- The impact of the microbiota in early-life on the developing immune system and optimal vaccine responses.
- How does the microbiota modulate vaccine responses in human infants: A systems vaccinology approach.
- Vaccine non-specific effects and trained innate immunity.
- The impact of the microbiota on the efficacy and toxicity of cancer immunotherapies.
- InnateDB an internationally recognised platform facilitating systems-level analyses of innate immunity.
- Gnotobiotic (germ-free) mouse models.
Bioinformatics and Computational Biology
- The development of novel software applications and resources for proteomics, pathway analysis, network analysis and visualisation (e.g. DyNet; CHAT; SIGORA; HiQuant).
- Protein-Protein Interaction Network Rewiring in Cancer (International PRIMES consortium).
- Patient-Specific Network Rewiring.
- Transcriptional and metabolic reprogramming of colorectal cancer cells expressing the oncogenic KRASG13D mutation.
- Novel co-extinction strategies for treatment of prostate cancer.
- Network visualization and analysis of spatial omics data.
David has an international track record in applying computational and experimental systems biology approaches to investigate the immune system.
Following a PhD in computational immunology 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. He was also awarded a Michael Smith Foundation for Health Research postdoctoral fellowship during this time.
In 2009, he was appointed as a “Vision” Group Leader in Computational Biology at the Irish agriculture and food research agency (Teagasc), where his group developed computational and experimental approaches (particularly NGS based) to investigate the immune response to several bovine infectious diseases. Within 3 years here, he built up a group of eight people and attracted more than €1.5 million in funding. He also continued to collaborate extensively in the area of human infectious disease. In 2011, he was awarded the Teagasc Excellence in Research Award.
In 2014, he was appointed as EMBL Australia Group Leader in the Infection and Immunity Theme at the South Australian Health and Medical Research (SAHMRI). He also holds a joint faculty appointment as Professor at the College of Medicine and Public Health, Flinders University
At SAHMRI, David’s group is a multi-disciplinary group that is equally divided between bioinformatics and experimental 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, vaccines and the immune system. On the bioinformatics side, his group leads the development of InnateDB.com, an internationally recognised systems biology platform for innate immunity networks (10,000 users worldwide).
David also leads the computational biology aspects of the €12 million European Commission funded project called PRIMES, which is investigating how to model and subsequently therapeutically target protein interaction networks in cancer.
mSystems (2019) 4(5) pii: e00484-19.
|Changes in the composition of the gut microbiota and the blood transcriptome in preterm infants <29 weeks gestation diagnosed with bronchopulmonary dysplasia|
British Journal of Cancer (2019) 121(1): 37–50.
|Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation|
Cell Host & Microbe (2018) 23(5): 653-660.
|Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice|
Cell Systems (2018) 6(5): 626-630.
|Network visualization and analysis of spatially aware gene expression data with InsituNet|
Nucleic Acids Research (2013) 41(D1):D1228-33.
|InnateDB: systems biology of innate immunity and beyond. Nucleic Acids Research|