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BiCoN: Network-constrained biclustering of patients and omics data

Unsupervised learning approaches are frequently employed to stratify patients into clinically relevant subgroups and to identify biomarkers such as disease-associated genes. However, clustering and biclustering techniques are oblivious to the …

DIGGER: exploring the functional role of alternative splicing in protein interactions

Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of …

MiRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice

The transcriptome of non-coding RNA (ncRNA) species is increasingly focused in Alzheimer’s disease (AD) research. NcRNAs comprise, among others, transfer RNAs, long non-coding RNAs and microRNAs (miRs), each with their own specific biological …

EpiGEN: an epistasis simulation pipeline

**Summary** Simulated data is crucial for evaluating epistasis detection tools in genome-wide association studies. Existing simulators are limited, as they do not account for linkage disequilibrium (LD), support limited interaction models of single …

Genetic Studies of Urinary Metabolites Illuminate Mechanisms of Detoxification and Excretion in Humans

The kidneys integrate information from continuous systemic processes related to the absorption, distribution, metabolism and excretion (ADME) of metabolites. To identify underlying molecular mechanisms, we performed genome-wide association studies of …

Impaired Exocrine Pancreatic Function Associates With Changes in Intestinal Microbiota Composition and Diversity

Changes in intestinal microbiome composition are associated with inflammatory, metabolic, and malignant disorders. We studied how exocrine pancreatic function affects intestinal microbiota. We performed 16S ribosomal RNA gene sequencing analysis of …

Mendelian randomization evaluation of causal effects of fibrinogen on incident coronary heart disease.

Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

C-reactive protein (CRP) is a sensitive biomarker of chronic low-grade inflammation and is associated with multiple complex diseases. The genetic determinants of chronic inflammation remain largely unknown, and the causal role of CRP in several …

A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome

Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based …

Empowering thyroid hormone research in human subjects using OMICs technologies

OMICs subsume different physiological layers including the genome, transcriptome, proteome and metabolome. Recent advances in analytical techniques allow for the exhaustive determination of biomolecules in all OMICs levels from less invasive human …