The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
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Updated
Apr 23, 2017 - Perl
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
Using graph database techniques to understand the infectious relationships between bacteria and phages.
A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).
Identify phage regions in bacterial genomes for masking purposes
2020 International Genetically Engineered Machine competition
Old repository comprising code for my HTHSCI 3BM6 phage modelling project.
From protein to phage phylogeny in single line!
Quick and dirty scripts for simple biology
This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048
This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
Prediction of bacterial host for phage
A toy MC model studying bacteria-phage coevolution dynamics. Code is meant to be readable instead of performant, or, well, good. Good for beginners in ABM
A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure
.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
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