Understanding the regulation of the immune system from a systems-level perspective
The Lynn group is a multi-disciplinary group that is equally divided between computational systems biology and experimental immunology.
On the wet-lab side, the 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, Lynn’s group leads the development of InnateDB, an internationally recognised systems biology platform for innate immunity networks.
David Lynn also leads the computational biology aspects of a €12 million European Commission-funded project called PRIMES, which is investigating how to model, and subsequently therapeutically target, protein interaction networks in cancer.
The Lynn Group is continuing their work investigating the role that the microbiota in early-life plays in shaping the developing immune system, and how this influences responses to vaccination. To do this, they will continue to employ mouse models (including germ-free) and run a large clinical study in human infants.
On the bioinformatics side of the group, they recently developed a novel application for spatial transcriptomics and will continue to develop novel software to facilitate systems-level analysis.
- 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.
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|