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Connections Hypothesis Provider
Connections Hypothesis Provider (CHP) is a service built by Dartmouth College (PI – Dr. Eugene Santos) and Tufts University (Co-PI – Joseph Gormley) in collaboration with the National Center for Advancing Translational Sciences (NCATS). In its current version, CHP supports queries pertaining to tissue and gene specificity. A gene’s specificity to a tissue is determined both by its level of expression, and how specific that expression is to a particular tissue. For more detailed information on our tissue-gene specificity app see our README for that service. Our long term aim is to leverage clinical data along with structured biochemical knowledge to derive a computational representation of pathway structures and molecular components to support human and machine-driven interpretation, enable pathway-based biomarker discovery, and aid in the drug development process. We represent Gene Regulatory Networks (GRNs) via a probabilistic graphical model called the Bayesian Knowledge Base (BKB). We use the BKB to interrogate the data and discover motifs of gene regulation, constrained around biochemical context. We wrap our GRN model, as well as several other state of the art GRN learning algorithms into our service, GenNIFER. For more detailed information on GenNIFER please see our README for that service.
Eugene Santos Jr - PI (Dartmouth
Joseph Gormley – Co PI (Tufts)
Eugene Hinderer – Bioinformaticist (Tufts)
Tom Zisk – Developer (Tufts)
Dan Corkill – AI Research Scientist (Tufts)
Keumjoo Kim – Researcher (Dartmouth)
Chase Yakaboski – Graduate Assistant (Dartmouth)
Gregory Hyde – Graduate Assistant (Dartmouth)
Anthony Ragazzi - Graduate Assistant (Dartmouth)
All results from our services are precomputed and exposed in a Translator Reasoner API (TRAPI) compliant format. For details on how to use our service see our Smart-API page or reference the documentation for each of our individual services:
Tissue – Gene Specificity: https://github.com/di2ag/gene-specificity
GenNIFER: https://github.com/di2ag/gennifer
GenNIFER also has an external interface for interrogating transcriptomic data via our BKB Learning algorithm: https://chp.thayer.dartmouth.edu/ui
Dr. Eugene Santos (PI): [email protected]
Joseph Gormley (Co-PI): [email protected]
http://smart-api.info/registry?q=23f770568b92b7a82063989b3ddd9706
1.4.0
Genotype-Tissue Expression (GTEx) project: https://www.gtexportal.org/home/
Genomic Data Commons (GDC): https://portal.gdc.cancer.gov/
Reactome: https://reactome.org/