Tommaso Andreani

AXIS converts published QSP models and their companion publications into executable simulation configurations by integrating entity grounding, scenario extraction, and parameter assignment.

Talk2Biomodels provides an AI platform for interacting with biological models using natural language, enhancing accessibility and FAIR principles.

The paper investigates harmonin expression and localization in human retinas to understand USH1C pathophysiology and potential gene therapy approaches.

This paper benchmarks six computational methods for reconstructing B-cell receptors from scRNA-seq data, finding BALDR, BASIC, and BRACER perform best overall.

SIMPA imputes missing regions in scChIP-seq data using machine learning models trained on bulk data, improving clustering and pathway gene identification while enabling model interpretation.

The paper develops a method to identify cell-specific variable regions in ChIP-seq data by integrating replicated experiments, finding regions with variable occupancy that may have functional significance.

The paper benchmarks 10 scATAC-seq analysis methods on synthetic and real datasets, finding SnapATAC, Cusanovich2018, and cisTopic perform best in separating cell populations across varying coverage and noise levels.