This repository contains code and results from the Pacific Symposium of Biocomputing 2021 paper:

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2−human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan Lavista Ferres, Gregory R. Bowman, Judith Klein-Seetharaman

Paper (PDF): https://psb.stanford.edu/psb-online/proceedings/psb21/kshirsagar.pdf
Online: https://www.worldscientific.com/doi/abs/10.1142/9789811232701_0015

The features are not available here due to github's size limits, here is a link to a dropbox folder: https://www.dropbox.com/sh/tx73tx355z8klrh/AADl0MyptAGZSucaKOMnpiX4a?dl=0
The README.txt file therein should describe the various files. Please email me if you have any further questions: mekshirs AT microsoft DOT com

Plots

PCA/T-SNE interactive plot is in the allviruses_plot.html html file and should be downloaded and opened in a browser to visualize. Also available are GO enrichment visualizations.

Predictions

Predictions from the model on all pairs of virus-human proteins are in the results directory

GO Enrichment analysis

Detailed GO enrichment analysis results and plots are in the enrichment_analysis directory