Rick Jansen

Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

Transcriptomic and Metabolomic analyses in Monozygotic and Dizygotic twins.

The paper compares transcriptomic and metabolomic data from monozygotic and dizygotic twins to identify molecular biomarkers of twinning, finding no replicable transcript-level differences but highlighting potential pathways.

Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data

The paper develops interpretable neural networks for multi-omics data to predict smoking status, age, and LDL levels, showing improved performance and generalizability across cohorts.

Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins

This study identifies proteins and genes associated with BMI and its changes in twins, showing shared genetic and environmental factors across proteome, transcriptome, and metabolome layers.

OTTERS: A powerful TWAS framework leveraging summary-level reference data

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

This study identifies 43 genomic loci associated with reproductive success in 785,604 individuals, showing ongoing natural selection at the FADS locus.

Multimodal Data Integration Advances Longitudinal Prediction of the Naturalistic Course of Depression and Reveals a Multimodal Signature of Disease Chronicity

This study uses machine learning to predict 2-year MDD chronicity by integrating proteomics with clinical data, showing improved accuracy over psychiatrists' predictions.

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

The paper uses blood eQTL meta-analysis to explore the polygenic architecture of complex traits, finding that trans-eQTLs are more informative for identifying causal genes than cis-eQTLs.

Alterations in Acylcarnitines, Amines, and Lipids Inform about Mechanism of Action of Citalopram/Escitalopram in Major Depression

The paper uses targeted metabolomics to analyze changes in acylcarnitines, amines, and lipids in response to citalopram/escitalopram treatment in MDD patients, identifying metabolic correlates of treatment response.

A novel Mendelian randomization method identifies causal relationships between gene expression and low-density lipoprotein cholesterol levels.

This paper introduces MR-link, a Mendelian randomization method that identifies causal relationships between gene expression and LDL-C levels, finding 19 causally linked genes including PVRL2.

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference

The paper identifies 818 genes influencing DNA methylation in blood using genetic anchors and causal inference, revealing both transcription factors and non-DNA-binding proteins with regulatory roles.

DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan

This paper identifies DNA methylation sites associated with aggression through a meta-analysis of epigenome-wide studies across different age groups and tissues.

A phenome-wide association and Mendelian Randomisation study of polygenic risk for depression in UK Biobank

This study identifies traits associated with polygenic risk for depression using UK Biobank data and finds causal links between depression risk and brain structure, as well as environmental interactions.

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group

The paper reports epigenome-wide meta-analyses of blood DNA methylation with subcortical brain volumes, identifying significant associations with hippocampal volume and potential biological mechanisms.

Mendelian Randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

This paper introduces TWMR, a Mendelian Randomization method that identifies gene-trait associations by integrating GWAS and eQTL data, revealing 3,913 novel associations across 43 human phenotypes.

RNA-Seq in 296 phased trios provides a high resolution map of genomic imprinting

The paper uses RNA-Seq data from 296 family trios to identify genomic imprinting by analyzing allelic expression and parental haplotypes, finding 45 imprinted genes and one novel imprinted transcript.

Novel DNA methylation sites of glucose and insulin homeostasis: an integrative cross-omics analysis

This study identifies nine novel DNA methylation sites associated with fasting glucose and insulin levels by integrating cross-omics data from multiple cohorts.

Variably methylated regions in the newborn epigenome: environmental, genetic and combined influences

The paper examines how genetic and environmental factors influence DNA methylation at variably methylated regions in neonatal blood, finding that combined effects best explain methylation variability.

Applying polygenic risk scoring for psychiatric disorders to a large family with Bipolar Disorder and Major Depressive Disorder

The paper applies polygenic risk scoring to a large family with bipolar and depressive disorders to study genetic risk patterns and anticipation.

Genome-wide identification of directed gene networks using large-scale population genomics data

The paper identifies 49 gene drivers of downstream transcriptional changes using population genomics data and RNA-sequencing from 3,072 individuals.

Novel susceptibility loci and genetic regulation mechanisms for type 2 diabetes

This study identifies 139 common and 4 rare genetic variants associated with type 2 diabetes through GWAS and integrates gene expression and epigenomic data to highlight potential functional genes and regulatory mechanisms.

Stratified Linkage Disequilibrium Score Regression reveals enrichment of eQTL effects on complex traits is not tissue specific

The paper uses SLDSR to show that eQTL effects on complex traits are not tissue-specific, supporting the use of accessible tissues like blood for eQTL discovery.

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

The paper identifies gene targets for brain-related traits using transcriptomic and methylomic data from blood, finding strong correlations between genetic effects in brain and blood tissues.

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

Genome-wide association meta-analysis of 130,664 major depression cases and 330,470 controls identifies 44 independent risk loci enriched in cortical neurons, conserved mammalian regions, splicing networks, and antidepressant targets.

Novel blood pressure locus and gene discovery using GWAS and expression datasets from blood and the kidney

This study identifies 6 new blood pressure loci and 48 genes involved in BP regulation using GWAS and gene expression data from blood and kidney tissues.

Multivariate Genome-wide and integrated transcriptome and epigenome-wide analyses of the Well-being spectrum.

The paper identifies 63 genetic signals associated with well-being traits using genome-wide analyses and links them to gene expression and methylation in brain tissues.

Integrative approaches for large-scale transcriptome-wide association studies

The paper integrates gene expression and GWAS data to identify novel genes associated with obesity-related traits.