The paper introduces Aster, a statistical framework for accurately classifying antimalarial drug efficacy outcomes by accounting for complexity of infection and genotyping limitations.

Antimicrobial Agents and Chemotherapy · Apr 13, 2026Peer-reviewedGenetics

Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health

Andrés Aranda-Díaz, Eric Neubauer Vickers, Kathryn Murie, Brian Palmer, Nicholas J. Hathaway, Inna Gerlovina, Simone Salvador Boene, Manuel II García-Ulloa, Pau Cisteró, Thomas Katairo, Francis D Semakuba, Bienvenu Nsengimaana, Hazel B. Gwarinda, Carla García-Fernández, William Louie, , Bryan Greenhouse

The paper develops MAD4HatTeR, an amplicon sequencing panel and analysis pipeline for detecting Plasmodium falciparum diversity, resistance markers, and gene duplications/deletions, showing high sensitivity and reproducibility across settings.

Scientific Reports · Mar 28, 2025Peer-reviewedGenomics

Plasmodium falciparum transmission in the highlands of Ethiopia is driven by closely related and clonal parasites

Aurel Holzschuh, Yalemwork Ewnetu, Lise Carlier, Anita Lerch, Inna Gerlovina, Sarah Cate Baker, Delenasaw Yewhalaw, Werissaw Haileselassie, Nega Berhane, Wossenseged Lemma, Cristian Koepfli

The paper analyzes P. falciparum genetic diversity and transmission patterns in Ethiopian highlands, finding local transmission and clonal parasite spread.

Molecular Ecology · Feb 9, 2024Peer-reviewedGenomics

Highly multiplexed ddPCR-amplicon sequencing reveals strong Plasmodium falciparum population structure and isolated populations amenable to local elimination efforts in Zanzibar

Aurel Holzschuh, Anita Lerch, Inna Gerlovina, Bakar Shariff Fakih, Abdul-wahid H. Al-mafazy, Erik J. Reaves, Abdullah Ali, Faiza Abbas, Mohamed Haji Ali, Mohamed Ali Ali, Manuel W. Hetzel, Joshua O. Yukich, Cristian Koepfli

This study uses ddPCR-amplicon sequencing to analyze Plasmodium falciparum genetic structure in Zanzibar, revealing isolated populations and transmission patterns relevant to malaria elimination.

bioRxiv · Jan 5, 2023 · PreprintGenomics

Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections

Inna Gerlovina, Boris Gerlovin, Isabel Rodríguez-Barraquer, Bryan Greenhouse

Dcifer calculates genetic distance between polyclonal infections using IBD-based methods, showing higher statistical power than identity by state approaches and detecting related infections.

Genetics · Aug 24, 2022Peer-reviewedGenetics