Dénes Türei

Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz

The paper introduces MetaProViz, an R package for metabolomics data analysis that integrates prior knowledge to generate mechanistic hypotheses, using kidney cancer data to demonstrate its capabilities.

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.

CROssBARv2: A Unified Computational Framework for Heterogeneous Biomedical Data Representation and LLM-Driven Exploration

CROssBARv2 integrates heterogeneous biomedical data into a knowledge graph with embeddings and LLM-driven tools for predictive modeling and question-answering.

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.

NeKo: a tool for automatic network construction from prior knowledge

NeKo automates biological network construction by integrating molecular interactions from databases, enabling efficient network building for research applications.

Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression

This paper uses time-resolved multi-omics analysis of kidney fibrosis to identify novel mechanisms and validate transcription factors involved in collagen deposition.

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.

Modeling causal signal propagation in multi-omic factor space with COSMOS

The paper introduces COSMOS+ to integrate mechanistic prior knowledge with multi-omics data analysis to generate mechanistic hypotheses about disease resistance mechanisms.

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

MetalinksDB provides a comprehensive database of metabolite-protein interactions, enabling context-specific analysis of metabolite-mediated cell-cell communication.

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.

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.

Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data

The paper compares 15 resources and 6 methods for inferring cell-cell communication from single-cell RNA data, finding significant variation in predicted interactions and biological interpretations.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.

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.

Benchmark and integration of resources for the estimation of human transcription factor activities

The paper benchmarks and integrates TF regulon resources to assess their impact on TF activity estimation in human gene expression data.

Integration of Structured Biological Data Sources using Biological Expression Language

The paper introduces Bio2BEL, a set of Python packages that convert multi-modal biological data into Biological Expression Language for integration and analysis.

SignaFish: a zebrafish-specific signaling pathway resource

SignaFish provides a zebrafish-specific signaling pathway resource built on the SignaLink framework, offering curated and additional interactions for pathway analysis.