DylanSteinecke's repositories
BE298FinalProject
Fall 2022 Bioengineering 298 Final Project: using protein networks to understand drug and disease mechanisms
calcium_proteins_os_cvd
Calcium-binding and -signaling proteins in oxidative stress and cardiovascular disease
caseolap
CaseOLAP: A cloud computing platform for phrase mining. This consists of downloading, parsing, and indexing of data, text-cube creation, entity count with search functionality, and caseOLAP score calculation.
caseolap_lift
Fall 2022 Project collaborating with Alexander Pelletier et al. to improve CaseOLAP's input data quantity, result quality, and usability.
gene_to_anatomy_text_mining
Uses PubTator3 to identify genes in PubMed articles. Uses PubMed API and MeSH annotations to identify articles studying anatomies. Uses co-occurrence of gene mentions and anatomy topics to calculate gene-anatomy associations. Allows users to choose anatomies (MeSH) and to choose genes (NCBI) or automatically curate genes via GO terms
grape
🍇 GRAPE is a Rust/Python Graph Representation Learning library for Predictions and Evaluations
Know2BIO
Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs
knowledge_graph_of_text_mined_pubmed
knowledge_graph_of_text_mined_pubmed
metapaths
Augmenting a network to find metapaths that capture a Drugs MoA
TextMining_NDMDs
Summer 2021: CaseOLAP-based protein and pathway analyses on neurodegenerative mitochondrial disease publications
PubMed_PMID_to_PMC
Take PubMed IDs and map them to PubMed Central IDs
superSTR
A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.
UCLA_Assignments
Some homework assignments to be shared