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Project Title Work Group(s) Status Collaborator Project Deliverables
OpenGWAS Phenotype Mapping
  • Knowledge Representation
Ongoing MRC Integrative Epidemiology Unit, University of Bristol Tool for ontology mapping; and mappings of OpenGWAS phenotypes
23andMe Phenotype Mapping
  • Knowledge Representation
Ongoing 23andMe Mappings of 23andMe GWAS phenotypes
Benchmark of Ontology Mapping Tools
  • Knowledge Representation
Ongoing Kohane Lab, Department of Biomedical Informatics, Harvard Medical School Survey and benchmark test of ontology mapping tools
Programmatic Interface to HuBMAP Ontology
  • Knowledge Representation
Ongoing Cyberinfrastructure for Network Science Center, Indiana University Tool for programmatic interaction with HuBMAP ontology
Drugging the undruggable – machine-learning-based cancer immunotherapy design
  • Computational Biology,
  • Data & Analytics Platforms
Ongoing Ming-Ru Wu, MD, PhD Promoter visualization platform
Leveraging geographic information systems for spatial transcriptomics
  • Data & Analytics Platforms,
  • Computational Biology
Ongoing Harvey Mudd College Implement a GIS database-backend to represent and analyse spatial transcriptomics data
Whole-genome sequencing analysis of fluoroquinolone resistance acquisition in Mycobacterium tuberculosis
  • Computational Biology
Ongoing Maha Farhat, MD MSc Wrangle data to construct fully-processed & analysis-ready large WGS MTB sample constructed phylogenies that relate thousands of MTB isolates from different genetic backgrounds dated phylogenies and identification of key mutations based of phylogeny dating tools, identification of FLQ antibiotic resistance emergence in time and geographically
Single-cell characterization of acute inflammation in patients with COVID-19
  • Computational Biology
Ongoing Jonathan Kagan, PhD An assessment of the quality of the scRNA-seq data obtained for the first 10 samples; 2) a characterization of the cell type composition of the first 10 samples; and 3) a statistical analysis of differential cell type abundance and investigation of T-cell receptor sequencing data and cytokine measurements between samples for defined contrasts.
Thyroid hormone influence on the brain
  • Computational Biology
Ongoing Bernardo Sabatini, PhD Gene expression quantification and quality control for 16 bulk RNA-seq samples obtained from 8 mice; 2) differential expression analysis for defined contrasts; and 3) an exploration of alternative splicing for the ROBO3 gene
Transparency In Coverage
  • Data & Analytics Platforms
Ongoing Mike Chernew, PhD, Healthcare Policy Data warehouse for insurance cost-sharing data
Computational pipeline for whole-genome sequencing analysis of yeast strains
  • Computational Biology
Ongoing Fred Winston, PhD Computational pipeline for whole-genome sequencing data analysis of yeast strains on HMS’ O2 cluster.
C elegans Database
  • Data & Analytics Platforms
Complete Max Heiman, PhD Database
Proteome-scale protein-protein interaction networks from the BioPlex project
  • Computational Biology
Complete Steven Gygi, PhD and Wade Harper, PhD R & Python packages
RNA sequencing atlas of vascular endothelial cells
  • Computational Biology
Complete Ulrich von Andrian, PhD O2-based RNA-seq pipeline & interactive data exploration platform
Harvey Mudd College CS Clinic 21/22
  • Knowledge Representation
Complete Harvey Mudd College Components of ontology mapping tool
Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH)
  • Computational Biology,
  • Image Analysis & Processing
Complete Jeffrey Moffitt, PhD R/Bioconductor package, Repository of applications & downstream analyses and Interactive gallery of publicly available MERFISH datasets
AlphaFold & ColabFold
  • Computational Biology
Complete Research Computing and Edward Huttlin, PhD Modules on the O2 HPC cluster
Designmatch Container
  • Data & Analytics Platforms
Complete José R. Zubizarreta, PhD Develop a Docker image to collect and install all the necessary resources to run Designmatch in R.