Wolfgang K. Huber

diffTF quantifies differential transcription factor activity and classifies TFs as activators or repressors using multi-omics data, identifying known and novel TFs in two case studies.

This paper introduces NPARC, a non-parametric method for analyzing thermal proteome profiles to identify drug-binding proteins with improved specificity and sensitivity.

This study quantifies ATP's proteome-wide interactions with protein solubility and thermal stability, revealing concentration-dependent roles in protein structure, complex stability, and phase transitions.

This study identifies vault RNA1-1 as a riboregulator of autophagy by interacting with p62, showing that it modulates autophagic flux.

This study shows that deleting Ncaph2 in mouse hepatocytes does not alter chromatin folding or gene expression, suggesting condensin II's role in interphase may be limited.

MOFA, a sparse Bayesian factor model with mixed likelihoods, separates shared from modality-specific multi-omic variation, recovering IGHV, trisomy 12 and oxidative-stress axes in 200 leukaemia samples.

This study identifies MDM4 as a critical target of 1q gain in TP53wt Burkitt lymphoma, showing its role in evading cell cycle arrest and highlighting its therapeutic potential.

The paper investigates transcript isoform diversity across human tissues and finds that alternative transcription start and termination sites drive most tissue-dependent isoform usage, with splicing playing a minor role.

This study shows that cohesin removal leads to loss of TADs and loops but preserves compartments, revealing two independent modes of chromosome organization.

The paper introduces a method to improve statistical power in multiple testing by weighting hypotheses based on covariates, while controlling the false discovery rate.

FourCSeq identifies specific genomic interactions in 4C sequencing data and detects changes across conditions using statistical methods.

DESeq2 uses empirical Bayes priors to shrink negative binomial dispersions and log fold changes, giving reproducible effect sizes and error-controlled differential expression calls for RNA-seq.

HTSeq provides a Python framework for handling high-throughput sequencing data, including tools for RNA-Seq preprocessing and differential expression analysis.

The paper identifies transcript isoform changes in UQCC and RPL31 associated with SF3B1 mutations in CLL and uveal melanoma, suggesting common molecular effects across cancer types.

The paper uses TCC sequencing to study 3D chromatin organization during neural induction in mouse cells, finding widespread changes in inter-chromosomal contacts and a role for euchromatic domains in pluripotent cells.