drug-resistance

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

Minor Variant Calling and Phasing Tools

Drug Response Estimation from single-cell Expression Profiles

Genome classificator using machine learning and SNP markers

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

Generate a rich feature space describing all possible mutations in a given protein sequence (+ structure)

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

Multipurpose tool for targeted variant calling of genetic polymorphisms in Mycobacterium Tuberculosis

Data and analysis scripts used in Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

A GLUE project for Hepatitis C virus (HCV)

A robust, Dockerized WDL/Cromwell workflow for Mycobacterium tuberculosis complex genomic surveillance, integrating read trimming, QC, species typing, TB-Profiler resistance & lineage profiling, NTM/MTBC identification, mutation evidence reporting, core-SNP phylogenomics, SNP distance analysis & interactive HTML reporting for TB AMR surveillance.

Structural bioinformatics analysis of the EGFR T790M drug-resistance mutation using BioPython, protein structure analysis, ligand interaction mapping, and mutation characterization.

A method to predict activating, deactivating and resistance mutations in kinases

Benchmark for evaluating sequence-based ML and foundation models for tuberculosis drug-resistance prediction and WHO-catalogued variant recovery.

This project contains the code for the manuscript "Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning" by Heller et al. published 2026 in Molecular Systems Biology (https://doi.org/10.1038/s44320-026-00187-9).

A GLUE project for hepatitis B virus (HBV).

Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. It translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.

This study assessed the spatial genetic variation in P. falciparum populations in Mali

Clusters phosphoproteomics data based on a combination of the sequence information and abundance changes over conditions.

HCV drug resistance extension based on collaboration with PHE.