List of works - Ramnik J Xavier

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

scientific article

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

scientific article

Guidelines for the use and interpretation of assays for monitoring autophagy

scientific article

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

scientific article

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

scientific journal article

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

scientific article

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

scientific article

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

scientific article

Genetics and pathogenesis of inflammatory bowel disease

scientific article (publication date: 15 June 2011)

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

scientific article (publication date: 16 April 2012)

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

scientific article (publication date: 13 November 2008)

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

scientific journal article

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

scientific article

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

scientific article

CRISPR-Cas9 knockin mice for genome editing and cancer modeling

scientific article

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

scientific article

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

scientific article published on February 19, 2014

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on September 17, 2012

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

scientific article published on September 2014

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

scientific article

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

scientific article

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

scientific article published on September 2008

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

scientific article

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

scientific article (publication date: 11 September 2008)

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages

scientific article published on 21 September 2016

The effect of host genetics on the gut microbiome

scientific article published on 03 October 2016

Identification of a candidate therapeutic autophagy-inducing peptide

scientific journal article

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

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

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

scientific article

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

scientific article

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

scientific article published on August 2012

The Human Cell Atlas

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

scientific article

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

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

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

scientific article published on 09 May 2016

Proton pump inhibitors affect the gut microbiome

scientific article published on 9 December 2015

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

scientific article published on June 2016

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

scientific article

Identification of a novel Ras-regulated proapoptotic pathway

scientific article (publication date: 19 February 2002)

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

scientific article

List of works by Ramnik J Xavier

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

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

Guidelines for the use and interpretation of assays for monitoring autophagy

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

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

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

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

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

Genetics and pathogenesis of inflammatory bowel disease

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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

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

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

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

CRISPR-Cas9 knockin mice for genome editing and cancer modeling

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

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

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

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

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

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

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

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

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

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

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

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

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

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages

The effect of host genetics on the gut microbiome

Identification of a candidate therapeutic autophagy-inducing peptide

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

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

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

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

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

The Human Cell Atlas

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

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

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

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

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

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

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

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

Proton pump inhibitors affect the gut microbiome

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

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

Identification of a novel Ras-regulated proapoptotic pathway

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