An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

CCR5 expression in inflammatory bowel disease and its correlation with inflammatory cells and β-arrestin2 expression

(2017) Xiaoyan Ye et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Proteomic profiling identifies markers for inflammation-related tumor–fibroblast interaction

(2017) Daniel Drev et al.   Clinical Proteomics

Exome Analysis of Rare and Common Variants within the NOD Signaling Pathway

(2017) Gaia Andreoletti et al.   Scientific Reports

E3 Ubiquitin ligase RNF183 Is a Novel Regulator in Inflammatory Bowel Disease

(2016) Qiao Yu et al.   Journal of Crohns & Colitis

The Comparative Toxicogenomics Database: update 2017

(2016) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis

(2016) Mari H. Tervaniemi et al.   Scientific Reports

Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls

(2016) Carolin Knecht et al.   Scientific Reports

Role of Protein Tyrosine Phosphatases in Regulating the Immune System

(2015) Marianne R. Spalinger et al.   INFLAMMATORY BOWEL DISEASES

Epithelial IL-1R2 acts as a homeostatic regulator during remission of ulcerative colitis

(2015) R Mora-Buch et al.   Mucosal Immunology

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Role of necroptosis in the pathogenesis of solid organ injury

(2015) H Zhao et al.   Cell Death & Disease

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

(2014) Alvin Leung et al.   BIOINFORMATICS

Predicting disease associations via biological network analysis

(2014) Kai Sun et al.   BMC BIOINFORMATICS

The Diagnostic Approach to Monogenic Very Early Onset Inflammatory Bowel Disease

(2014) Holm H. Uhlig et al.   GASTROENTEROLOGY

The Transcription Factor IRF8 Activates Integrin-Mediated TGF-β Signaling and Promotes Neuroinflammation

(2014) Yuko Yoshida et al.   IMMUNITY

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

Chemokines in Cancer

(2014) M. T. Chow et al.   Cancer Immunology Research

Polyglucosan body myopathy caused by defective ubiquitin ligase RBCK1

(2013) Johanna Nilsson et al.   ANNALS OF NEUROLOGY

Up-regulation and Pre-activation of TRAF3 and TRAF5 in Inflammatory Bowel Disease

(2013) Jun Shen et al.   International Journal of Medical Sciences

Gene expression of tumor necrosis factor receptor associated-factor (TRAF)-1 and TRAF-2 in inflammatory bowel disease

(2013) Yu Qi Qiao et al.   Journal of Digestive Diseases

Discovering disease-disease associations by fusing systems-level molecular data

(2013) Marinka Žitnik et al.   Scientific Reports

Common and specific signatures of gene expression and protein–protein interactions in autoimmune diseases

(2012) T Tuller et al.   GENES AND IMMUNITY

The Core Diseasome

(2012) Vuk Janjić et al.   Molecular BioSystems

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

(2012) Luke Jostins et al.   NATURE

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Analysis of IL12B Gene Variants in Inflammatory Bowel Disease

(2012) Jürgen Glas et al.   PLoS One

Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions

(2011) Tamir Tuller et al.   HUMAN MOLECULAR GENETICS

Pathway-based analysis of GWAS datasets: effective but caution required

(2011) Peilin Jia et al.   INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY

Finding disease similarity based on implicit semantic similarity

(2011) Sachin Mathur et al.   JOURNAL OF BIOMEDICAL INFORMATICS

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

(2011) Carl A Anderson et al.   NATURE GENETICS

Dominating Biological Networks

(2011) Tijana Milenković et al.   PLoS One

Prediction of Disease and Phenotype Associations from Genome-Wide Association Studies

(2011) Stephanie N. Lewis et al.   PLoS One

Regulation of induced colonic inflammation by Lactobacillus acidophilus deficient in lipoteichoic acid

(2011) M. Mohamadzadeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased expression of chemokine receptor CCR3 and its ligands in ulcerative colitis: the role of colonic epithelial cells in in vitro studies

(2010) P. Manousou et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

A multivariate regression approach to association analysis of a quantitative trait network

(2009) S. Kim et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Identifying disease associations via genome-wide association studies

(2009) Wenhui Huang et al.   BMC BIOINFORMATICS

Platelet-activating factor-induced NF-κB activation and IL-8 production in intestinal epithelial cells are Bcl10-dependent

(2009) Alip Borthakur et al.   INFLAMMATORY BOWEL DISEASES

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

A Pathway-Based View of Human Diseases and Disease Relationships

(2009) Yong Li et al.   PLoS One

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

A navigator for human genome epidemiology

(2008) Wei Yu et al.   NATURE GENETICS

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

(2008) Jeffrey C Barrett et al.   NATURE GENETICS

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA