Wolfgang K. Huber

Time-resolved single-cell screening reveals the dynamic regulatory architecture of human cardiogenesis

This study uses time-resolved single-cell CRISPR screening and a multiome atlas to uncover dynamic gene regulatory networks in human cardiogenesis, identifying stage-specific regulators and CHD-linked gene functions.

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data

The paper introduces spatialproteomics, a Python toolbox for analyzing highly multiplexed fluorescence images, demonstrating its use on lymph node and lymphoma data.

Proliferation and differentiation of intestinal stem cells depends on the zinc finger transcription factor BCL11/Chronophage

This study identifies Cph as a key regulator of intestinal stem cell proliferation and differentiation, showing its role in maintaining ISC and EE populations and remodeling progenitor transcriptomes.

Cancer pathway connectivity resolved by drug perturbation and RNA sequencing

The paper uses drug perturbations and RNA sequencing to map pathway connectivity in CLL, showing how genetic aberrations modulate drug responses and pathway interactions.

Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines

The paper benchmarks deep learning models against linear baselines for predicting gene perturbation effects and finds they do not outperform simple models.

Analysis of multi-condition single-cell data with latent embedding multivariate regression

LEMUR identifies gene expression changes across conditions using a continuous latent space, improving analysis of multi-condition single-cell RNA-seq data.

Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data

SOFA identifies novel sources of variation in multi-omic data by incorporating known covariates and focusing on unexplained factors.

Feature selection by replicate reproducibility and non-redundancy

The paper introduces RNR, a feature selection algorithm that prioritizes reproducibility across replicates and non-redundancy, applied to microscopy and proteomics data.

Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq

This paper introduces SDR-seq, a multiomic scDNA-scRNA-seq method to link genotypes with gene expression, showing variants affect expression in iPSCs and B-cell lymphoma.

SpatialData: an open and universal data framework for spatial omics

SpatialData, a Zarr/OME-NGFF-based format plus Python library, unifies images, labels, points, shapes and tables across spatial omics platforms with coordinate alignment, lazy loading and cross-modal aggregation.

Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq

DEWSeq improves eCLIP data analysis by increasing the detection of RNA-binding protein binding sites and their functional elements.

MsQuality - an interoperable open-source packagefor the calculation of standardized quality metricsof mass spectrometry data

MsQuality calculates 40 standardized quality metrics for mass spectrometry data using the mzQC vocabulary to improve data quality assessment and comparability across datasets.

Comparison of Transformations for Single-Cell RNA-Seq Data

The paper compares transformation methods for single-cell RNA-seq data and finds that a simple log transformation with pseudo-count and PCA performs as well as more complex approaches.

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

The paper develops a method to infer tumor-specific molecular dependencies by integrating drug response assays with protein-drug affinity profiles, identifying known and novel dependencies in cancer types.

MatrixQCvis: shiny-based interactive data quality exploration for omics data

MatrixQCvis provides interactive visualization of data quality metrics for omics data using R's shiny framework, facilitating quality assessment and integration into existing workflows.

Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia

This study identifies subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia using RNA-sequencing and genomic data.

glmGamPoi: Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data

The paper introduces a new R package for efficiently fitting Gamma-Poisson models to single-cell RNA-seq data, improving speed and accuracy over existing methods.

Computational analysis of ligand dose range thermal proteome profiles

The paper develops a statistical method to analyze thermal proteome profiles and identifies off-target drug interactions in epigenetic drugs.

Pairwise genetic interactions modulate lipid plasma levels and cellular uptake

The paper identifies genetic and RNAi-based pairwise interactions between lipid-related genes that modulate plasma and cellular lipid levels, suggesting potential drug target pairs for lipid-lowering therapies.

Developmental gene expression differences between humans and mammalian models

The paper identifies developmental gene expression differences between humans and mammalian models, finding that half of human genes differ from their mouse orthologs in temporal trajectories, particularly for disease-related genes.

Single cell 3'UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism

The paper analyzes 3'UTR changes during neuronal differentiation and in ASD, finding longer 3UTRs in ASD patients and a role for CPEB4 and APLP1 in APA regulation.

A user's guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

This study shows that reduced proteasome activity in aging brains leads to ribosome stoichiometry loss and aggregation, increasing mortality risk in killifish.

Modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection

The paper develops a statistical test to improve hit detection in CRISPR screens by accounting for asymmetric gRNA abundance changes, allowing smaller experiment sizes.

Orchestrating Single-Cell Analysis with Bioconductor

This paper provides an overview of single-cell RNA sequencing analysis using Bioconductor, highlighting its tools and methods for handling high-dimensional data.

Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF

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.

Non-Parametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-Binding Proteins

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

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP

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.

The small non-coding vault RNA1-1 acts as a riboregulator of autophagy

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