Martina Kutmon

Downregulation of Trpv4 and Klf2 in brain microvessels is associated with the progression of neurovascular dysfunction and cognitive impairment in a model of heart failure with preserved ejection fraction.

This study shows that reduced Trpv4 and Klf2 in brain microvessels correlates with neurovascular dysfunction and cognitive decline in an HFpEF rat model.

GSEA and the coexpression network approach identify novel pathway connections of molecular processes affected in Porto-sinusoidal vascular disease.

The paper uses GSEA and WGCNA to identify dysregulated pathways in Porto-sinusoidal vascular disease, revealing immune, signaling, and metabolic dysfunctions.

User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams

The paper describes the development and evaluation of an agentic framework using LLMs to explore molecular interaction maps through user-driven prototyping and testing.

The guardians of mitochondrial dynamics: a novel role for intermediate filament proteins

The paper identifies ITPRIPL2 as a novel protein involved in mitochondrial dynamics through computational interaction analysis and shows its role in vimentin-associated intermediate filament structure.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

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

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

The paper semantifies and harmonizes biological pathway diagrams from WikiPathways to enable semantic querying and integration with linked data.

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.

History of rare diseases and their genetic causes - a data driven approach

This paper provides a dataset linking rare monogenic diseases to their causative genes, revealing the timeline of discoveries and their relation to methodological and database advancements.

A protocol for adding knowledge to Wikidata, a case report

The paper describes a protocol for enhancing Wikidata with structured knowledge using Shape Expressions, demonstrating its application to SARS-CoV-2 and other coronaviruses.

25 Years of Pathway Figures

The paper identifies and analyzes pathway figures from 1995 to 2019, extracting human gene content and disease terms to create a resource for pathway knowledge.

ComMet: A method for comparing metabolic states in genome-scale metabolic models

ComMet is a method for analyzing and comparing metabolic flux states in genome-scale models, identifying distinct network modules and differences in human adipocyte metabolism under varying amino acid uptake conditions.