David Lynn

Professor, BA MSc PhD

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Research activity per year

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David has an international track record (having worked in Canada, Ireland and Australia) in applying computational and experimental systems biology approaches to investigate the immune system and more recently, cancer. Following a PhD in computational immunology at University College Dublin and a postdoctoral position in population immunogenomics at Trinity College Dublin, he moved to Vancouver (SFU & UBC) where he was the lead computational biologist on a Grand Challenges in Global Health Initiative project investigating how to modulate the innate immune response to several pathogens of major importance to global health. Since 2014, David is a European Molecular Biology Laboratory (EMBL) Australia Group Leader at the South Australian Health and Medical Research Institute (SAHMRI). EMBL Australia Group Leader positions are prestigious positions (only 15 awarded in Australia) which come with up to 9 years of funding for the group. In 2019, David was promoted to Director of the Computational and Systems Biology Program at SAHMRI, one of the 16 Programs/Divisions in the Institute. He also holds a full academic faculty position as Professor at the Flinders University School of Medicine.

David’s group is a multi-disciplinary group that is equally divided between computational and experimental systems biology. On the wet-lab side, his group employs in vitro and in vivo experimental and clinical models coupled with systems biology approaches to investigate the interplay between the microbiome and the immune system. For example, we have recently shown that early life antibiotic exposure in mice leads to significantly impaired vaccine antibody responses to commercial vaccines administered to millions of infants worldwide (Cell Host Microbe, 2018). This has led to a new, NHMRC-funded (2019-2021 as CIA), clinical trial in human infants and is informing new research on microbiota-targeted interventions to boost vaccine efficacy.

On the bioinformatics side, his group has developed a wide-range of bioinformatics software and online resources, which are all open source and open access. These include InnateDB.com, an internationally recognised systems biology platform for network and pathway analysis (40,000 users worldwide; >800 citations). We have also developed a range of software in the network biology space including applications for dynamic network analysis and visualisation (DyNet). We have also developed software for proteomics (HiQuant) and recently published one of the first bioinformatics tools for the analysis of spatial transcriptomics data (published in Cell Systems). His group has also led the computational biology aspects of a €12 million European funded project investigating how to model and subsequently therapeutically target protein interaction networks in colorectal cancer.


Education/Academic qualification

PhD, Bioinformatic Discovery & Evolutionary Analysis of Novel Innate Immunity Genes, University College Dublin


Masters, A Comparative Analysis of Synonymous Codon Usage Patterns in Forty Completely Sequenced Bacterial Genomes, University of Ottawa


Bachelor's Degree (Honours), Investigation of the Effect of GC Skew in Two Completely Sequenced Chlamydia Genomes, Trinity College Dublin


External positions

Professor, School of Medicine, Flinders University, Flinders University

1 Jan 2019 → …

Associate Professor, School of Medicine, Flinders University

201431 Dec 2018

Adjunct Lecturer, School of Biochemistry & Immunology, Trinity College Dublin


Vision Appointment in Computational Biology, Teagasc


Postdoctoral Research Associate, Simon Fraser University


Honorary Research Associate, University of British Columbia


Postdoctoral Fellow, Trinity College Dublin



  • systems immunology
  • bioinformatics
  • vaccine biology
  • cancer biology
  • microbiota
  • genomics
  • systems biology
  • mouse models
  • immunotherapy

Collaborations and top research areas from the last five years

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