Integrating pathways and related knowledge in a multilayer framework
Automatic context-specific network inference.
Analysis pipeline for single-cell RNA sequencing (scRNA-seq) data focused on T cells in COVID-19. Includes scripts and workflows for data processing, visualization, and identifying immune cell signatures and responses. Designed to accelerate reproducible research in immunology and single-cell genomics.
A matrix factorization model for multi-omic data and biological pathways
SpatialTranscriptFormer: A biologically-informed transformer architecture for spatial transcriptomics. Features Quad-Flow Interaction (P↔P, P↔H, H→P, H↔H) and a pathway bottleneck using MSigDB Hallmarks. Integrated with pathology foundation models (CTransPath/Phikon).
Reactome — independent third-party profile of a public API surface, by API Evangelist. Reactome is a free, open-source, curated, and peer-reviewed biological pathway database. It provides comprehensive pathway data covering human biology and orthologous reactions for over 14 non-human species including mouse, rat, yeast, and fruit fly.
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