Alexander Lachmann

Rare loss-of-function variants in POLD1, PMS1 and FAN1 modify age at onset of motor symptoms in Huntington's disease

The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

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

ChEA-KG: Human Transcription Factor Regulatory Network with a Knowledge Graph Interactive User Interface

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: Automatic Mining of Human and Mouse Gene Sets from GEO

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

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

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

PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data

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

Systematic Elucidation and Validation of OncoProtein-Centric Molecular Interaction Maps

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: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud

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: RNA-seq Alignment in the Cloud

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.

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

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