Benjamin M. Gyori

MSstatsBioNet integrates differential proteomics results with biomolecular networks to enable mechanistic interpretation of biological changes.

This paper shows that kinase inhibitors commonly target multiple kinases, independent of approval status, and highlights the need for better understanding of their polypharmacology.

The paper quantifies variation in gut microbial metabolism of dietary compounds and identifies compounds specific to few species, proposing a method for synbiotic design.

The paper introduces SeMRA, a tool for integrating biomedical identifier mappings across resources, enabling large-scale data interoperability.

This paper introduces INDRA, a system that uses NLP and probability models to assemble high-quality molecular mechanisms from text and databases, improving accuracy over machine reading alone.

Biomappings predicts and curates missing biomedical identifier mappings between ontologies, providing curated and predicted mappings for use in data integration.

NDEx IQuery provides a tool for network-based gene set analysis using diverse pathways and integrates with existing resources to enhance pathway interpretation.

The paper constructs a database of receptor-ligand pairs and uses single-cell transcriptomics to identify injury-specific neuroimmune interactomes in inflammatory pain.

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

The paper introduces the Bioregistry, an open metaregistry that integrates and expands existing biomedical entity registries to improve interoperability and data reuse.

The paper develops ProtMapper to normalize phosphosite positions from databases and text mining, creating a comprehensive corpus of regulatory annotations.

The paper introduces STonKGs, a Transformer model trained on biomedical text and knowledge graphs, which outperforms single-modality models in classification tasks.

Gilda is a tool that normalizes biomedical entity names using machine-learned disambiguation models and provides a web service for this task.

The paper introduces Biofactoid, a tool that crowdsources structured biological knowledge from authors, enabling efficient human-computer interaction and expanding existing pathway databases.

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.

GeneWalk identifies gene functions relevant to a biological context using network representation learning and validates it on RNA-seq and NET-seq data from human and mouse samples.

The paper analyzes parameter geography in PTM systems to assess robustness, finding that bistability is rare under realistic enzyme mechanisms.

This paper refines the definition of the human kinome, identifies understudied kinases, and highlights their potential as drug targets through differential expression, essentiality, and mutation data.

The paper develops workflows to re-curate and enrich knowledge graphs encoded in Biological Expression Language using automated and manual methods.

FamPlex improves named entity recognition and grounding for protein families and complexes in biomedical text by providing a manually curated resource with hierarchical organization and curated patterns.

The paper introduces INDRA, a tool that converts natural language descriptions of molecular mechanisms into executable computational models of biological networks.