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List of works by Ramnik J Xavier

A Common Mechanism Links Activities of Butyrate in the Colon

scientific article published on 10 April 2018

A Functional Genomic Screen Identifies Cellular Cofactors of Hepatitis C Virus Replication

scientific article

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

scientific article published on November 2016

A Microbiome Foundation for the Study of Crohn's Disease

scientific article published on March 2017

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-γ-Activated Human Cells

scientific article

A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition

scientific article

A common mechanism links activities of butyrate in the colon

scientific article published in 2017

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

scientific article published on 23 January 2019

A genome-wide genetic screen for host factors required for hepatitis C virus propagation

scientific article

A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions

scientific article published on June 2010

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

scientific article (publication date: 13 November 2008)

A locus at 7p14.3 predisposes to refractory celiac disease progression from celiac disease

A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity

scientific article published on 02 November 2020

A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands

scientific article published on 6 July 2006

A non-canonical autophagy-dependent role of the ATG16L1 variant in urothelial vesicular trafficking and uropathogenic Escherichia coli persistence

scientific article published on 08 November 2018

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

scientific article

A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy

scientific article published on April 2009

A novel role for KLF14 in T regulatory cell differentiation

scientific article

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

scientific article published on 09 August 2016

A role for bacterial urease in gut dysbiosis and Crohn's disease.

scientific article

A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.

scientific article published on 25 April 2018

A single-cell survey of the small intestinal epithelium

scientific article published on 8 November 2017

A systems biology viewpoint on autophagy in health and disease

scientific article published on July 2010

ABCA3 inactivation in mice causes respiratory failure, loss of pulmonary surfactant, and depletion of lung phosphatidylglycerol

scientific article published in December 2006

AKAP13, a RhoA GTPase-specific guanine exchange factor, is a novel regulator of TLR2 signaling

scientific article

ATG5 regulates plasma cell differentiation

scientific article published on 17 January 2013

Adaptive Evolution within Gut Microbiomes of Healthy People

scientific article published on 23 April 2019

Adaptive evolution within the gut microbiome of individual people

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

scientific article

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis

scientific article published in March 2019

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis

scientific article published on 01 June 2019

Allergic asthma is distinguished by sensitivity of allergen-specific CD4+ T cells and airway structural cells to type 2 inflammation

scientific article

Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases

scientific article published on 14 March 2020

An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread

scientific article published on 26 November 2018

An alteration in ATG16L1 stability in Crohn disease

scientific article published on 12 August 2014

An image-based genetic assay identifies genes in T1D susceptibility loci controlling cellular antiviral immunity in mouse

scientific journal article

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

scientific article published on 02 June 2009

An integrative view of microbiome-host interactions in inflammatory bowel diseases

scientific article published on May 2015

Angiotensin II drives the production of tumor-promoting macrophages

scientific article published on 17 January 2013

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes

scientific article published on 22 October 2018

Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease

scientific article published on 01 February 2019

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

scientific article published on 8 April 2015

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense

scientific article

Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection

scientific article published on 21 August 2013

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease

scientific article published on 01 May 2019

Author Correction: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

scientific article published in 2021

Author Correction: Trained immunity, tolerance, priming and differentiation: distinct immunological processes

scientific article published in 2021

Autophagy and checkpoints for intracellular pathogen defense

scientific article

Autophagy and the Immune System ⬇️

scientific article published on January 1, 2012

Autophagy as an important process in gut homeostasis and Crohn's disease pathogenesis

scientific article published on 13 February 2008

Autophagy at the crossroads of metabolism and cellular defense.

scientific article

Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases

scientific article published on January 2010

Autophagy controls BCG-induced trained immunity and the response to intravesical BCG therapy for bladder cancer

scientific article

Autophagy is essential for cardiac morphogenesis during vertebrate development

scientific article published on 14 January 2014

Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1β (IL-1β)

scientific article published on 5 February 2013

Autophagy suppresses interleukin-1β (IL-1β) signaling by activation of p62 degradation via lysosomal and proteasomal pathways.

scientific article published on 13 December 2011

Autophagy, immunity and human disease

scientific article

Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9. ⬇️

scientific article

Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia

scientific article

BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity

scientific article published in January 2018

BCG-induced trained immunity in NK cells: Role for non-specific protection to infection

scientific article published on 25 October 2014

Bacille Calmette-Guérin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes ⬇️

scientific article published on September 17, 2012

Bacterial and host determinants of MAL activation upon EPEC infection: the roles of Tir, ABRA, and FLRT3

scientific article

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis

scientific article published on 01 May 2019

Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism

scientific article

Beth Cindy Levine (1960-2020)

scientific article published on 01 July 2020

Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease

scientific article

Building complex biological networks based upon model organisms: mapping the human autophagy interactome via a hybrid yeast-human protein interaction network

scientific article

C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions.

scientific article

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

scientific article published on 09 May 2016

CARMA1 is critical for the development of allergic airway inflammation in a murine model of asthma

scientific article

CARMA1 is necessary for optimal T cell responses in a murine model of allergic asthma

scientific article published on 9 November 2011

CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.

scientific article published on 3 June 2015

CARMA3 Mediates Allergic Lung Inflammation in Response to Alternaria alternata

scientific article published on 01 December 2018

CARMA3 mediates lysophosphatidic acid-stimulated cytokine secretion by bronchial epithelial cells.

scientific article published on 28 August 2008

CHOP is a critical regulator of acetaminophen-induced hepatotoxicity.

scientific article published on 9 May 2013

CRISPR-Cas9 knockin mice for genome editing and cancer modeling

scientific article

Ca2+/calmodulin-dependent protein kinase II is a modulator of CARMA1-mediated NF-kappaB activation

scientific article

Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses

scientific article published on 08 October 2019

Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes.

scientific article published on August 2012

Card9 mediates intestinal epithelial cell restitution, T-helper 17 responses, and control of bacterial infection in mice

scientific article published on 31 May 2013

Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A

scientific article published on 10 June 2020

Characterization and analysis of human chordoma cell lines

scientific article published in June 2010

Characterization of candidate genes in inflammatory bowel disease-associated risk loci

scientific article published on 18 August 2016

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level

scientific article published on 10 June 2020

Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2

article published in the Proceedings of the National Academy of Sciences of the United States of America

Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes

scientific article published on 3 May 2016

Clinical and Genomic Correlates of Neutrophil Reactive Oxygen Species Production in Pediatric Patients with Crohn's Disease

scientific article published on 15 February 2018

Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study

scientific article published on 29 March 2019

Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing

scientific article published on 27 January 2022

Colonic epithelial functional phenotype varies with type and phase of experimental colitis.

scientific article

Commensal flora: wolf in sheep's clothing

scientific article published in April 2005

Common alleles that influence autophagy and the risk for inflammatory bowel disease

scientific article published on 05 October 2012

Common variants at five new loci associated with early-onset inflammatory bowel disease

scientific article

Complex host genetics influence the microbiome in inflammatory bowel disease

scientific article

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

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

ConStrains identifies microbial strains in metagenomic datasets

scientific article

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis

scientific article published on 28 February 2021

Control and manipulation of pathogens with an optical trap for live cell imaging of intercellular interactions

scientific article (publication date: 2010)

Control of NOD2 and Rip2-dependent innate immune activation by GEF-H1 ⬇️

scientific article published on September 1, 2011

Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

correction of a scientific article; published on 30 May 2019

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

scientific article published on 2 March 2015

Corrigendum: SIKs control osteocyte responses to parathyroid hormone

scientific article published on 22 February 2017

Crohn disease: a current perspective on genetics, autophagy and immunity

scientific article

Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly

scientific article

Cutting Edge: Cell-Autonomous Control of IL-7 Response Revealed in a Novel Stage of Precursor B Cells ⬇️

scientific article published on February 18, 2013

Cytokine release and gastrointestinal symptoms after gluten challenge in celiac disease

scientific article published on 07 August 2019

DLG1 is an anchor for the E3 ligase MARCH2 at sites of cell-cell contact

scientific article

DLGH1 is a negative regulator of T-lymphocyte proliferation

scientific journal article

Dectin-1-dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages.

scientific article

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

scientific article

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis

scientific article

Defective signal transduction in B lymphocytes lacking presenilin proteins

scholarly article

Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis

scientific article

Defining trained immunity and its role in health and disease

scientific article published on 04 March 2020

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

scientific article published on September 2008

Delivery Mode Affects Stability of Early Infant Gut Microbiota

scientific article published on 22 December 2020

Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function in Vivo

scientific article published on 25 May 2016

Difference in clinical course, genetics, and the microbiome between familial and sporadic inflammatory bowel diseases.

scientific article published on 14 November 2017

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits

scientific article

Differential effect of genetic burden on disease phenotypes in Crohn's disease and ulcerative colitis: analysis of a North American cohort

scientific article

Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression

scientific article published in June 2010

Differential requirement for CARMA1 in agonist-selected T-cell development

scientific article published on January 2009

Discovery of a Small-Molecule Probe for V-ATPase Function

scientific article published on 20 April 2015

Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter

scientific article

Disease-specific alterations in the enteric virome in inflammatory bowel disease

scientific article

Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1

scientific article published on 26 August 2019

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

scientific article

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

scientific article

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

scientific article (publication date: 16 April 2012)

Early life environment and natural history of inflammatory bowel diseases

scientific article

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

scientific article published in October 2017

Enhanced Tim3 activity improves survival after influenza infection

scientific article

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

scientific article published on September 2014

Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies

scientific article published on 11 May 2017

Erratum to: Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

scientific article published on 18 November 2016

Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

scientific article published on 13 September 2016

Erratum: Corrigendum: Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi

article

Erratum: Corrigendum: Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

scholarly article published in Nature Genetics

Erratum: Genome-wide association identifies multiple ulcerative colitis susceptibility loci

scholarly article published in Nature Genetics

Essential cell-autonomous role for interferon (IFN) regulatory factor 1 in IFN-γ-mediated inhibition of norovirus replication in macrophages

scientific article

Essential role for Vav1 in activation, but not development, of gammadelta T cells

scientific article published on 01 February 2003

Establishment and characterization of a novel chordoma cell line: CH22.

scientific article

Failure and exploitation of autophagy in human pathologies—cellular integrity between inflammation, infection, and cell survival ⬇️

scientific article published on November 25, 2010

Fine-mapping inflammatory bowel disease loci to single-variant resolution

scientific article

Flow Cytometric Analysis of Mononuclear Phagocytes in Nondiseased Human Lung and Lung-Draining Lymph Nodes

scientific article published on 9 November 2015

From genetics of inflammatory bowel disease towards mechanistic insights ⬇️

scientific article published on April 30, 2013

Fruit and vegetable consumption is associated with lower prevalence of asymptomatic diverticulosis: a cross-sectional colonoscopy-based study

scientific article published on 11 July 2020

Functional and Genomic Architecture of Borrelia burgdorferi-Induced Cytokine Responses in Humans.

scientific article published on November 2016

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst

scientific article

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans

scientific article published on January 2013

Functional profiling of the gut microbiome in disease-associated inflammation

scientific article published on 31 July 2013

GSDMD is critical for autoinflammatory pathology in a mouse model of Familial Mediterranean Fever.

scientific article

Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor

scientific article

Gene networks that compensate for crosstalk with crosstalk

scientific article published on 06 September 2019

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease

scientific article

Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk

scientific article published on 6 June 2016

Genetic Markers Predict Primary Non-Response and Durable Response To Anti-TNF Biologic Therapies in Crohn's Disease

scientific article published on 6 September 2016

Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis

scientific article published on 01 July 2018

Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte-Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn's Disease

scientific article published on 01 February 2019

Genetic effects on the commensal microbiota in inflammatory bowel disease patients

scientific article published on 08 March 2019

Genetic polymorphisms in metabolizing enzymes modifying the association between smoking and inflammatory bowel diseases

scientific article

Genetic risk factors for serious infections in inflammatory bowel diseases

scientific article published on 5 February 2017

Genetic variants synthesize to produce paneth cell phenotypes that define subtypes of Crohn's disease.

scientific article

Genetics and pathogenesis of inflammatory bowel disease

scientific article (publication date: 15 June 2011)

Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism

scientific article published on 14 October 2014

Genome-wide analysis of immune system genes by expressed sequence Tag profiling

scientific article published on 24 April 2013

Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.

scientific article

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

scientific article

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

scientific article

Genome-wide association studies: a new window into immune-mediated diseases

scientific article published on August 2008

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

scientific article

Genome-wide enhancer maps link risk variants to disease genes

scientific article published on 07 April 2021

Genome-wide expression profiling implicates a MAST3-regulated gene set in colonic mucosal inflammation of ulcerative colitis patients ⬇️

scientific article published on October 12, 2011

Genome-wide siRNA screen for mediators of NF-κB activation

scientific article published on 17 January 2012

Genomic and Expression Analyses Identify a Disease-Modifying Variant for Fibrostenotic Crohn's Disease.

scientific article published in April 2018

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

scientific article published on 17 December 2018

Global chemical effects of the microbiome include new bile-acid conjugations

scientific article published on 26 February 2020

Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity

scientific article published on 16 November 2016

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease

scientific article published on 20 January 2020

Guidelines for the use and interpretation of assays for monitoring autophagy

scientific article

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

scientific article

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk

scientific article published on 11 April 2019

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases

scientific article published on May 2017

Gut bacterial metabolites modulate endoplasmic reticulum stress

scientific article published on 15 October 2021

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

scientific article published on 11 August 2020

Gut microbiome structure and metabolic activity in inflammatory bowel disease

scientific article published on 10 December 2018

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

scientific article published in 2021

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

scientific article published on 01 December 2018

Helminth Infection Impairs Autophagy-Mediated Killing of Bacterial Enteropathogens by Macrophages ⬇️

scientific article published on June 25, 2012

Host and Environmental Factors Influencing Individual Human Cytokine Responses

scientific article published on November 2016

Host genetic variation and its microbiome interactions within the Human Microbiome Project

scientific article published on 29 January 2018

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

scientific article

How Does Genotype Influence Disease Phenotype in Inflammatory Bowel Disease? ⬇️

scientific article published on August 1, 2013

Human genome-wide RNAi screen identifies an essential role for inositol pyrophosphates in Type-I interferon response

scientific article (publication date: February 2014)

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

scientific article

IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans

scientific article published on 18 February 2014

IL-22 ameliorates intestinal inflammation in a mouse model of ulcerative colitis

scientific article

IRGM Gene Variants Modify the Relationship Between Visceral Adipose Tissue and NAFLD in Patients With Crohn's Disease

scientific article published on 01 September 2018

Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes.

scientific article published on 10 July 2009

Identification of a candidate therapeutic autophagy-inducing peptide

scientific journal article

Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway

scientific article

Identification of a novel Ras-regulated proapoptotic pathway

scientific article (publication date: 19 February 2002)

Identification of host proteins required for HIV infection through a functional genomic screen

scientific article

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

scientific article published on 29 September 2022

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions

scientific article

Image-based genome-wide siRNA screen identifies selective autophagy factors

scientific article

Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes

scientific article published on 21 June 2006

Impact of Specialized Inpatient IBD Care on Outcomes of IBD Hospitalizations: A Cohort Study

scientific article published on August 2016

Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome

scholarly article by Jane M. Natividad published in July 2018

Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease

scientific article published on 7 March 2016

Impaired autophagy in macrophages promotes inflammatory eye disease

scientific article published on 27 July 2016

Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant

scientific article

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease

scientific article published on September 2016

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation

scientific article published on July 2017

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

preprint published 25 September 2016

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

scientific article

Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy

scientific article published on 18 June 2015

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses

scientific article published on 21 May 2018

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi

scientific article published on 4 July 2016

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

scientific article published on 8 October 2016

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

scientific article published on 10 July 2017

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

scientific article published on 01 July 2019

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

scientific article published on 01 January 2019

LRRK2 is involved in the IFN-gamma response and host response to pathogens

scientific article

Large-scale screens for cDNAs with in vivo activity

scientific article published on 01 January 2005

Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs

scientific article (publication date: 2014)

Leucine-rich repeat (LRR) proteins: Integrators of pattern recognition and signaling in immunity ⬇️

scientific article published on September 1, 2011

Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease

scientific article published on 26 August 2020

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity ⬇️

scientific article

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

scientific article published on 01 December 2016

Long-lasting effects of BCG vaccination on both heterologous Th1/Th17 responses and innate trained immunity

scientific article published on 30 October 2013

Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways.

scientific article

Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140

scientific article published on 3 March 2017

Mechanisms and function of autophagy in intestinal disease

scientific article published on 13 November 2017

Mechanisms of Pediatric Inflammatory Bowel Disease

scientific article published on May 2016

Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice

scientific article published on 06 May 2019

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

scientific journal article

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease

scientific article published on 26 May 2016

Microbial genes and pathways in inflammatory bowel disease

scientific article published on 01 August 2019

Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines

scientific article published on 03 November 2020

Molecular pathogenesis of inflammatory bowel disease: genotypes, phenotypes and personalized medicine

scientific article published on January 2007

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

article

Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse

scientific article published on 07 August 2020

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

scientific article published on 29 May 2019

Multiomics Analyses to Deliver the Most Effective Treatment to Every Patient With Inflammatory Bowel Disease

scientific article published on 02 August 2018

Multivariate inference of pathway activity in host immunity and response to therapeutics

scientific article

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

scientific article

MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties

scientific article published on 6 June 2011

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

scientific article published on June 2016

Neither hide nor hair: the difficulty of identifying useful disease biomarkers

scientific article published on 16 May 2008

Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes

scientific article published on 01 July 2018

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

scientific article

Nondegradative role of Atg5-Atg12/ Atg16L1 autophagy protein complex in antiviral activity of interferon gamma

scientific article

Novel mechanism of tumor suppression by polarity gene discs large 1 (DLG1) revealed in a murine model of pediatric B-ALL.

scientific article

Obesity, but not physical activity, is associated with higher prevalence of asymptomatic diverticulosis

scientific article published on 9 September 2017

On the level: IRGM gene function is all about expression

scientific article published on 25 January 2009

PDZ domains and the politics of polarity in lymphocytes

scientific article published on 01 June 2005

Paneth cell defects in Crohn's disease patients promote dysbiosis

scientific article published on 02 June 2016

Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine.

scientific article

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

scientific article

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

article

Pathway paradigms revealed from the genetics of inflammatory bowel disease

scientific article published on 26 February 2020

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

scientific article

Phosphoprotein Associated with Glycosphingolipid-Enriched Microdomains Differentially Modulates Src Kinase Activity in Brain Maturation ⬇️

scientific article published on September 6, 2011

Polarity gene discs large homolog 1 regulates the generation of memory T cells ⬇️

scientific article published on 09 April 2013

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

scientific article

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study

scientific article published on March 2017

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

scientific article published on 17 July 2019

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks

scientific article published on 13 June 2016

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology

scientific article

Proton pump inhibitors affect the gut microbiome

scientific article published on 9 December 2015

Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

scientific article published on 01 March 2019

Publisher Correction: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

scientific article published in 2021

Pyruvate Kinase M2 Regulates Hif-1α Activity and IL-1β Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages.

scientific article published on 3 February 2015

Pyruvate kinase M2 regulates Hif-1α activity and IL-1β induction and is a critical determinant of the warburg effect in LPS-activated macrophages

scientific article published on January 2015

QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis

scientific article published on 01 January 2021

RNA interference screen for human genes associated with West Nile virus infection

scientific article (publication date: 11 September 2008)

RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy

scientific article

Rassf family of tumor suppressor polypeptides.

scientific article published on 17 December 2008

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.

scientific article

Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection

scientific article published on 24 March 2013

Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas ⬇️

scientific article published on May 13, 2011

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

scientific journal article

Regulation of monocyte functional heterogeneity by miR-146a and Relb

scientific article published in April 2012

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease.

scientific article published on April 2017

Reverse metabolomics for the discovery of chemical structures from humans

Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions

scholarly article

Role of Autophagy in the Maintenance of Intestinal Homeostasis

scientific article

Role of tumor necrosis factor receptor 2 (TNFR2) in colonic epithelial hyperplasia and chronic intestinal inflammation in mice

scientific article

SIKs control osteocyte responses to parathyroid hormone

scientific article published on 19 October 2016

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects

scientific article published in PLoS ONE

SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn's disease

scientific article

SNPping away at the pathogenesis of Crohn's disease

scientific article published on 01 January 2008

SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter

scientific journal article

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential

scientific article published on 24 August 2018

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential: (Trends Endocrinol. Metab. 29, 723-735, 2018)

scientific article published on 02 March 2019

Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota.

scientific article published on 24 May 2017

Selective modulation of autophagy, innate immunity, and adaptive immunity by small molecules

scientific article

Sex-Specific Regulation of Inflammation and Metabolic Syndrome in Obesity

scientific article published on 28 May 2020

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing

scientific article published on 19 May 2016

Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets

scientific article published on 02 November 2018

Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions

scientific article published on 26 March 2021

Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses

scientific article

Small-molecule control of cytokine function: new opportunities for treating immune disorders

scientific article

Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics

scientific article published on 20 July 2015

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease

scientific article

Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells

scientific article

Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells.

scientific article published on 14 August 2017

Sorting nexin 5 mediates virus-induced autophagy and immunity

scientific article published on 16 December 2020

Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity

scientific article published on 12 February 2019

Spinophilin and the immune synapse

scientific article published on 14 April 2008

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

scientific article published in February 2018

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

article

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes

scientific article published on 17 February 2016

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages

scientific article published on 21 September 2016

Systems immunology reveals markers of susceptibility to West Nile virus infection

scientific article

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

scientific article published on 01 November 2018

TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41

scientific article published on 01 November 2020

TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation

scientific article published in December 2016

Targeting innate immunity for tuberculosis vaccination

scientific article published on 01 September 2019

Temporal development of the gut microbiome in early childhood from the TEDDY study

scientific article published in Nature

Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses to Candida albicans

scientific article published on 22 April 2019

The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response

January 2019 scholarly article in eLife

The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors

scientific article

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

scholarly article published by Päivi Pöhö in 2016

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids

scientific article published on 10 September 2015

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

scientific article published on 21 August 2020

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus

scientific article

The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular Salmonella Typhimurium

scientific article

The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells.

scholarly article

The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections

scientific article published on 13 January 2015

The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).

scientific article

The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.

scientific article published on 08 June 2016

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense

scientific article published on 14 December 2016

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense

scientific article published in September 2017

The causes and consequences of variation in human cytokine production in health

article

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools

scholarly article by Peggy S Lai et al published June 2018 in The Journal of Allergy and Clinical Immunology

The cytoskeletal scaffold Shank3 is recruited to pathogen-induced actin rearrangements

scientific article published on 14 April 2009

The dichotomous pattern of IL-12r and IL-23R expression elucidates the role of IL-12 and IL-23 in inflammation

scientific article

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes

scientific article published on 5 February 2015

The effect of host genetics on the gut microbiome

scientific article published on 03 October 2016

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study

scientific article published in Nature

The influence of the gut microbiome on BCG-induced trained immunity

scientific article published in 2021

The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells

scientific article published on 22 May 2015

The microbiome in inflammatory bowel disease: current status and the future ahead

scientific article

The treatment-naive microbiome in new-onset Crohn's disease

scientific article

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships

scientific article published on 01 August 2019

Trained immunity, tolerance, priming and differentiation: distinct immunological processes

scientific article published on 08 December 2020

Trained immunity: A program of innate immune memory in health and disease.

scientific article

Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo

scientific article published on 24 October 2017

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

scientific article published on 01 October 2019

Transforming growth factor-beta mediates intestinal healing and susceptibility to injury in vitro and in vivo through epithelial cells

scientific article published on February 2003

Tribbles 2 (Trib2) is a novel regulator of toll-like receptor 5 signaling ⬇️

scientific article published on January 23, 2012

USP15 Deubiquitinates CARD9 to Downregulate C-Type Lectin Receptor-Mediated Signaling

scientific article published on 22 October 2020

Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation

scientific article published on October 2015

Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection

scientific article

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response

scientific article published in Nature Communications

Understanding human immune function using the resources from the Human Functional Genomics Project

scientific article published on August 2016

Use of an Optical Trap for Study of Host-Pathogen Interactions for Dynamic Live Cell Imaging ⬇️

scientific article published on July 28, 2011

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

scientific article

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

scientific article published on 01 June 2016

Vav proteins control MyD88-dependent oxidative burst

scientific article published on 7 December 2006

Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

scientific article published on 28 October 2016

Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine

scientific article

Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

scientific article published on 22 November 2016

Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD

scientific article published on 10 July 2020

Wiskott Aldrich syndrome protein (WASP) and N-WASP are critical for T cell development.

scholarly article

Without Adaptive Immunity, There's a Cost to Responding STAT

scientific article published on 01 April 2018

Wnt signaling regulates mitochondrial physiology and insulin sensitivity

scientific journal article

mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity.

scientific article

p40 phox -Deficient Mice Exhibit Impaired Bacterial Clearance and Enhanced Pro-inflammatory Responses during Salmonella enterica serovar Typhimurium Infection

scientific article published on 9 October 2017

p40phox expression regulates neutrophil recruitment and function during the resolution phase of intestinal inflammation.

scientific article published on 22 August 2012

αv Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells

scientific article published on 11 March 2016

ω-6 Polyunsaturated fatty acids extend life span through the activation of autophagy

scientific article published on 7 February 2013

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