Alexander R. Pico

The paper identifies genetic regulators of neuronal survival across different metabolic environments using CRISPRi screens in human neurons.

This paper introduces PFOCR, a pathway database derived from published figures, and demonstrates its utility in cancer subtype and grade prediction.

NDEx IQuery provides a tool for network-based gene set analysis using diverse pathways and integrates with existing resources to enhance pathway interpretation.

The paper identifies and analyzes pathway figures from 1995 to 2019, extracting human gene content and disease terms to create a resource for pathway knowledge.

The paper describes Wikidata as a FAIR knowledge graph for life sciences, showcasing its breadth, tools for integration, and use cases in biomedical analysis.

RCy3 provides R access to Cytoscape's network biology tools, enabling reproducible workflows through automation and integration with existing packages.

pathwayPCA is an R package that performs integrative pathway analysis with modern PCA methods and gene selection, enabling multi-omics data analysis and sample-specific pathway activity estimation.

This study benchmarks four methods for assigning cell type labels to cell clusters in scRNA-seq data, showing high performance but variability in precision-recall across methods and datasets.

The paper identifies genes in published pathway figures using OCR and pathway modeling, finding 29,189 gene symbols across 3982 figures, significantly expanding gene associations beyond existing databases.