Reid, Adam James
I want to better understand how parasites are able to infect people and how they avoid being killed by the immune system. To do this I am taking advantage of the power of DNA sequencing technologies and computational analysis to identify the genes important for these interactions.
My primary interest is in identifying genes involved in host-parasite interactions. I am currently working on malaria and several species of nematode worm. The first goal in this process is to produce a high quality, annotated genome sequence for the parasite species of interest describing the layout of the genome and all the genes in the parasites arsenal. Once this is achieved, functional genomics approaches such as gene expression analysis can be used to determine genes of particular importance for host-parasite interactions (Reid et al., 2015; Reid & Berriman, 2013).
In collaboration with the Lawnizcak group at WTSI, I have been involved in developing a protocol for single-cell RNA-sequencing of Plasmodium cells. We have used this to shed new light on control of gene expression and to highlight roles for multigene families such as var and pir in sexual stages. This work has been published on bioRxiv: https://www.biorxiv.org/content/early/2017/02/10/105015.
In collaboration with the Langhorne group at The Francis Crick Institute I am currently working on understanding how malaria parasites are able to establish chronic infections, increasing their chance of transmission (Brugat*, Reid* et al., in preparation). This has stemmed from work where I was involved in identifying a role for the pir gene family in virulence and the importance of mosquito transmission on controlling gene expression in the parasite (Spence et al., 2013).
The SIMS project is a multi-centre systems immunology collaboration (The Kenya Medical Research Institute, Oxford University, the Francis Crick Institute, University of Exeter) funded by the Medical Research Council to understand why some children are more susceptible to malaria than others. I am coordinating sequencing and analysis of the data for this project.
I have also lead projects to develop reference genome sequences for several distant relatives of the malaria parasite. In collaboration with Fiona Tomley and Damer Blake of the Royal Veterinary College, London and Arnab Pain at King Abdulla University of Saudi Arabia we sequenced the genomes of all seven chicken-infecting parasites of the genus Eimeria (Reid et al., 2014). Prior to that we generated a reference genome for the cattle parasite Neospora with Jonathan Wastling at University of Liverpool (Reid et al., 2012).
In collaboration with, amongst others, Mark Viney from University of Bristol and Taisei Kikuchi from University of Miyazaki, we have sequenced the genomes of several species of the parasitic nematode Strongyloides and identified genes involved in the transition from a free-living to a parasitic life style (Hunt*, Tsai*, Coghlan*, Reid* et al., 2016). I am also interested in how the host reacts to infection with parasites and based on previous work in collaboration with Richard Grencis at University of Manchester (Foth*, Tsai*, Reid*, Bancroft* et al., 2014) we are exploring the genes involved in chronic whipworm infection, collaborating also with the group of Gordan Dougan here at the Sanger Institute. Previously I have been involved in producing and analyzing reference genome sequences for the plant-infecting nematodes Bursephelenchus (Kikuchi et al., 2011) and Globodera (Cotton et al., 2014) and the sheep-infecting barber pole worm Haemonchus (Laing et al., 2013)
The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.
Science (New York, N.Y.) 2019;365;6455
Repeated clinical malaria episodes are associated with modification of the immune system in children.
BMC medicine 2019;17;1;60
Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.
Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection.
Nature microbiology 2017;2;16276
The genomic basis of parasitism in the Strongyloides clade of nematodes.
Nature genetics 2016;48;3;299-307
Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa.
Parasitology 2015;142 Suppl 1;S57-70
Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Genome research 2014;24;10;1676-85
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.
Nature genetics 2014;46;7;693-700
Vector transmission regulates immune control of Plasmodium virulence.
Genes involved in host-parasite interactions can be revealed by their correlated expression.
Nucleic acids research 2013;41;3;1508-18
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.
PLoS pathogens 2012;8;3;e1002567
RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.
BMC genomics 2013;14;822
Genome sequencing gets func-y.
Nature reviews. Microbiology 2011;9;6;401
The evolution of protein functions and networks: a family-centric approach.
Biochemical Society transactions 2009;37;Pt 4;745-50
Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone.
Bioinformatics (Oxford, England) 2007;23;18;2353-60