David Lynn

Professor

  • 4314 Citations
  • 29 h-Index
20022019
If you made any changes in Pure these will be visible here soon.

Personal profile

Public Profile

 

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.

 

Education/Academic qualification

PhD, University College Dublin

20012004

Masters, University of Ottawa

20002001

Bachelor's Degree (Honours), Trinity College Dublin

19962000

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, Ireland.

20122013

Vision Appointment in Computational Biology, Teagasc

20092014

Postdoctoral Research Associate, Simon Fraser University

20072009

Honorary Research Associate, University of British Columbia

20072009

Postdoctoral Fellow, Trinity College Dublin, Ireland.

20042006

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Research Output 2002 2019

4 Citations (Scopus)

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

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. I., Jurisica, I., Hermjakob, H., Orchard, S., Porras, P., Khadake, J., Meldal, B., Panni, S., Thorneycroft, D. & 23 othersvan 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. & authors, IME. C. C., 2019, In : Nature Communications. 10, 1

Research output: Contribution to journalArticle

Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia

Ryan, F. J., Drew, D. P., Douglas, C., Leong, L. E. X., Moldovan, M., Lynn, M., Fink, N., Sribnaia, A., Penttila, I., McPhee, A. J., Collins, C. T., Makrides, M., Gibson, R. A., Rogers, G. B. & Lynn, D. J., 29 Oct 2019, In : mSystems. 4, 5

Research output: Contribution to journalArticle

2 Citations (Scopus)

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation

Charitou, T., Srihari, S., Lynn, M., Jarboui, M. A., Fasterius, E., Moldovan, M., Shirasawa, S., Tsunoda, T., Ueffing, M., Xie, J., Xin, J., Wang, X., Proud, C., Boldt, K., Al-Khalili Szigyarto, C., Kolch, W. & Lynn, D., 2 Jul 2019, In : British Journal of Cancer. 121, 1, p. 37-50 14 p.

Research output: Contribution to journalArticle

Analysis and visualization of dynamic networks using the DyNet App for cytoscape

Salamon, J., Goenawan, I. H. & Lynn, D., 31 Aug 2018, In : Current Protocols in Bioinformatics. 30168906.

Research output: Contribution to journalArticle

Open Access
File