Tamas Douglas Korcsmaros

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

This paper identifies a microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state linked to mucosal inflammation and treatment resistance in ulcerative colitis.

The paper identifies a stromal remodelling programme in ulcerative colitis patients who failed prior anti-TNF therapy, linking it to MAPK/EGFR signalling and suggesting MEK/EGFR inhibitors as potential treatments.

The paper identifies cytokine interaction networks, not individual cytokines, as the driver of anti-TNF non-response in Crohn's disease using single-cell RNA sequencing data.

This paper identifies non-coding SNPs affecting epithelial regulatory networks in UC and links them to clinical outcomes using iSNP analysis.

OmniPath Metabo integrates metabolomics data with prior knowledge to enable mechanistic analysis of the metabolome through harmonized databases and network construction.

SalmonAct infers transcription factor activities in Salmonella using prior knowledge, aiding in interpreting high-dimensional transcriptomic data and uncovering regulatory mechanisms.

The paper maps cytokine interaction networks in ulcerative colitis to uncover novel pathogenic mechanisms and therapeutic targets.

The paper investigates how antibiotic resistance affects the MexT regulatory switch in Pseudomonas aeruginosa, leading to phenotypic plasticity in virulence and antibiotic resistance.

The paper models the impact of non-coding SNPs on gene regulatory networks in IBD to stratify patients based on gene dysregulation and therapeutic response.

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.

This study shows that PYK2 and FAK regulate breast cancer metastasis through distinct mechanisms, with PYK2 affecting motility and FAK reducing tumor size and metastasis.

AutophagyNet is an updated database providing curated interactions and annotations for autophagy proteins, enabling analysis of autophagy regulation across different contexts.

This study shows that extracellular vesicles from Bacteroides thetaiotaomicron affect host immune pathways differently in various cell types and disease states, with implications for IBD therapy.

SalmoNet2 provides an updated multi-layered network resource for 20 Salmonella strains, enhancing strain comparisons through protein-protein, transcriptional regulatory, and metabolic interactions.

CytokineLink maps cytokine interactions to analyze immune responses in inflammatory and infectious diseases, revealing rewiring in ulcerative colitis and cytokine storm patterns in COVID-19.

This study uses single-cell RNA-seq data to analyze how SARS-CoV-2 infection alters intestinal epithelial-immune cell interactions and identifies potential drug targets and repurposing strategies for COVID-19.

The paper integrates intra- and intercellular signaling knowledge into a database for multicellular omics analysis, demonstrating its application to SARS-CoV-2 infection and ulcerative colitis.

ViralLink is a systems biology workflow that reconstructs and analyzes intracellular signaling networks affected by viruses, using transcriptomics data to identify key pathways and proteins in the cellular response to infection.

The paper identifies distinct regulatory mechanisms and functions of ULK1 and ULK2, showing they are less redundant than previously thought.

MicrobioLink integrates microbial-host protein interactions with host networks to predict functional effects on cellular processes using network diffusion, applied to Crohn's disease gut metaproteomic data.

The paper uses transcriptomics and network analysis to study regulatory networks in Paneth and goblet cell enriched gut organoids, identifying key regulators and their links to inflammatory bowel disease.

This paper introduces iSNP, a workflow to identify patient-specific pathogenic pathways in ulcerative colitis by integrating SNP profiles with regulatory networks.

This study shows that antibiotics disrupt the gut microbiota, leading to faster breast tumour growth and metabolic changes in mice.

The paper introduces CausalTAB, an updated format for representing causal signaling interactions, enhancing the precision and coverage of signaling network modeling.

The paper integrates proteomic and transcriptomic data from intestinal organoids to identify autophagy-dependent processes in Paneth cells, showing that autophagy impairment affects protein abundance and key cellular functions.