Projects
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CCB is here to support your data science and computational needs. If interested in collaborating or need any related assistance, please email the details to ccbhelp@hms.harvard.edu.
Additional information can be found on our Collaboration Page.
Our Work Groups
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Status
| Project Title | Work Group(s) | Status | Collaborator(s) | Project Deliverables |
|---|---|---|---|---|
| OpenGWAS Phenotype Mapping |
|
Ongoing |
|
Tool for ontology mapping; and mappings of OpenGWAS phenotypes |
| 23andMe Phenotype Mapping |
|
Ongoing |
|
Mappings of 23andMe GWAS phenotypes |
| Benchmark of Ontology Mapping Tools |
|
Ongoing |
|
Survey and benchmark test of ontology mapping tools |
| Programmatic Interface to HuBMAP Ontology |
|
Ongoing |
|
Tool for programmatic interaction with HuBMAP ontology |
| Single-cell characterization of acute inflammation in patients with COVID-19 |
|
Ongoing |
|
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. |
| Transparency In Coverage |
|
Ongoing |
|
Data warehouse for insurance cost-sharing data |
| HSDM Research Data Repository |
|
Ongoing |
|
Data warehouse containing copy of production EHR data to support research activities |
| Research Design and Analysis - R Component |
|
Ongoing |
|
R programming workshop as a supplementary component to the Research Design and Analysis Course |
| Identification of cell-cell interactions from high-resolution spatial transcriptomics data |
|
Ongoing |
|
Develop an open-source Python package and publish it on the Python Package Index (PyPI) |
| Aging intervention multi-omics data integration and biomarker discovery |
|
Ongoing |
|
To develop an R/Bioconductor experimental data package, integrate signals from multiple aging intervention omics datasets and identify biomarker sets through machine learning and gene set analysis, and develop a data portal that enables interactive exploration of the data. |
| Extensions and updates to the BioPlex R and Python packages |
|
Ongoing |
|
Update the BioPlex R and Python packages to provide access to newly generated PPI, TMT, and PTM datasets |
| C elegans Database |
|
Complete |
|
Database |
| Proteome-scale protein-protein interaction networks from the BioPlex project |
|
Complete |
|
R & Python packages |
| RNA sequencing atlas of vascular endothelial cells |
|
Complete |
|
O2-based RNA-seq pipeline & interactive data exploration platform |
| Harvey Mudd College CS Clinic 21/22 |
|
Complete |
|
Components of ontology mapping tool |
| Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH) |
|
Complete |
|
R/Bioconductor package, Repository of applications & downstream analyses and Interactive gallery of publicly available MERFISH datasets |
| AlphaFold & ColabFold |
|
Complete |
|
Modules on the O2 HPC cluster |
| Drugging the undruggable – machine-learning-based cancer immunotherapy design |
|
Complete |
|
Promoter visualization platform |
| Designmatch Container |
|
Complete |
|
Develop a Docker image to collect and install all the necessary resources to run Designmatch in R. |
| Leveraging geographic information systems for spatial transcriptomics |
|
Complete |
|
Implement a GIS database-backend to represent and analyse spatial transcriptomics data |
| Whole-genome sequencing analysis of fluoroquinolone resistance acquisition in Mycobacterium tuberculosis |
|
Complete |
|
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 |
| Thyroid hormone influence on the brain |
|
Complete |
|
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 |
| Computational pipeline for whole-genome sequencing analysis of yeast strains |
|
Complete |
|
Computational pipeline for whole-genome sequencing data analysis of yeast strains on HMS’ O2 cluster. |
| MERFISH Mouse Brain Data Viewer |
|
Complete |
|
Posit Connect interface that enables interactive exploration of the data |
| Single-cell atlas of human variation in hematopoietic tissue |
|
Complete |
|
Processing, analysis, annotation, visualization, and exploration of a large single-cell hematopoiesis reference dataset |