Balázs Bohár

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.

Epithelial regulatory networks link non-coding genetic variation to clinical heterogeneity in ulcerative colitis

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

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome

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

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.

Decoding Non-coding SNPs: Systems Genomics Modelling Dissects the Heterogeneity of IBD

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: 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.

Pathogen genomic surveillance as a scalable framework for precision phage therapy

This paper develops a scalable framework for precision phage therapy by combining genomic surveillance and phage typing to target carbapenem-resistant Acinetobacter baumannii.

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.

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.

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions

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.