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 August 2019, the Malaria Cell Atlas includes data from our eLife and Biorxiv papers, which describe methods we have used and optimised to generate single cell transcriptomes for malaria parasites. Our Atlas includes single cell RNA-sequencing data covering all stages of the life cycle in both Anopheles vector and mammalian host tissues, spans both cell sorting and droplet-based scRNAseq and includes four Plasmodium species, including three human pathogens. It also includes the first single cell data from parasites isolated directly from clinical samples.

Download and Installation

VISUALISE DATA <- explore how genes are expressed over thousands of individual Plasmodium parasites from across the life cycle.

DOWNLOAD DATA <- Our Github contains gene count tables for all scRNAseq data.

eLife RAW DATA <- European Nucleotide Archive accession ERP021229

Biorxiv RAW DATA <-  European Nucleotide Archive accession ERP110344

eLife paper <- Further information about this study.

Biorxiv 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.


For comments and questions, please contact us at


Sanger Contributors

Rayner, Julian C

Dr Julian C Rayner
Senior Group Leader and Director of Wellcome Genome Campus Connecting Science

Related Programmes, Associate Research 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