Anna Niarakis

TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual

TabularQual provides a spreadsheet-based format for annotating logical models, with tools to convert between spreadsheets and SBML-qual, enhancing model reuse and interoperability.

The SjD Map: An interactive pathway tour into Sjogren's disease signalling mechanisms

The paper develops a molecular interaction map of Sjogren's disease using transcriptomic data and literature, integrating pathway analysis and experimental data for therapeutic insights.

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.

Large-scale computational modelling of the M1 and M2 synovial macrophages in Rheumatoid Arthritis

This study develops a computational framework to model M1 and M2 macrophages in RA, identifying potential therapeutic targets through Boolean modeling and gene expression validation.

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

The paper develops a Boolean model of RA-FLS to predict drug synergies and identify therapeutic targets for rheumatoid arthritis.

Hybrid computational modeling highlights reverse Warburg effect in breast cancer-associated fibroblasts

This paper develops a hybrid computational model of breast cancer-associated fibroblasts to identify HIF-1 as a driver of the reverse Warburg effect.

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.

Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach

This paper develops a hybrid model of RASFs integrating signaling, gene regulation, and metabolism to simulate metabolic reprogramming and hypothesize a reverse Warburg effect in RA.

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.

Inference of an integrative, executable network for Rheumatoid Arthritis combining data-driven machine learning approaches and a state-of-the-art mechanistic disease map

This paper integrates machine learning and a mechanistic disease map to infer an executable network for RA, identifying key transcription factors and treatment responses.