Malaria Cell Atlas

Malaria Cell Atlas

Malaria Cell Atlas


The Malaria Cell Atlas aims to provide a resource of single cell transcriptomic data across the full lifecycle of the parasite. At the Sanger Institute, we are using single cell RNAsequencing to understand parasite developmental decision making in the host and the vector in both lab and natural infections. More widely, we aim for the Malaria Cell Atlas to be beneficial to all malaria researchers, from those focused on particular gene families, to those developing novel drugs and vaccines. Nearly half of the world’s population remains at risk for malaria with 216 million reported cases in 2016 and over 400,000 deaths. Understanding transcriptional diversity across the lifecycle under different disease settings will help in the fight to eliminate and eventually eradicate this disease.

As of March 2018, the Malaria Cell Atlas includes data from our eLife Paper, which also describes the method we have used to generate single cell transcriptomes for malaria parasites. In the near future, our Atlas will also include single cell RNA-sequencing data covering more stages from different Plasmodium species as well as Anopheles and mammalian host tissues that play a role in the parasite's lifecyce.

MalariaAlex Cagan

Download and Installation

VISUALISE DATA <- explore how genes are expressed across more than 500 individual Plasmodium parasites.

DOWNLOAD DATA <- contains gene count tables for Plasmodium berghei and falciparum scRNAseq data. (Specifically, this download contains (a) Read counts for P. berghei mixed blood stages (b) read counts for P. falciparum asexual parasites and (c) read counts for P. falciparum gametocytes.

RAW DATA <- European Nucleotide Archive accession ERP021229

eLife paper <- Further information about this study.

Learn and Support

The Malaria Cell Atlas is supported by Wellcome (WT098051) and by a Medical Research Council Career Development Award (G1100339) to Mara Lawniczak. The authors would like to thank the staff of the Illumina Bespoke Sequencing and Core Cytometry teams at the Wellcome Sanger Institute for their contribution.


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Sanger Contributors

Related Programmes and Facilities


  • Genetic diversity of the African malaria vector Anopheles gambiae.

    Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections—Angola:, Burkina Faso: et al.

    Nature 2017;552;7683;96-100

  • A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum.

    Lawniczak MK and Eckhoff PA

    Malaria journal 2016;15;1;487

  • Gametocytogenesis: the puberty of Plasmodium falciparum.

    Talman AM, Domarle O, McKenzie FE, Ariey F and Robert V

    Malaria journal 2004;3;24