The IBD interactome: an integrated view of aetiology, pathogenesis and therapy

Serologic microbial associated markers can predict Crohn's disease behaviour years before disease diagnosis

(2016) R. S. Choung et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

(2016) Romain Banchereau et al.   CELL

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility

(2016) Byong Duk Ye et al.   Expert Review of Clinical Immunology

Electronic Sorting of Immune Cell Subpopulations Based on Highly Plastic Genes

(2016) Pingzhang Wang et al.   JOURNAL OF IMMUNOLOGY

Environmental Immunology: Lessons Learned from Exposure to a Select Panel of Immunotoxicants

(2016) Joanna M. Kreitinger et al.   JOURNAL OF IMMUNOLOGY

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

(2016) David Ellinghaus et al.   NATURE GENETICS

The cellular composition of the human immune system is shaped by age and cohabitation

(2016) Edward J Carr et al.   NATURE IMMUNOLOGY

Genomic Classification and Prognosis in Acute Myeloid Leukemia

(2016) Elli Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

Gene-environment interplay

(2016) J. Berg   SCIENCE

Writ large: Genomic dissection of the effect of cellular environment on immune response

(2016) N. Yosef et al.   SCIENCE

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

(2016) Alexandra Zhernakova et al.   SCIENCE

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

(2016) H. Chu et al.   SCIENCE

Exposing the exposures responsible for type 2 diabetes and obesity

(2016) P. W. Franks et al.   SCIENCE

Transgenerational inheritance: Models and mechanisms of non-DNA sequence-based inheritance

(2016) E. A. Miska et al.   SCIENCE

Going global by adapting local: A review of recent human adaptation

(2016) S. Fan et al.   SCIENCE

Endophenotype Network Models: Common Core of Complex Diseases

(2016) Susan Dina Ghiassian et al.   Scientific Reports

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

(2015) Jung Hoon Woo et al.   CELL

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

MicroRNA214 Is Associated With Progression of Ulcerative Colitis, and Inhibition Reduces Development of Colitis and Colitis-Associated Cancer in Mice

(2015) Christos Polytarchou et al.   GASTROENTEROLOGY

Genetics of Inflammatory Bowel Diseases

(2015) Dermot P.B. McGovern et al.   GASTROENTEROLOGY

Exposome in IBD

(2015) Gerhard Rogler et al.   INFLAMMATORY BOWEL DISEASES

A MicroRNA Signature in Pediatric Ulcerative Colitis

(2015) Georgios Koukos et al.   INFLAMMATORY BOWEL DISEASES

Beyond the genome

(2015)   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6

(2015) Qian Zhang et al.   NATURE

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

Therapeutic genome editing: prospects and challenges

(2015) David Benjamin Turitz Cox et al.   NATURE MEDICINE

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Immunopathogenesis of IBD: current state of the art

(2015) Heitor S. P. de Souza et al.   Nature Reviews Gastroenterology & Hepatology

Multiple Molecular Data Sets and the Classification of Adult Diffuse Gliomas

(2015) David W. Ellison   NEW ENGLAND JOURNAL OF MEDICINE

A Bronchial Genomic Classifier for the Diagnostic Evaluation of Lung Cancer

(2015) Gerard A. Silvestri et al.   NEW ENGLAND JOURNAL OF MEDICINE

Precision Medicine — Personalized, Problematic, and Promising

(2015) J. Larry Jameson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

(2015) Chen Davidovich et al.   RNA

CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks

(2014) M. A. Moni et al.   BIOINFORMATICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Systems biology in inflammatory bowel diseases

(2014) Christos Polytarchou et al.   CURRENT OPINION IN GASTROENTEROLOGY

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

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Tralokinumab for moderate-to-severe UC: a randomised, double-blind, placebo-controlled, phase IIa study

(2014) Silvio Danese et al.   GUT

Two-stage Genome-wide Methylation Profiling in Childhood-onset Crohnʼs Disease Implicates Epigenetic Alterations at the VMP1/MIR21 and HLA Loci

(2014) Alex T. Adams et al.   INFLAMMATORY BOWEL DISEASES

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

iPOP Goes the World: Integrated Personalized Omics Profiling and the Road toward Improved Health Care

(2013) Jennifer Li-Pook-Than et al.   CHEMISTRY & BIOLOGY

Complex diseases require complex therapies

(2013) Ravi Iyengar   EMBO REPORTS

Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine

(2013) Boyko Kabakchiev et al.   GASTROENTEROLOGY

MicroRNA-124 Regulates STAT3 Expression and Is Down-regulated in Colon Tissues of Pediatric Patients With Ulcerative Colitis

(2013) Georgios Koukos et al.   GASTROENTEROLOGY

Beyond Gene Discovery in Inflammatory Bowel Disease: The Emerging Role of Epigenetics

(2013) Nicholas T. Ventham et al.   GASTROENTEROLOGY

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

Personalizing medicine for autoimmune and inflammatory diseases

(2013) Andrew C Chan et al.   NATURE IMMUNOLOGY

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies

(2013) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

Pattern discovery and cancer gene identification in integrated cancer genomic data

(2013) Qianxing Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

iFad: an integrative factor analysis model for drug-pathway association inference†

(2012) Haisu Ma et al.   BIOINFORMATICS

iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data

(2012) Wenting Wang et al.   BIOINFORMATICS

Metformin in early breast cancer: a prospective window of opportunity neoadjuvant study

(2012) Saroj Niraula et al.   BREAST CANCER RESEARCH AND TREATMENT

Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations

(2012) Núria Planell et al.   GUT

Secukinumab, a human anti-IL-17A monoclonal antibody, for moderate to severe Crohn's disease: unexpected results of a randomised, double-blind placebo-controlled trial

(2012) Wolfgang Hueber et al.   GUT

Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy

(2012) Natasha S. Stephens et al.   Journal of Crohns & Colitis

Quantitative Metabolomic Profiling of Serum, Plasma, and Urine by 1H NMR Spectroscopy Discriminates between Patients with Inflammatory Bowel Disease and Healthy Individuals

(2012) Rudolf Schicho et al.   JOURNAL OF PROTEOME RESEARCH

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Integrative Subtype Discovery in Glioblastoma Using iCluster

(2012) Ronglai Shen et al.   PLoS One

Abundant Pleiotropy in Human Complex Diseases and Traits

(2011) Shanya Sivakumaran et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2011) Thaddeus S. Stappenbeck et al.   Autophagy

Metformin Decreases the Dose of Chemotherapy for Prolonging Tumor Remission in Mouse Xenografts Involving Multiple Cancer Cell Types

(2011) D. Iliopoulos et al.   CANCER RESEARCH

DNA methylation of colon mucosa in ulcerative colitis patients: Correlation with inflammatory status

(2011) Shunsuke Saito et al.   INFLAMMATORY BOWEL DISEASES

Genome-wide methylation profiling in Crohnʼs disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway

(2011) Elaine R. Nimmo et al.   INFLAMMATORY BOWEL DISEASES

Metabolomics of Fecal Extracts Detects Altered Metabolic Activity of Gut Microbiota in Ulcerative Colitis and Irritable Bowel Syndrome

(2011) Gwénaëlle Le Gall et al.   JOURNAL OF PROTEOME RESEARCH

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Genomics Is Not Enough

(2011) A. Chakravarti   SCIENCE

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

(2010) Jing Gao et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Proteomic profiling of mucosal and submucosal colonic tissues yields protein signatures that differentiate the inflammatory colitides

(2010) Amosy E. MʼKoma et al.   INFLAMMATORY BOWEL DISEASES

Upregulation of DNA Methyltransferase-Mediated Gene Silencing, Anchorage-Independent Growth, and Migration of Colon Cancer Cells by Interleukin-6

(2010) E. Foran et al.   MOLECULAR CANCER RESEARCH

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

(2009) Uma T Shankavaram et al.   BMC GENOMICS

Metformin Selectively Targets Cancer Stem Cells, and Acts Together with Chemotherapy to Block Tumor Growth and Prolong Remission

(2009) H. A. Hirsch et al.   CANCER RESEARCH

Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor

(2009) Erik-Oliver Glocker et al.   NEW ENGLAND JOURNAL OF MEDICINE

OmicsViz: Cytoscape plug-in for visualizing omics data across species

(2008) T. Xia et al.   BIOINFORMATICS

Proteomics for prediction and characterization of response to infliximab in Crohn's disease: A pilot study

(2008) Marie-Alice Meuwis et al.   CLINICAL BIOCHEMISTRY

MicroRNAs Are Differentially Expressed in Ulcerative Colitis and Alter Expression of Macrophage Inflammatory Peptide-2α

(2008) Feng Wu et al.   GASTROENTEROLOGY

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

(2008) Zoltán Kutalik et al.   NATURE BIOTECHNOLOGY

From Genotype to Phenotype: Systems Biology Meets Natural Variation

(2008) P. N. Benfey et al.   SCIENCE