Theme Member
Professor David Lynn

Position 

Director, Computational & Systems Biology Program. Precision Medicine Theme.

Group Leader, SAHMRI Microbiome & Host Health Program.

EMBL Australia Group Leader.

Professor, College of Medicine & Public Health, Flinders University.

Contact

P +61 881 284 053

E david.lynn@sahmri.com

David Lynn Track Record & Research Interests

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 (10,000 users worldwide; >500 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 inCell 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.

David's Group Members

Alumni

Software & Resources:

www.innatedb.com – systems biology platform for innate immunity and beyond. Pathway, Gene Ontology and Network Analysis & Visualisation tools all freely available. >30,000 molecular interactions of relevance to innate immunity manually annotated plus another 300,000 imported interactions representing the entire human and mouse interactome.

http://apps.cytoscape.org/apps/dynet - DyNet is a Cytoscape application that provides a range of functionalities for the visualization, realtime synchronization, and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most ‘rewired’ nodes across many network states.

http://www.innatedb.com/CerebralWeb/ - CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualisation of molecular interaction networks stratified based on subcellular localisation or other custom annotation. The application is designed to be easily integrated into any website and is configurable to customise the network visualisation.

www.primesdb.eu/ – platform for investigating dynamic re-wiring of PPI networks in cancer. Not currently publically available.

chat.primesdb.eu – Contextual hub analysis tool (CHAT). Find nodes in a network that are more connected to contextually relevant nodes than statistically expected by chance.

hiquant.primesdb.eu – High-throughput SILAC analysis tool.

https://code.google.com/p/sigora/ - R-based Pathway Analysis tool. Uses statistically over-represented gene-pair signatures to identify more biologically relevant pathways in omics datasets.

http://apps.cytoscape.org/apps/chat - The Contextual Hub Analysis Tool (CHAT) enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance.

http://apps.cytoscape.org/apps/insitunet - InsituNet converts in situ sequencing data into interactive network-based visualizations, where each transcript is a node in the network and edges represent the spatial co-expression relationships between transcripts. InsituNet profiles and facilitates comparison of different 2D tissue regions by identifying spatial co-expressions that occur between transcripts both significantly more, and less, than statistically expected, given the frequency of the transcripts in the tissue.

Grant Funding & Awards (last 5 years):

2019-2021 National Health & Medical Research Council (NHMRC) Project Grant (APP1156415). “How does the microbiota modulate vaccine responses in human infants: A systems vaccinology approach.”($858,033). Role: CIA. CIs: David Lynn, Geraint Rogers, Helen Marshall, Damon Tumes.

2019-2023 EMBL Australia Group Leader Funding (SAHMRI/Flinders University). “Emergent Properties of Complex Systems”. ($2,845,108). Role: CIA.

2019-2019 Flinders University NHMRC Near Miss Funding Scheme. "Characterising the mechanisms through which early-life dysbiosis modulates B and T cell responses to vaccination." ($25,000). Role: CIA.

2018 Australian Bioinformatics and Computational Biology Society Mid-Career Researcher Award.

2018 Australian Cancer Research Foundation. “ACRF Centre for Integrated Cancer Systems Biology.” ($2.5 million). CIs: Hughes, Zannettino, White, Proud, Wesselingh, Lynn*, Butler, Gronthos, Tilley, Price, Worthley, Bulone. * Leads computational & systems biology aspects.

2018-2018 The Flinders Foundation Health Seed Research Grant. “The role of the gut microbiota in the efficacy and toxicity of agonistic antibody cancer immunotherapies”($22,890). Role: CIA. CIs: David Lynn

2018-2021 Medical Research Future Fund (APP1152268). “Using metagenomics and the Registry of Ageing South Australians to understand carriage and transmission of antimicrobial resistance in the elderly”. ($1,414,049.50). Role: CIG.

2018-2020 Cancer Australia Project Grant (APP1138766). "Novel co-extinction strategies for treatment of prostate cancer". ($596,409). Role: CIB.

2018-2018 Flinders University NHMRC Near Miss Funding Scheme. “A systems vaccinology study to uncover how dysregulation of the infant gut microbiome leads to impaired vaccine responses.” ($30,000). Role: CIA.

2016-2018 National Health & Medical Research Council (NHMRC) Project Grant (APP1098429). "The impact of neonatal gut microbiome on specific and nonspecific vaccine responses". ($661,495.50). Role: CIA.

2016-2018 National Health & Medical Research Council (NHMRC) Project Grant (APP1104281). "Blood serum microRNA biomarkers for oesophageal cancer". ($495,432.60). Role: CID.

2015-2017 The Garnett Passe and Rodney Williams Memorial Foundation. "Blood serum microRNA biomarkers for detection of oropharyngeal cancer" ($372,375). Role: CID.

2014-2016 Australian Hotels Association (SA) - Hotel Care Community Projects. Funding for High Performance Computing Infrastructure for Bioinformatics at SAHMRI ($150,000).

2014-2019 EMBL Australia Group Leader Funding (~$3 million). Role: CIA.

2014-2014 NC3Rs (UK) CRACK IT Challenge 16 - Virtual Infectious Disease Research (£84,561). “Modelling of the molecular interactions between host and pathogen” Role: CI.

2011-2016 European Commission FP7-HEALTH-2011 (P#278568). "PRIMES: Protein interaction machines in oncogenic EGF receptor signalling" (€11,999,640). Role: CI/WP Leader ($1.2 million).

2011-2014 Teagasc Research Funding (RMIS6082). "MicroRNA regulation of the host response to bovine TB" (€92,282). Role: PI.

Publications:

Khadake J., Meldal B., Panni S., Thorneycroft D., van Roey K., Abbani S., Salwinski L., Pellegrini M., Iannuccelli M., Licata L., Cesareni G., Roechert B., Bridge A., Ammari M.G., McCarthy F., Broackes-Carter F., Campbell N.H., Melidoni A.N., Rodriguez-Lopez M., Lovering R.C., Jagannathan S., Chen C., Lynn D.J., Ricard-Blum S., Mahadevan U., Raghunath A.,del Toro N., Duesbury M., Koch M., Perfetto L., Shrivastava A., Ochoa D., Wagih O., Piñero J., Kotlyar M., Pastrello C., Beltrao P., Furlong L., Jurisica I., Hermjakob H., Orchard S., Porras P. (2019).Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications. 10 (2019).

Salamon J., Goenawan I.H., Lynn D.J. (2018). Analysis and visualization of dynamic networks using the DyNet App for cytoscape. Current Protocols in Bioinformatics 63(5): e55. Corresponding Author.

MacGregor S., Ong J.S., An J., Han X., Zhou T., Siggs O.M., Law M.H., Souzeau E., Sharma S., Lynn D.J., Beesley J., Sheldrick B., Mills R.A., Landers J., Ruddle J.B., Graham S.L., Healey P.R., White A.J.R., Casson R.J., Best S., Grigg J.R., Goldberg I., Powell J.E., Whiteman D.C., Radford-Smith G.L., Martin N.G., Montgomery G.W., Burdon K.P., Mackey D.A., Gharahkhani P., Craig J.E., Hewitt A.W. (2018). Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma. Nature Genetics 50(8):1067-1071.

Lynn M.A., Tumes D.J., Choo J.M., Sribnaia A., Blake S.J., Leong L.E.X., Young G.P., Marshall H.S., Wesselingh S.L., Rogers G.B., Lynn D.J. (2018). Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice. Cell Host & Microbe 23: 1-8. Corresponding Author.

Nguyen E., Centenera M., Moldovan M., Das R., Irani S., Vincent A., Chan H., Horvath L., Lynn D.J., Daly R., Butler L. (2018). 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 Apr 9. pii: mcp.RA118.000633 [Epub ahead of print].

Salamon J., Qian X., Nilsson M., Lynn D.J. (2018). Network visualization and analysis of spatially aware gene expression data with InsituNet. Cell Systems 6:1-5. Corresponding Author.

Dumousseau M., Alonso-López D., Ammari M., Bradley G., Campbell N.H., Ceol A., Cesareni G., Combe C., De Las Rivas .J, Del-Toro N., Heimbach J., Hermjakob H., Jurisica I., Koch M., Licata L., Lovering R.C., Lynn D.J., Meldal B., Micklem G., Panni, S., Porras P., Ricard-Blum S., Roechert B., Salwinski L., Shrivastava A., Sullivan J., Thierry-Mieg N., Yehudi Y., Van Roey K., Orchard S. (2018). Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics 19(1):134.

Gharahkhani P., Burdon K.P., Cooke Bailey J.N., Hewitt A.W., Law M.H., Pasquale L.R., Kang J.H., Haines J.L., Souzeau E., Zhou T., Siggs O.M., Landers J., Awadalla M., Sharma S., Mills R.A., Ridge B., Lynn D.J., NEIGHBORHOOD consortium, Casson R., Graham S.L., Goldberg I., White A., Healey P.R., Grigg J., Lawlor M., Mitchell P., Ruddle J., Coote M., Walland M., Best S., Vincent A, Gale J., Radford Smith G., Whiteman D.C., Montgomery G.W., Martin N.G., Mackey D.A., Wiggs J.L., MacGregor S., Craig J.E. (2018). Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma. Scientific Reports 8(1):3124.

Armstrong H.K., Gillis J., Johnson I.R.D., Nassar Z.D., Moldovan M., Levrier C., Sadowski M.C., Chin M.Y., Guns E.T., Tarulli G., Lynn D.J., Brooks D.A., Selth L.A., Centenera M.M., Butler L.M. (2018). Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion. Scientific Reports 8(1):2090.

Lynn D.J., Pulendran B. (2018). The potential of the microbiota to influence vaccine responses. Journal of Leukocyte Biology 103(2):225-231. Corresponding Author.

Smith J.R, Todd S., Ashander L.M., Charitou T., Ma Y., Yeh S., Crozier I., Michael M., Appukuttan B., Lynn D.J.*, Marsh G.A*. (2017). 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. * Joint-senior author.

Muetze T., Goenawan I.H., Wiencko H.L., Bernal-Llinares M., Bryan K., Lynn D.J. (2016) Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. F1000 Research 5: 1745. 

Goenawan I., Bryan K., Lynn D.J. (2016). DyNet: visualization and analysis of dynamic molecular interaction networks. Bioinformatics btw187. Corresponding Author.

Bryan K., Jarboui M., Bernal-Llinares M., Raso C., McCann B., Rauch J., Boldt, K. Lynn D.J. (2016) HiQuant: Rapid post-quantification analysis of large-scale MS-generated proteomics data. Journal of Proteome Research. (Epub. April 18). Corresponding Author.

Blohmke C.J., Darton T.C., Jones C., Suarez N.M., Waddington C.S., Angus B., Zhou L., Hill J., Clare S., Kane L., Mukhopadhyay S., Schreiber F., Duque-Correa MA., Wright J.C., Roumeliotis T.I., Yu L., Choudhary J.S., Mejias A., Ramilo O., Shanyinde M., Sztein M.B., Kingsley R.A., Lockhart S., Levine M.M., Lynn D.J., Dougan G., Pollard A.J. (2016). Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever. Journal of Experimental Medicine jem.20151025.

Richardson I.W., Berry D.P., Wiencko H.L., Higgins I.M., More S.J., McClure J., Lynn D.J., Bradley D.G. (2016). A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genetics, Selection & Evolution 48(1):19.

Charitou, T., Bryan, K., Lynn D.J. (2016). Using biological networks to integrate, visualize and analyze genomics data. Genetics, Selection & Evolution 48(1):27. Corresponding Author.

Dickinson P., Smith C., Forster T., Craigon M., Ross A., Khondoker M., Ivens A., Lynn D.J., Orme J., Jackson A., Lacaze P., Flanagan K., Stenson B., Ghazal P. (2015). Whole blood gene expression profiling of neonates with confirmed bacterial sepsis. Genomics Data 3:41-8.

Foley C., Chapwanya A., Callanan J.J., Whiston R., Miranda-CasoLuengo R., Lu J., Meijer W.J., Lynn D.J., O’ Farrelly C., Meade K.G. (2015). Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. BMC Genomics 16(1):811.

Frias S., Bryan K., Brinkman F.S.L., Lynn D.J. (2015). CerebralWeb: a Cytoscape.js plug-in to visualise networks stratified by subcellular localization. Database 2015:bav041. Corresponding Author.

Vegh P., Magee D.A., Nalpas N.C., Bryan K., McCabe M.S., Browne J.A., Conlon K.M., Gordon S.V., Bradley D.G., MacHugh D.E., Lynn D.J. (2015). MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking. Tuberculosis 95(1): 60-67. Corresponding Author.

Lawless N., Vegh P., O’Farrelly C., Lynn D.J. (2014). The role of microRNAs in bovine infection and immunity. Frontiers in Immunology 5:611. Corresponding Author.

Smith C., Dickinson P., Forster T., Craigon M., Ross A., Khondoker M., France R., Ivens A., Lynn D.J., Orme J., Jackson A., Lacaze P., Flanagan K., Stenson B., Ghazal P. (2014). Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nature Communications 5:4649.

Lawless N., Reinhardt T.A., Bryan K., Baker M., Pesch B., Zimmerman D., Zuelke K., Sonstegard T., O’Farrelly C., Lippolis J.D., Lynn D.J. (2014) MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. G3: Genes, Genomes, Genetics. 4(6):957-971. Corresponding Author. Featured in the Genetics/G3 special issue on the Genetics of Immunity.

Fatima A., Lynn D.J., O’Boyle P., Seoighe C, Morris D. (2014). The miRNAome of the postpartum dairy cow liver under negative energy balance. BMC Genomics 15(1): 279.

Foroushani A, Brinkman F.S.L., Lynn D.J. (2013). Pathway-GPS and SIGORA: Identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ 1e:229. Corresponding Author.

Meredith B.K., Berry D.P., Kearney J.F., Finlay E.K., Fahey A.G., Bradley D.G., Lynn D.J. (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. Frontiers in Genetics 4, 229. Corresponding Author.

Vegh P., Foroushani A.B.K., Magee D.A., McCabe M.S., Browne J.A., Nalpas N.C., Conlon K.M., Gordon S.V., Bradley D.G., MacHugh D.E., Lynn D.J. (2013). Profiling microRNA expression in bovine alveolar macrophages using RNA-seq. Veterinary Immunology and Immunopathology 155(4), 238-244. Corresponding Author.

Lawless N., Foroushani A.K., McCabe M., O’Farrelly C., Lynn D.J. (2013). Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection. PLOS ONE 8(3):e57543. Corresponding Author.

Breuer K., Foroushani A.K., Laird M.R., Chen C., Sribnaia A., Lo R., Winsor G.L., Hancock R.E.W., Brinkman F.S.L., Lynn D.J. (2012) InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation. Nucleic Acids Research, 2012, 41(D1):D1228-33. (Featured on NAR cover). Corresponding Author.

Tellam J., Lekieffre L., Zhong J., Lynn D.J., Khanna R. (2012). Messenger RNA Sequence Rather than Protein Sequence Determines the Level of Self-synthesis and Antigen Presentation of the EBV-encoded Antigen, EBNA1. PLoS Pathogens 8(12): e1003112.

Achtman A.H., Pilat S., Law C.W., Lynn D.J., Janot L., Mayer, M.L., Ma S., Kindrachuk J., Finlay B.B., Brinkman F.S.L, Smyth G.K., Hancock R.E.W., Schofield L. (2012). Effective adjunctive therapy by an innate defense regulatory Peptide in a preclinical model of severe malaria. Science Translational Medicine 4(135), 135ra64.

McCabe M.S., Waters S.M., Morris D.G., Kenny D.A., Lynn D.J., Creevey C. (2012). RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. BMC Genomics 13(1), 193.

O'Loughlin A., Lynn D.J., McGee M., Doyle S., McCabe M.S., Earley B. (2012). Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology. BMC Genomics 13(1), 250.

Orchard S., Kerrien S., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F.S.L., Cesareni G., Chatr-aryamontri A., Chautard E., Dumousseau M., Eisenberg D., Goll J., Hancock R.E.W., Hannick L.I., Jurisica I., Khadake J., Lynn, D.J., Mahadevan U., Perfetto L., Raghunath A., Ricard-Blum S., Salwinski L., Stümpflen V., Tyers M., Uetz P., Xenarios I., Hermjakob H. (2012). Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). Nature Methods 9(4), 345–350.

Meredith B.K., Kearney F.J, Finlay E.K., Bradley D.G., Fahey A.G., Berry D.P., Lynn D.J. (2012). Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland. BMC Genetics 13(1), 21. Corresponding Author.

Magee D.A., Taraktsoglou M., Killick K.E., Nalpas N.C., Browne J.A., Park S.D.E., Conlon K.M., Lynn D.J., Hokamp K., Gordon S.V., Gormley E., MacHugh D. (2012). Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis. PLOS ONE.7(2), e32034.

Aranda B., Blankenburg H., Kerrien S., Brinkman F.S.L., Ceol A., Chautard E., De La Rivas J., Galeota E, Gaulton A., Goll J., Hancock R.E.W., Isserlin R., Jimenez R., Lynn D.J., Michaut M., O’Kelly G., Ono K., Orchard S., Prieto C., Razick S., Rigina O., Salwinski L., Simonovic M., Winter A., Wu G., Bader G., Cesareni G., Donaldson I.M., Eisenberg D., Overington J., Ricard-Blum S., Tyers M., Albrecht M., Hermjakob H. (2011). PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods 8, 528-529.

Schreiber F., Lynn D.J., Houston A., Peters P., Mwafulirwa G., Finlay B.B., Brinkman F.S.L., Hancock R.E.W., Heyderman R.S., Dougan G., Gordon M.A. (2011). The Human Transcriptome During Nontyphoid Salmonella and HIV Coinfection Reveals Attenuated NF kappa B-Mediated Inflammation and Persistent Cell Cycle Disruption. Journal of Infectious Diseases 204(8),1237-1245.

Hoang L.T., Lynn D.J., Henn M., Birren B.W., Lennon N.J., Lee P.T., Duong K.T., Nguyen T.T., Mai L.N., Farrar J.J., Hibberd M.L., Simmons C.P. (2010). An Early Whole-blood Transcriptional Signature Associated with Progression to Dengue Shock Syndrome in Vietnamese Children. Journal of Virology 84(24), 12982-12994.

Whan V., Hobbs M., McWilliam S., Lynn D.J., Strandberg Lutzow Y., Khatkar M., Barendse W., Raadsma H., Tellam R.L. (2010). Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes. BMC Genomics 11(1), 654.

Lynn D.J., Chan C., Naseer M., Yau M., Lo R., Sribnaia A., Ring G., Que J., Wee K., Winsor G.L., Laird M.R., Breuer K., Foroushani A.K., Brinkman F.S.L., Hancock R.E.W. (2010). Curating the Innate Immunity Interactome. BMC Systems Biology 4(1):117. Corresponding Author.

Lynn D.J., Gardy J.L., Fjell CD, Hancock R.E.W., Brinkman F.S.L. (2010). Systems-Level Analyses of the Mammalian Innate Immune Response. Book Chapter in Systems Biology for Signaling Networks, Springer Publishing, N.Y. Volume 1, Part 3, 531-560. Corresponding Author.

Byrne K., Colgrave M.L., Vuocolo T., Pearson R., Bidwell C.A., Cockett N.E., Lynn D.J., Fleming-Waddell J.N., Tellam R.L. (2010). The Imprinted Retrotransposon-Like Gene PEG11 (RTL1) Is Expressed as a Full-Length Protein in Skeletal Muscle from Callipyge Sheep. PLOS ONE 5(1): e8638.

Thompson L.J., Dunstan S.J., Dolecek C., Perkins T., House D., Dougan G., Hue N.T., La T.T., Du D.C., Phuong L.T., Dung N.T., Hien T.T., Farrar J.J., Monack D., Lynn D.J., Popper S.J., Falkow S. (2009). Transcriptional Response in the Peripheral Blood of Patients Infected with Salmonella enterica serovar Typhi. Proceedings of the National Academy of Sciences USA 106(52), 22433-22438.

Gardy J.L., Lynn D.J., Brinkman F.S.L., Hancock R.E.W. (2009). Enabling a Systems Biology Approach to Immunology: Focus on Innate Immunity. Trends in Immunology 30(6), 249-262. Joint First Author.

Downing T., Lynn D.J., Connell S., Lloyd A.T., Bhuiyan A.K.F.H., Silva P., Naqvi A., Sanfo R., Sow R.S., Podisi B., Hanotte O., O’Farrelly C., Bradley D.G. (2009). Evidence of Balanced Diversity at the Chicken Interleukin 4 Receptor Alpha Chain Locus. BMC Evolutionary Biology 9(1):136.

The Bovine Genome Sequencing and Analysis Consortium (2009). The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science 324(5926), 522-528. Analysis Project Leader.

The Bovine HapMap Consortium (2009). Genome Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science 324(5926), 528-532.

Downing T., Lynn D.J., Connell S., Lloyd A.T., Bhuiyan A.K.F.H., Silva P., Naqvi A., Sanfo R., Sow R.S., Podisi B., O’Farrelly C., Hanotte O., Bradley D.G. (2009). Contrasting Evolution of Diversity at Two Disease-Associated Chicken Genes. Immunogenetics 61(4), 303-314.

Lemay D.G., Lynn D.J., Martin W.F., Casey T.M., Kriventseva E.V., Rincon G., Barris W., Hinrichs A.S., Molenaar A.J., Pollard K.S., Neville M.C., Maqbool N.J., Zdobnov E.M., Medrano J.F., Tellam R., German J.B., Rijnkels M. (2009). The Bovine Lactation Genome: Insights into the Evolution of Mammalian Milk. Genome Biology 10(4):R43.

Lynn D.J., Winsor G.L., Chan C., Richard N., Laird M.R., Barsky A., Gardy J.L., Roche F.M., Chan T.H.W., Shah N., Lo R., Naseer M., Que J., Yau M., Acab M., Tulpan D., Whiteside M.D., Chikatamarla A., Mah B., Munzner T., Hokamp K., Hancock R.E.W., Brinkman F.S.L. (2008). InnateDB - Facilitating Systems Level Analyzes of the Mammalian Innate Immune Response. Molecular Systems Biology 4:218 (www.nature.com/msb). Joint Corresponding Author. Review of InnateDB paper featured in Cell Host & Microbe. 2008 4(4):312-3.

Freeman A.R., Lynn D.J., Murray C., Bradley D.G. (2008). Detecting the Effects of Selection at the Population Level in Bovine Immune Genes. BMC Genetics 9:62. Joint First Author.

Lynn D.J., Higgs R., Lloyd A.T., Hervé-Grépinet V., Nys Y., Brinkman F.S.L., Yu P.L., Soulier A., Kaiser P., Zhang G., O’Farrelly C., Lehrer R.I. (2007). Avian Beta-Defensin Nomenclature: A Community Proposed Update. Immunology Letters 110(1), 86-89. Corresponding Author.

Higgs R., Lynn D.J., Cahalane S., James T., Lloyd A.T. and O’Farrelly C. (2007). Modification of chicken avian beta-defensin-8 at positively selected amino acid sites enhances specific antimicrobial activity. Immunogenetics 59(7), 573-580.

Lynn D.J., Bradley, D.G. (2007). Discovery of alpha-Defensins in Basal Mammals. Developmental & Comparative Immunology 31(10), 963-967. Corresponding Author.

Cruz F., Bradley D.G., Lynn D.J. (2007). Evidence of Positive Selection on the Atlantic Salmon CD3 Gene. Immunogenetics 59(3), 225-232. Corresponding & Senior Author.

Murphy A.M., MacHugh D.E., Park S.D.E., Scraggs E., Haley C.S., Lynn D.J., Boland M.P., Doherty M.L. (2007). Linkage Mapping of the Locus for Inherited Ovine Arthrogryposis (IOA) to Sheep Chromosome 5. Mammalian Genome 18(1) 43-52. (Featured on Mammalian Genome cover).

Higgs R., Cormican P., Cahalane S., Allan B., Lloyd A.T., Meade K., James T., Lynn D.J., Babiuk L., O'Farrelly C. (2006). Upregulation of a Novel Chicken TLR Following Salmonella enterica Serovar Typhimurium Infection. Infection and Immunity 74(3), 1692-1698.

Lynn D.J., Freeman A.R., Murray C.U., Bradley D.G. (2005). A Genomics Approach to the Detection of Positive Selection in Cattle – Adaptive Evolution of the T Cell and NK Cell Surface Protein, CD2. Genetics 170(3), 1189-1196.

Higgs R., Lynn D.J., Gaines S., McMahon J., Tierney J., James T., Lloyd A.T., Mulcahy G., O’Farrelly C. (2005). The Synthetic Form of a Novel Chicken -Defensin Identified in Silico is Predominantly Active against Intestinal Pathogens. Immunogenetics 57(1-2), 90-98.

Lynn D.J., Higgs R., Gaines S., Tierney J., James T., Lloyd A.T., Fares M.A., Mulcahy G., O’Farrelly C. (2004). Bioinformatic Discovery and Initial Characterisation of Nine Novel Antimicrobial Peptide Genes in the Chicken. Immunogenetics 56(3), 170-177.

Lynn D.J., Lloyd A.T., Fares M.A., O’Farrelly C. (2004). Evidence of Positively Selected Sites in Mammalian -Defensins. Molecular Biology and Evolution 21(5), 819-827.

Lynn D.J., Lloyd A.T., O’Farrelly C. (2003). In Silico Identification of Components of the Toll-Like Receptor (TLR) Signalling Pathway in Clustered Chicken Expressed Sequence Tags (ESTs). Veterinary Immunology & Immunopathology 93(3-4), 177-184.

Lynn D.J., Lloyd A.T., O’Farrelly C. (2003). Bioinformatics: Implications for Medical Research and Clinical Practice. Clinical Investigative Medicine 26(2), 70-74.

Duffy M.J., Lynn D.J., Lloyd A.T., O’Shea C.M. (2003). The ADAMs Family of Proteins: From Basic Studies to Potential Clinical Applications. Thrombosis and Haemostasis 89(4), 622-631.

Lynn D.J., Singer G.A.C., Hickey D.A. (2002). Synonymous Codon Usage is Subject to Selection in Thermophilic Bacteria. Nucleic Acids Research 30(19), 4272-4277.

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SAHMRI is located on the traditional lands of the Kaurna Nation.

The SAHMRI community acknowledges and respects the traditional owners, the family clans who are the Kaurna Nation from the Adelaide Plains region of South Australia. We acknowledge the clans of the Kaurna Nation and the sacred knowledge they hold for their country. We pay our respects to the Kaurna Nation, their ancestors and the descendants of these living family clans today.