Browse Projects


Work Group


Project Title Work Group Status Project Overview
Proteome-scale protein-protein interaction networks from the BioPlex project Genetics / Genomics Ongoing

Implement programmatic access to BioPlex from within R/Bioconductor and from within Python, along with a series of downstream applications of BioPlex,

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Ontology Phenotype Mapping Knowledge Representation Ongoing

Standardization of the phenotypes in 23andMe’s GWAS metadata with suitable symbols from ontologies

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OpenGWAS Ontology Mapping Knowledge Representation Ongoing

Mapping the traits in Open GWAS to ontologies

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Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH) Genetics / Genomics Ongoing

Make MERFISH datasets accessible to the wider R/Bioconductor community.

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AlphaFold & ColabFold Genetics / Genomics Ongoing

Developing a pair of modules on the O2 HPC cluster to facilitate protein structure prediction

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C elegans Database Data & Analytics Platforms Complete

Build a relational database to catalog and track ~5000 transgenic or mutant C. elegans strains.

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RNA sequencing atlas of vascular endothelial cells Genetics / Genomics Complete

Developed an O2-based RNA-seq pipeline that enabled efficient processing of raw sequencing output for 500 samples.

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Harvey Mudd College Computer Science Clinic Knowledge Representation Complete

Developing a tool that relies on NLP techniques, ontology semantics and automated reasoning to semi-automatically map concepts in bulk

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