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.


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.

Further information

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.


If you need help or have any queries, please contact us using the details below.

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Sanger Institute Contributors

Photo of Dr Martin Hemberg, PhD

Dr Martin Hemberg, PhD

CDF Group Leader

Photo of Dr Matt Berriman

Dr Matt Berriman

Senior Group Leader

Photo of Tallulah S. Andrews, Ph. D

Tallulah S. Andrews, Ph. D

Postdoctoral Fellow

Photo of Dr Adam James Reid

Dr Adam James Reid

Senior Staff Scientist

Photo of Dr Julian C Rayner

Dr Julian C Rayner

Honorary Faculty (formerly Senior Group Leader at the Sanger Institute) and Director of Wellcome Genome Campus Connecting Science

Photo of Dr Mara Lawniczak

Dr Mara Lawniczak

Group Leader

Photo of Dr Virginia Muriel Howick

Dr Virginia Muriel Howick

Postdoctoral Fellow

Previous contributors

Photo of Dr Oliver Billker

Dr Oliver Billker

Former Senior Group Leader

Photo of Dr Arthur M Talman

Dr Arthur M Talman

Postdoctoral Fellow

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