V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Source files for building the IDM EMOD disease transmission model.

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Network Models of HIV Transmission Dynamics among MSM and Heterosexuals

Point of care system for AMPATH clinics

A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8

FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

Clinical Trial Risk Tool for analysing clinical trial protocols using natural language processing and assessing the risk of ending uninformatively, developed by Fast Data Science

The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA structures and a limited understanding of the parameters that drive RNA recognition by small molecules, including a lack of validated quantitative structure-activity relationships (QSAR). Herein, we developed QSAR models that quantitatively predict both thermodynamic and kinetic-based binding parameters of small molecules and the HIV-1 TAR model system. Small molecules bearing diverse scaffolds was screened against the HIV-1 TAR using surface plasmon resonance. Then multiple linear regression (MLR) combined with feature selection was performed to afford robust models that allowed direct interpretation of properties critical for both binding strength and kinetic rate constants. These models were externally validated with new molecules and their accurate performance confirmed via comparison to ensemble tree methods.

A repository for the Advanced Programming Tutorial that teaches you how to develop an interactive model using Shiny

This repo contains the data and software used to run the analyses in the "Using machine learning and Big data to explore the drug resistance landscape in HIV"

a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows

Incidence Estimation Tools

A comprehensive pipeline for HIV drug resistance identification, variant evaluation, and surveillance.

🦠Research project in Bioinformatics Institute 2023-2024

Viral Load Sample Management - Machine Interfacing

A simple, open source Sample Management System for Viral Load, EID and Covid-19 testing.

RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins

Current development version of EvoNetHIV package

High accuracy single molecule Nanopore reads using the MrHAMER pipeline

Tutorial materials as referenced in IDM's documentation for EMOD, an agent-based disease dynamics model.

SEEPS: Sequence Evolution and Epidemiological Process Simulator

A toolkit for creating databases of viral integration sites in host genomes

Reconstruction and analysis of the HIV outbreak in Scott County, Indiana

Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV

HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.

Virology is the study of viruses – submicroscopic, parasitic particles of genetic material contained in a protein coat – and virus-like agents.

Webserver for storage [and analysis] of NGS-based HIVDR testing data