Adam Reid, PhD

Head of Bioinformatics, Gurdon Institute

The Gurdon Institute Bioinformatics group collaborates with scientists across the Institute to enhance research into developmental biology and cancer. We advise on experimental design, develop pipelines for data processing (with Nextflow, Python and R) and analyse data to generate novel biological findings.

The Institute has its own compute cluster, Illumina NovaSeq 6000 sequencer and 10X chromium single-cell platform, as well as access to wider University of Cambridge resources. Sequencing-based technologies such as whole genome sequencing, scRNA-seq, ATAC-seq, ChIP-seq and Hi-C are widely used at the Gurdon Institute and are the focus of much of our work. We provide supervision and training to staff in a variety of areas of bioinformatics.

Biography

Adam’s undergraduate degree was in Genetics at the University of Sheffield, after which he completed an MRes in Bioinformatics at the University of York. He worked at AstraZeneca as a Proteomics Bioinformatician, before going on to a PhD at University College London with Professor Christine Orengo. His thesis explored the evolution and functions of protein domain families.

He then spent a productive 12 years as postdoc and staff scientist in the Parasite Genomics group at the Wellcome Sanger Institute with Dr Matthew Berriman. There he studied the evolution and function of parasite genomes, using bioinformatics applied to whole genome sequencing, bulk and single-cell RNA-seq technologies. During this time he generated and analysed genome sequences for a wide range of species, identified the role of pir genes in establishing chronic infections in malaria parasites and published the first single-cell RNA-seq dataset for these parasites.

Publications

Key publications:

Aunin E et al. (2022) Characterising genome architectures using genome decomposition analysis. BMC Genomics 23(1): 398. DOI: 10.1186/s12864-022-08616-3.

Aunin E et al. (2020) Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PLoS Pathogens 16(8): e1008717. DOI: 10.1371/journal.ppat.1008717.

Howick VM et al. (2019) The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science 365: 6455. DOI: 10.1126/science.aaw2619.

International Helminth Genomes Consortium (2018) Comparative genomics of the major parasitic worms. Nature Genetics 51: 163-174. DOI: 10.1038/s41588-018-0262-1.

Reid AJ et al. (2018) Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. eLife 7: e33105. DOI: 10.7554/eLife.33105.

Brugat T et al. (2017) Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection. Nature Microbiology 2: 16276. DOI: 10.1038/nmicrobiol.2016.276.

Reid AJ (2014) Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa. Parasitology 142 (Suppl. 1): S57-70. DOI 10.1017/S0031182014001528.

Reid AJ et al. (2014) Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research 24: 1676-1685. DOI: 10.1101/gr.168955.113.

Teaching and Supervisions

Teaching:

2024/2025:

Managing bioinformatics software and pipelines - Trainer
Single-cell RNA-seq analysis - Training Lead, Trainer

2023/2024:

Analysis of Single-cell RNA-seq Data - Training Lead, Trainer
Analysis of Bulk RNA-seq Data - Training Lead, Trainer

2022/2023:

Analysis of Single-cell RNA-seq Data - Training Lead, Trainer

2021/2022:

Analysis of Single-cell RNA-seq Data - Training Lead, Trainer

Head of Bioinformatics, Gurdon Institute

Biography

Publications

Teaching and Supervisions

Contact Details

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Contact: bioinfotraining@bio.cam.ac.uk

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