Jörg Menche

The paper creates a comprehensive reference map of the RAS/RAF/MEK/ERK pathway interactomes and their mutation-driven rewiring, revealing new interactions and disease links.

This paper introduces a Nextflow pipeline to evaluate disease module detection methods, showing variability in results due to method, network, and seed differences.

reComBat-seq removes batch effects in transcriptomics data while preserving count data structure and compatibility with downstream analyses.

The paper identifies UBR4, UBR5, and HUWE1 as E3 ligases that degrade cancer-associated APOBEC3 proteins to prevent genome mutagenesis.

This study shows that tRNA thiolation defects in humans cause proteostasis and tissue homeostasis issues, but mice with similar defects develop normally.

The paper constructs and integrates protein-protein interaction networks across time and tissues to identify protein groups and networks associated with development and aging, and ranks anti-aging drug candidates.

The paper identifies a non-enzymatic role of NUDT5 in repressing purine de novo synthesis by scaffolding PPAT, with implications for cancer treatment and MTHFD1 deficiency.

The paper identifies SAT1 as a marker of skin-specific Treg dysfunction in TH17-mediated inflammation and shows targeting SSAT can rescue Treg function in a mouse model.

This study examines transcriptional changes in murine pneumonia models and identifies potential biomarkers for severe CAP by comparing gene expression with human plasma proteins.

This study profiles mutations in MMR-deficient human cells and identifies new mutational signatures linked to MMR deficiency and cancer development.

CellWhisperer enables chat-based exploration of single-cell RNA-seq data using natural language by connecting transcriptomes with text through multimodal learning.

The paper investigates how changes in large neutral amino acid metabolism during development affect neuronal excitability and survival, finding that Slc7a5 deletion disrupts lipid metabolism and leads to long-term circuit dysfunction.

BioProfiling.jl provides a Julia package for morphological profiling of high-content imaging data, enabling analysis of cell state changes and integration with molecular target networks.

The paper evaluates 24 network-based methods for predicting protein-protein interactions across five interactomes, identifies top-performing methods, and validates their predictions experimentally.

The paper identifies kinase-specific vulnerabilities and resistances in response to DNA damaging agents using kinase-deficient cell lines and validates gene-drug interactions.

The paper integrates existing interactome data with new experimental interactions to identify a COPD-related disease network module.

This study introduces PxEA, a network-based method to identify drugs targeting common pathways across diseases, demonstrating drug repurposing opportunities for autoimmune disorders and comorbid conditions like type 2 diabetes and Alzheimer's disease.

The paper identifies NFATC4 as a key regulator of Type 2 Diabetes genes by analyzing a gene regulatory network in pancreatic islets and linking it to eQTLs and differential expression.