Alexander Lachmann

The CFDE Workbench integrates metadata and processed data from Common Fund programs to enable FAIR and AI-ready cross-program knowledge discovery.

ChEA-KG constructs a human transcription factor regulatory network using gene set enrichment analysis and provides an interactive web interface for network exploration and analysis.

RummaGEO automatically mines gene sets from GEO RNA-seq studies for human and mouse, enabling signature search and metadata analysis.

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

PrismExp improves gene function prediction by partitioning RNA-seq co-expression data into tissue-specific segments, outperforming cross-tissue approaches across multiple domains.

The paper introduces an algorithm to reconstruct context-specific molecular interaction maps centered on oncoproteins, validating it with KRAS in lung adenocarcinoma and identifying novel synthetic lethal proteins.

BioJupies automates the creation of interactive Jupyter Notebooks for RNA-seq analysis, enabling users to generate reproducible reports from raw data to visualizations and differential expression analyses.

Elysium provides a cloud-based RNA-seq alignment service with a GUI, allowing users to upload FASTQ files and obtain aligned results without needing programming skills or Amazon credentials.

The paper develops ARCHS4, a resource that provides uniformly processed RNA-seq data from human and mouse, enabling easier integration and analysis.