Reinhard Schneider

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

This study uses Boolean modeling on PD cohorts to show sex-specific miRNA dysregulation affects mitochondrial biogenesis, mitophagy, and autophagy in Parkinson's disease.

This paper constructs and compares computational disease maps of ulcerative colitis and atopic dermatitis to identify shared and unique molecular mechanisms and potential therapeutic targets.

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

The paper presents the ISD map, an interactive resource modeling molecular mechanisms of psoriasis and atopic dermatitis, and identifies potential therapeutic targets through hypothesis generation.

The paper develops a systems immunotoxicology workflow to model and predict adverse outcomes in immunotoxicology using a molecular interaction model and the MINERVA Platform.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

This study uses Boolean models to analyze Parkinson's disease progression and identifies subtype-specific regulatory modules and biomolecules.

The paper assesses the FAIRness of the MINERVA platform using the RDA FAIR Data Maturity Model, focusing on the Parkinson's Disease Map and the COVID-19 Disease Map.

This study uses Boolean modeling to analyze Parkinson's disease mechanisms, identify drug targets, and simulate treatment responses using the PD-map framework.

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

Arena3Dweb provides an interactive 3D visualization tool for multi-layered networks with clustering, directional connections, and integration capabilities.

COBREXA.jl is a Julia package for scalable constraint-based metabolic modeling, designed for high-performance computing environments and multi-organism community models.

OnTheFly2.0 automates biomedical entity recognition and analysis from documents, revealing inflammatory and senescence pathways in severe COVID-19.

Arena3Dweb provides an interactive 3D web tool for visualizing multilayered networks, supporting drug repurposing and GPCR signaling pathway analysis.

The paper evaluates the reusability and composability of manually-built RAS-RAF-MEK-ERK signaling pathway maps from three databases to improve disease model assembly.

PredictProtein provides protein sequence analysis tools, offering structure and function predictions with updates including deep learning and DNA/RNA/protein binding predictions.

GigaSOM.jl provides a scalable solution for clustering and visualizing large cytometry datasets, achieving high performance with distributed computing.

BioKC provides a collaborative platform for curating and annotating systems biology models using SBML standards.

The paper introduces the Virtual Metabolic Human database, which integrates human and gut microbiome metabolism with nutrition and disease data to support biomedical research.