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.
CURRENT RESEARCH:
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.
Systems Immunology
- 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.
Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice. Cell Host & Microbe, 23(5): 653-660. Corresponding Author. |
Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice. |
Analysis and visualization of dynamic networks using the DyNet App for Cytoscape. Current Protocols in Bioinformatics, 63(5): e55. Corresponding Author. |
Analysis and visualization of dynamic networks using the DyNet App for Cytoscape. |
Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma. Nature Genetics, 50(8): 1067-1071. |
Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma. |
Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants. Molecular & Cellular Proteomics, 17(8): 1470-1486. |
Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants. |
Network visualization and analysis of spatially aware gene expression data with InsituNet. Cell Systems, 6(5): 626-630. Corresponding Author. |
Network visualization and analysis of spatially aware gene expression data with InsituNet. |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1):134. |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. |
Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma. Scientific Reports, 8(1): 3124. |
Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma. |
Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion. Scientific Reports, 8(1): 2090. |
Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion. |
The potential of the microbiota to influence vaccine responses. Journal of Leukocyte Biology, 103(2): 225-231. Corresponding Author. |
The potential of the microbiota to influence vaccine responses. |
Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye. Translational Vision Science & Technology, 6(12): doi :10.1167/tvst.6.4.12. |
Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye. |
Identification of Contextually Relevant Hubs using the Contextual Hub Analysis Tool (CHAT) in Cytoscape. Current Protocols in Bioinformatics, 59 8.24.1 – 8.24.13 doi : 10.1002/cpbi.35. Corresponding Author. |
Identification of Contextually Relevant Hubs using the Contextual Hub Analysis Tool (CHAT) in Cytoscape. |
Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma. PLoS One, 12(3): e0172427. |
Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma. |
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. F1000 Research 2016 (In press). |
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. |
DyNet: visualization and analysis of dynamic molecular interaction networks. Bioinformatics. 2016 Sep 1;32(17):2713-5. doi: 10.1093/bioinformatics/btw187. Epub 2016 May 3. |
DyNet: visualization and analysis of dynamic molecular interaction networks. |
HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data. J Proteome Res. 2016 Jun 3;15(6):2072-9. doi: 10.1021/acs.jproteome.5b01008. Epub 2016 May 16. |
HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data. |
Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever. J Exp Med. 2016 May 30;213(6):1061-77. doi: 10.1084/jem.20151025. Epub 2016 May 23. |
Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever. |
Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol. 2016 Mar 31;48:27. doi: 10.1186/s12711-016-0205-1. |
Using biological networks to integrate, visualize and analyze genomics data. |
A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genet Sel Evol. 2016 Mar 9;48:19. doi: 10.1186/s12711-016-0197-x. |
A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. |
Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. BMC Genomics. 2015 Oct 19;16:811. doi: 10.1186/s12864-015-1967-5. |
Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. |
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database (Oxford). 2015 May 7;2015:bav041. doi: 10.1093/database/bav041. Print 2015. |
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. |
Profiling microRNA expression in bovine alveolar macrophages using a next-generation sequencing based approach. Tuberculosis (Edinb). 2015 Jan;95(1):60-7. |
Profiling microRNA expression in bovine alveolar macrophages using a next-generation sequencing based approach. |
MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. G3 (Bethesda). 2014 Jan 27;4(6):957-71. doi: 10.1534/g3.113.009936. |
MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. |
The miRNAome of the postpartum dairy cow liver under negative energy balance. BMC Genomics. 2014 Apr 12;15:279. doi: 10.1186/1471-2164-15-279. |
The miRNAome of the postpartum dairy cow liver under negative energy balance. |
Pathway-GPS and SIGORA: Identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ. 2013 Dec 19;1:e229. doi: 10.7717/peerj.229. eCollection 2013. |
Pathway-GPS and SIGORA: Identifying relevant pathways based on the over-representation of their gene-pair signatures. |
A Genome-wide association study for somatic cell score using the illumina high-density bovine BeadChip identifies several novel QTL potentially related to mastitis susceptibility. Front Genet. 2013 Nov 6;4:229. doi: 10.3389/fgene.2013.00229. eCollection 2013. |
A Genome-wide association study for somatic cell score using the illumina high-density bovine BeadChip identifies several novel QTL potentially related to mastitis susceptibility. |
Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection. PLoS One. 2013;8(3):e57543. doi: 10.1371/journal.pone.0057543. Epub 2013 Mar 5. |
Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection. |
Effective adjunctive therapy by an innate defense regulatory Peptide in a preclinical model of severe malaria. Sci Transl Med. 2012 May 23;4(135):135ra64. doi: 10.1126/scitranslmed.3003515. |
Effective adjunctive therapy by an innate defense regulatory Peptide in a preclinical model of severe malaria. |
Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. |
Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). |
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. |
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. |
Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24;324(5926):528-32. doi: 10.1126/science.1167936. |
Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. |
Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome, 6(1), p.68. |
Reproducible protocols for metagenomic analysis of human faecal phageomes. |
Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice. eLife, 7, p.e33070. |
Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice. |
Viromes of one-year-old infants reveal the impact of birth mode on microbiome diversity. PeerJ, 6, p.e4694. |
Viromes of one-year-old infants reveal the impact of birth mode on microbiome diversity. |
Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut, 66(4), pp.633-643. |
Tumour-associated and non-tumour-associated microbiota in colorectal cancer. |
Regulation of prefrontal cortex myelination by the microbiota. Translational Psychiatry, 6(4), p.e774. |
Regulation of prefrontal cortex myelination by the microbiota. |
SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinformatics,16(1), p.324. |
SPINGO: a rapid species-classifier for microbial amplicon sequences. |
Suppression of the ATP-binding cassette transporter ABCC4 impairs neuroblastoma growth and sensitises to irinotecan in vivo. Eur J Cancer, 2017 Sep; 83:132-141. |
Suppression of the ATP-binding cassette transporter ABCC4 impairs neuroblastoma growth and sensitises to irinotecan in vivo. |
Rhubarb extract partially improves mucosal integrity in chemotherapy-induced mucositis. World J Gastroenterol, 2016 Oct 7; 22(37):8322-8333. |
Rhubarb extract partially improves mucosal integrity in chemotherapy-induced mucositis. |
Emu oil combined with Lyprinol™ reduces small intestinal damage in a rat model of chemotherapy-induced mucositis. Nutr Cancer, 2016 Oct; 68(7);1171. |
Emu oil combined with Lyprinol™ reduces small intestinal damage in a rat model of chemotherapy-induced mucositis. |