Marton L. Olbei

The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut

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.

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

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

Cytokine interaction networks, not individual cytokines, drive anti-TNF response in Crohn's disease

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.

SalmonAct Deciphers Transcription Factor Regulatory Activity in Salmonella Transcriptomics

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

Decoding Cytokine Networks in Ulcerative Colitis to Identify Pathogenic Mechanisms and Therapeutic Targets

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

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.

mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction

mulea provides an R package for enrichment analysis across multiple ontologies with empirical FDR correction to address limitations in traditional gene set enrichment methods.

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

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

Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

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

CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases

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.

Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection

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.

Integrated intra- and intercellular signaling knowledge for multicelullar omics analysis

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: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

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.

ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins

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

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches

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.