Sjoerd Viktor Beentjes

Seven replicated genomic associations of myalgic encephalomyelitis/chronic fatigue syndrome: a biobank study

Targeted-learning GWAS of 1,268 UK Biobank ME/CFS cases found 176 FDR-significant variants; seven replicated in disjoint UK Biobank or All of Us cohorts.

Morphological profiling of all human and mouse miRNAs in 24M cells

The paper profiles the morphological effects of 2,565 human and 1,900 mouse miRNAs on 24 million cells across five cell lines, finding that 9% and 15% of miRNA mimics significantly alter cell morphology.

Epistatic contributions to human traits via transcription factor mechanisms

The paper identifies epistatic interactions among DNA variants affecting human traits by combining machine learning with experimentally verified transcription factor binding data.

Initial findings from the DecodeME genome-wide association study of myalgic encephalomyelitis/chronic fatigue syndrome

This study conducts a genome-wide association study (GWAS) of ME/CFS, identifying eight genetic loci associated with the disease, suggesting involvement of immune and neurological processes.

Systematic identification of context-dependent gene essentiality in Glioblastoma: The GBM-CoDE platform

The paper identifies context-dependent gene essentiality in GBM using CRISPR screening and develops a platform to link biomarkers to therapeutic targets.

High order expression dependencies finely resolve cryptic states and subtypes in single cell data

Stator identifies cell types, subtypes, and states in single-cell data by analyzing higher-order gene expression dependencies, revealing cryptic states and subtypes not captured by proximity-based clustering.

Dual site proteomic analyses reveal potential drug targets for cardiovascular disease

This paper uses Mendelian randomisation to identify potential drug targets for cardiovascular disease by analysing protein levels in plasma and PBMCs from large cohorts.

Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering

The paper investigates oncogene expression from extrachromosomal DNA in glioblastoma and finds that copy number amplification, not spatial clustering, drives high transcriptional output.

Dispensing with unnecessary assumptions in population genetics analysis

TarGene is a statistical workflow that estimates effect sizes and epistatic interactions without parametric assumptions, validated on UK Biobank data and showing genetic non-linearity and epistasis.