Falk Schreiber

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.

Brainacle: Interactive delineation and quantification of anatomical structures with virtual reality

Brainacle enables interactive delineation and quantification of anatomical structures in 3D data using virtual reality, validated on brain regions of African cichlid fish.

MeTrEx: Membrane Trajectory Explorer

MeTrEx is a Python-based software for analyzing MD simulation data, focusing on ligand-membrane interactions, with tools for visualization, analysis, and comparative studies.

The (α, β)-k Boolean Signatures of Molecular Toxicity: Microcystin as a Case Study

The paper applies (α, β)-k feature sets to identify toxicity-related substructures in Microcystin congeners using extended connectivity fingerprints.

Creating Aesthetically Pleasing SBGN Visualisations for Presentation and Exploration

The paper provides layout guidelines and workflows for creating aesthetically pleasing SBGN maps using SBGN-ED for presentation and exploration.

Automated Integration of Multi-Slice Spatial Transcriptomics Data in 2D and 3D

VR-Omics automates integration of multi-slice spatial transcriptomics data in 2D and 3D, revealing dysregulated metabolic networks in paediatric cardiac rhabdomyomas.

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.

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.