Sophia Müller‐Dott

OmniPath: integrated knowledgebase for multi-omics analysis

OmniPath integrates molecular knowledge from 168 resources to support multi-omics analysis, offering curated data, predictions, and tools for causal modeling across bulk, single-cell, and spatial data.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

This paper evaluates kinase activity inference methods using phosphoproteomics data and benchmarking approaches, finding that curated kinase-substrate libraries significantly impact results.

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

NetworkCommons integrates prior knowledge, omics data, and network inference methods to build and evaluate context-specific biological networks.

Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data

The paper benchmarks methods for inferring gene regulatory networks from multimodal single-cell data and introduces a framework called GRETA to evaluate their performance and limitations.

PhosX: data-driven kinase activity inference from phosphoproteomics experiments

PhosX infers kinase activity changes from phosphoproteomics data using substrate sequence specificity, outperforming existing methods without requiring prior kinase-substrate knowledge.

Evaluating signaling pathway inference from kinase-substrate interactions and phosphoproteomics data

The paper evaluates methods for inferring kinase-driven signaling pathways using phosphoproteomics data and kinase-substrate networks, finding that literature-curated networks with network propagation best recover ground truth interactions.

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities

CollecTRI-derived signed regulons, spanning 1,183 transcription factors (TFs) and 45,856 TF-gene links, outperform DoRothEA, ChEA3, RegNetwork and Pathway Commons at identifying perturbed TFs in KnockTF data.

decoupleR: Ensemble of computational methods to infer biological activities from omics data

decoupleR evaluates methods for inferring biological activities from omics data, finding simple linear models and consensus scores perform best in perturbation experiments.

GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.