design

scientific article

Host-microbe interaction: Rules of the game for microbiota

scientific article

How informative is the mouse for human gut microbiota research?

scientific article

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data

scientific article

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

scientific article

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 18 November 2020

Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases: protocol for a prospective cohort study of prognostic factors and personalised medicine.

scientific article published on 8 February 2018

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

In silico analyses of pericycle cell populations reinforce their relation with associated vasculature in Arabidopsis

scientific article

In vitro ecology: a discovery engine for microbiome therapies

scientific article published on 15 September 2020

Induction of bone loss by pathobiont-mediated Nod1 signaling in the oral cavity

scientific article published on May 2013

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

scientific article

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

scientific article published on 16 October 2018

Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease

scientific article

Interactions between soil compositions and the wheat root microbiome under drought stress: From an <i>in silico</i> to <i>in planta</i> perspective

scientific article published on 24 July 2021

Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model

scientific article published on 20 May 2015

Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena?

scientific article

Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community

scientific article published on 09 September 2018

Investigating ancient duplication events in the Arabidopsis genome

scientific article

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota

scholarly article by Kim De Paepe et al published 2019 in PeerJ

Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis

article published in 2018

Local immune response to food antigens drives meal-induced abdominal pain

scientific article published on 13 January 2021

LotuS: an efficient and user-friendly OTU processing pipeline.

scientific article published on 30 September 2014

Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC.

scientific article

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.

scientific article

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

scientific article published on 22 January 2016

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases

scientific article published on 18 July 2019

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

scientific article published on 18 September 2013

Metagenomics meets time series analysis: unraveling microbial community dynamics

scientific article published on 22 May 2015

Metformin induces weight loss associated with gut microbiota alteration in non-diabetic obese women: a randomized double-blind clinical trial

scientific article published on 01 December 2018

Microbial co-occurrence relationships in the human microbiome

scientific article

Microbial communities of the house fly Musca domestica vary with geographical location and habitat

scientific article published on 08 November 2019

Microbial interactions: from networks to models

scientific article

Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine

scientific article

Microbiology: Crowdsourcing Earth's microbes.

scientific article published in November 2017

Microbiome and metabolome features of the cardiometabolic disease spectrum

scientific article published on 17 February 2022

Microbiome-based companion diagnostics: no longer science fiction?

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

scientific article published on 3 June 2008

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Modeling gene and genome duplications in eukaryotes

scientific article

Molecular characterization of Arabidopsis PHO80-like proteins, a novel class of CDKA;1-interacting cyclins

scientific article published in June 2004

Molecular eco-systems biology: towards an understanding of community function

scientific article published in September 2008

Multi-stability and the origin of microbial community types

scientific article published on 5 May 2017

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition

scientific article

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

scientific article published on 15 March 2015

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

scientific article (publication date: 2006)

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets

scientific article

Nonsense-mediated mRNA decay: target genes and functional diversification of effectors

article

Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin

scientific article published on 28 June 2021

Ocean plankton. Determinants of community structure in the global plankton interactome

scientific article published on May 2015

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

scientific article published on May 2015

Ocean plankton. Structure and function of the global ocean microbiome

scientific article published on May 2015

Perspectives and pitfalls of microbiome research through home based fecal sampling: the Flemish Gut Flora Project experience.

scientific article

Plankton networks driving carbon export in the oligotrophic ocean

scientific article

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

scientific article

Population-level analysis of gut microbiome variation

scientific article published on 28 April 2016

Population-level analysis ofBlastocystissubtype prevalence and variation in the human gut microbiota

scientific article published on 31 August 2018

Practical considerations for large-scale gut microbiome studies

scientific article

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes

scientific article

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota

scientific article

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours

scientific journal article

Prediction of effective genome size in metagenomic samples

scientific article published on January 2007

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD

scientific article

Protein function space: viewing the limits or limited by our view?

scientific article published on 15 June 2007

Publisher Correction: Enterotypes in the landscape of gut microbial community composition

scientific article published on 13 February 2018

Quantifying environmental adaptation of metabolic pathways in metagenomics

scientific article

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

scientific article (publication date: 23 February 2007)

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

scientific article (publication date: 23 August 2007)

Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses

scientific article published on 17 June 2019

Quantitative microbiome profiling links gut community variation to microbial load.

scientific article

Reconciliation between operational taxonomic units and species boundaries

scientific article

Red Wine Consumption Associated With Increased Gut Microbiota α-Diversity in 3 Independent Cohorts

scientific article published on 28 August 2019

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 27 August 2018

Relationship between genome and epigenome--challenges and requirements for future research

scientific article published on 18 June 2014

Richness and ecosystem development across faecal snapshots of the gut microbiota

article

Richness of human gut microbiome correlates with metabolic markers

scientific article (publication date: 29 August 2013)

SmashCell: a software framework for the analysis of single-cell amplified genome sequences

scientific article

SmashCommunity: a metagenomic annotation and analysis tool

scientific article

Soil microbiome responses to the short-term effects of Amazonian deforestation.

scientific article published on 21 April 2015

Species-function relationships shape ecological properties of the human gut microbiome

scientific article published on 13 June 2016

Species-sorting and mass-transfer paradigms control managed natural metacommunities

scientific article published on 23 June 2016

Sputum Bacterial Metacommunities in Distinguishing Heterogeneity in Respiratory Health and Disease

scientific article published on 31 March 2022

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

scientific article published on 06 May 2020

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

scientific article published on 11 June 2015

Structure, function and diversity of the healthy human microbiome

scientific article

Successional Stages in Infant Gut Microbiota Maturation

scientific article published on 14 December 2021

Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study

scientific article published on 01 July 2019

Synthetic ecology of the human gut microbiota

scientific article published on 02 October 2019

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

scientific article published on 18 November 2021

The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity

scientific article

The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders

scientific article published on 2 August 2017

The Human Gut Microbiome: From Association to Modulation

scientific article published in March 2018

The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers

scientific article published on 21 September 2016

The TORNADO1 and TORNADO2 genes function in several patterning processes during early leaf development in Arabidopsis thaliana.

scientific article

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

scientific article published on November 2002

The chemical interactome space between the human host and the genetically defined gut metabotypes

scientific article published on 22 November 2012

The gut microbiome - a new target for understanding, diagnosing and treating disease

scientific article published on 6 June 2014

The human microbiome in health and disease: hype or hope

article

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

scientific article

The neuroactive potential of the human gut microbiota in quality of life and depression

scientific article published on 04 February 2019

The resilience of the intestinal microbiota influences health and disease

scientific article

The skin microbiome of caspase-14-deficient mice shows mild dysbiosis.

scientific article

The virota and its transkingdom interactions in the healthy infant gut

scientific article published on 23 March 2022

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data ⬇️

scientific article (publication date: 16 April 2014)

Towards biome-specific analysis of meta-omics data

scientific article

Towards microbial fermentation metabolites as markers for health benefits of prebiotics

scientific article published on June 2015

Tracking humans and microbes

scientific article published on 01 May 2019

Transcriptome analysis during cell division in plants

scientific article

Translating the human microbiome

scientific article published in April 2013

Universally distributed single-copy genes indicate a constant rate of horizontal transfer

scientific article

Variation and transmission of the human gut microbiota across multiple familial generations

scientific article published on 30 December 2021

Water activity does not shape the microbiota in the human colon

scientific article published on 6 January 2017

Worldwide trends in scientific publications on association of gut microbiota with obesity

scientific article published on 01 January 2019

Zinc inhibits lethal inflammatory shock by preventing microbe-induced interferon signature in intestinal epithelium

scientific article published on 11 September 2020

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