Creates a construct developed by the Niles Lab at MIT, designed to deliver a 3' UTR post-transcriptional regulatory element payload to a specific given gene in Plasmodium falciparum.
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.
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
Nextflow pipeline for analyzing empirical WGS data for the effect of positive selection on IBD-based inference
Bio-informed QSAR framework integrating P. falciparum transcriptomic signatures with molecular descriptors for enhanced antimalarial activity prediction (6.1% improvement, 98.3% feature reduction)
This repository contains data and code for our analysis of the genome of a Plasmodium falciparum strain with reduced susceptibility to Artemisinin-Based Combination Therapy (ACT) drugs. We performed whole-genome sequencing of the HSOG3 clinical isolate and compared it with a large dataset of global P. falciparum samples.
Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy - By Dieng and Ford et al.
An integrated computational pipeline for CRISPR-Cas13a (SHERLOCK) malaria diagnostics and trans-kingdom neuro-immune mapping, linking PfK13-driven pathogen detection to microglial homeostatic (CX3CR1/Iba1) set-points and Gut-Brain Axis (GBA) dysregulation.
Modeling Plasmodium falciparum Diagnostic Test Sensitivity using Machine Learning with Histidine-Rich Protein 2 Variants
Computational structural characterisation of PfMSP3.1 SPAM, including modelling, MD, docking, AlphaFold and experimental NMR-restraint reassessment.
Calculating the coverage depth for each coding gene and the percentage of each gene covered at ≥ 10X depth.
Effect of temperature stress on Plasmodium Falciparum. Code for data analysis. Rshiny app for data exploration.
Utilizing 3D GCN machine learning models to expedite and improve malaria drug discovery through efficient inhibitor detection
Mechanistic molecule→parasite-exposure→function→phenotype engine for P. falciparum (open-source)
Comprehensive transcriptomic analysis of host response to Plasmodium falciparum infection. This study identifies key immune pathways, differential gene expression patterns, and potential biomarkers associated with malaria pathogenesis.
Plasmodium Protein Domain Annotation Pipeline with Streamlit
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