SPARC CCF Multi-omics analysis

Evaluating the generalizability of graph neural networks for predicting collision cross section

Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"

Scripts and notebooks from Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation

Source code and data for "Exploring the known chemical space of the plant kingdom: Insights into taxonomic patterns, knowledge gaps, and bioactive regions"

Source code and data for "Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses"

On the correspondence between the transcriptomic response of a compound and its targets

MultiGML

Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"

A comprehensive 10-page probability cheatsheet that covers a semester's worth of introduction to probability.

Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly…

Python notebooks for analyses and simulating drug response on patient-specific pathway signatures

Fastest network node embeddings in the west

Supplementary code for the paper: Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

A programmatic interface for generating and handling OBO in Python.

A Python package for drug discovery by analyzing causal paths on multiscale networks

Resources for grounding protein families and complexes from text and describing their hierarchical relationships.

Curation of mechanistic relations from roles in ChEBI and MeSH

Functions for scraping git commits from repositories associated with a PhD (or anything else) and plotting them.