Projects
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Additional information can be found on our Collaboration Page.
Our Work Groups
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Status
| Project Title | Work Group(s) | Status | Collaborator | Project Deliverables |
|---|---|---|---|---|
| OpenGWAS Phenotype Mapping |
|
Ongoing | MRC Integrative Epidemiology Unit, University of Bristol | Tool for ontology mapping; and mappings of OpenGWAS phenotypes |
| 23andMe Phenotype Mapping |
|
Ongoing | 23andMe | Mappings of 23andMe GWAS phenotypes |
| Benchmark of Ontology Mapping Tools |
|
Ongoing | Kohane Lab, Department of Biomedical Informatics, Harvard Medical School | Survey and benchmark test of ontology mapping tools |
| Programmatic Interface to HuBMAP Ontology |
|
Ongoing | Cyberinfrastructure for Network Science Center, Indiana University | Tool for programmatic interaction with HuBMAP ontology |
| Single-cell characterization of acute inflammation in patients with COVID-19 |
|
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. |
| Transparency In Coverage |
|
Ongoing | Mike Chernew, PhD, Healthcare Policy | Data warehouse for insurance cost-sharing data |
| HSDM Research Data Repository |
|
Ongoing | Jane Barrow | Data warehouse containing copy of production EHR data to support research activities |
| MERFISH Mouse Brain Data Viewer |
|
Ongoing | Jeffrey Moffitt, PhD | Posit Connect interface that enables interactive exploration of the data |
| Single-cell atlas of human variation in hematopoietic tissue |
|
Ongoing | Allon Klein, PhD | Processing, analysis, annotation, visualization, and exploration of a large single-cell hematopoiesis reference dataset |
| Harvard School of Dental Medicine- Dental Project |
|
Ongoing | Jennifer L Gibbs, PhD | To analyze the data that Dr. Gibbs’ group has to identify the relationship between psychosocial and demographic variables and cytokine features that can explain pain resolution. |
| Research Design and Analysis - R Component |
|
Ongoing | Catherine Hayes, DMD, SM, DMSc | 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 | Martin Hemberg, PhD | Develop an open-source Python package and publish it on the Python Package Index (PyPI) |
| C elegans Database |
|
Complete | Max Heiman, PhD | Database |
| Proteome-scale protein-protein interaction networks from the BioPlex project |
|
Complete | Steven Gygi, PhD and Wade Harper, PhD | R & Python packages |
| RNA sequencing atlas of vascular endothelial cells |
|
Complete | Ulrich von Andrian, PhD | O2-based RNA-seq pipeline & interactive data exploration platform |
| Harvey Mudd College CS Clinic 21/22 |
|
Complete | Harvey Mudd College | Components of ontology mapping tool |
| Multiplexed Error Robust Fluorescence in Situ Hybridization(MERFISH) |
|
Complete | Jeffrey Moffitt, PhD | R/Bioconductor package, Repository of applications & downstream analyses and Interactive gallery of publicly available MERFISH datasets |
| AlphaFold & ColabFold |
|
Complete | Research Computing and Edward Huttlin, PhD | Modules on the O2 HPC cluster |
| Drugging the undruggable – machine-learning-based cancer immunotherapy design |
|
Complete | Ming-Ru Wu, MD, PhD | Promoter visualization platform |
| Designmatch Container |
|
Complete | José R. Zubizarreta, PhD | 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 | 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 |
|
Complete | 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 |
| Thyroid hormone influence on the brain |
|
Complete | 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 |
| Computational pipeline for whole-genome sequencing analysis of yeast strains |
|
Complete | Fred Winston, PhD | Computational pipeline for whole-genome sequencing data analysis of yeast strains on HMS’ O2 cluster. |
| Parabiosis single-cell data viewer |
|
Complete | Lee Rubin, PhD | Posit Connect interface that enables interactive exploration of the data |