Simon J. van Heeringen

The paper integrates single cell transcriptomics and chromatin accessibility data to uncover the regulatory logic of planarian stem cell differentiation, validating predictions with TF knockdown experiments.

The paper identifies gene regulatory differences between primary human hepatocytes and organoid-derived hepatocytes using integrative omics analysis.

This study uses multi-omics to show ONECUT2 restricts M cell differentiation in mouse intestinal organoids by acting downstream of RANK/RANKL signaling.

The paper identifies transcription factor interplay in corneal epithelial fate determination and disease using multi-omics analyses of limbal stem cells and epidermal keratinocytes.

The paper quantifies how chromatin context affects transcription factor binding affinities genome-wide and shows DNA accessibility is the main determinant.

ANANSE predicts key transcription factors in cell fate determination by analyzing enhancer-based regulatory networks across 18 human tissues.

The paper investigates how transcription factor combinations acting on open chromatin influence early cellular heterogeneity and organizer mesendoderm specification in Xenopus during gastrulation.

The paper compares Bayesian Linear Mixed Models and Ridge Regression for motif activity analysis, finding no performance gain in real data due to similar covariance structures.

The paper uses single-cell RNA-seq to identify a reversible epithelial-mesenchymal transition in p63 mutation-induced differentiation defects of human iPSCs.

The paper identifies Brca1, Bard1, and Wdr5 as factors linking DNA damage response to MET during reprogramming, using siRNA screening and colony morphology analysis.

GimmeMotifs bundles motif discovery, scanning, clustering and benchmarking; across 495 ENCODE ChIP-seq peak sets, the best motif from 14 finders out-scored BioProspector, the top single finder, on ROC AUC.

The paper identifies ZMAT2 as a regulator of human epidermal differentiation through interactions with epigenetic modifiers and the pre-spliceosome, highlighting joint control of cell adhesion genes.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.