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Published Online: 22 February 2022

GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum

Publication: The CRISPR Journal
Volume 5, Issue Number 1


Functional characterization of the multitude of poorly described proteins in the human malarial pathogen, Plasmodium falciparum, requires tools to enable genome-scale perturbation studies. Here, we present GeneTargeter (, a software tool for automating the design of homology-directed repair donor vectors to achieve gene knockouts, conditional knockdowns, and epitope tagging of P. falciparum genes. We demonstrate GeneTargeter-facilitated genome-scale design of six different types of knockout and conditional knockdown constructs for the P. falciparum genome and validate the computational design process experimentally with successful donor vector assembly and transfection. The software's modular nature accommodates arbitrary destination vectors and allows customizable designs that extend the genome manipulation outcomes attainable in Plasmodium and other organisms.

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Information & Authors


Published In

cover image The CRISPR Journal
The CRISPR Journal
Volume 5Issue Number 1February 2022
Pages: 155 - 164
PubMed: 35191751


Published online: 22 February 2022
Published in print: February 2022


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Pablo Cárdenas
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Lisl Y. Esherick
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Gaël Chambonnier
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Sumanta Dey
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Present address: Pfizer, Inc., Cambridge, Massachusetts, USA.
Christopher V. Turlo
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Armiyaw Sebastian Nasamu
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Present address: Center for Global Infectious Disease Research, Seattle, WA, USA.
Jacquin C. Niles* [email protected]
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.


Address correspondence to: Jacquin C. Niles, MD, PhD, Department of Biological Engineering, Massachusetts Institute of Technology, Room 56-341, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA, [email protected]

Author Disclosure Statement

J.C.N. is listed as one of the inventors on a patent of the genetically encoded protein-binding RNA aptamer technology utilized. No other authors have competing interests to declare.

Funding Information

This work was supported by grants from the Bill and Melinda Gates Foundation (OPP1162467 and OPP1158199); Broad Next10; National Institute of General Medical Sciences Center for Integrative Synthetic Biology Grant (P50 GM098792); National Institutes of Environmental Health Sciences Core Center Grant (P30-ES002109) and National Institutes of Environmental Health Sciences Training Grant (T32-ES007020 (L.Y.E.).

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