Professor Justin Martin O'Sullivan

BSc (Hons), PhD

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Deputy Director


After completing my PhD at The University of Otago with Richard Cannon in 1998, I held postdoctoral positions in the laboratories of Professor Mick Tuite (University of Kent) and Professor Nick Proudfoot (University of Oxford).

I returned to New Zealand in 2004 to take up a faculty position at Massey University, and moved to the Liggins Institute in 2012. I was appointed the Associate Director for Research at the Liggins Institute in 2016.

I was awarded the Life Technologies Award for excellence in molecular biology research in 2010, and a Massey University Early Career Research Medal (2005).


My group takes a holistic approach to understand genomes and cell structure formation, function, and inheritance. We use discovery-based approaches and hypothesis testing to interpret the relationships between what a cell’s DNA codes for (the genotype) and what we actually see (the phenotype). Our goal is to enhance our abilities to identify what is dysfunctional and make that information accessible to clinicians - for precision medicine. To do this we use and develop methods and technologies from molecular biology, bioinformatics, and computational biology to integrate the spatial organization of genomes with measures of their function and complex meta-data – commonly called “Big data”. We specialize in the meta-analyses that integrate novel experimental and in silico techniques. Our research relies on empirical descriptions of chromosome folding and packing within eukaryotes. In our models, the chromosomes act as a scaffold for the nuclear functions that decode the information they contain (PMID: 19628047, 24815909, & 27503698). We have identified functional regulatory connections between mitochondrial DNA and nuclear genes in eukaryotic cells (PMID: 27503698) and shown that nuclear functions (transcription and replication) occur in localized environments where groups of similarly regulated genes cluster to enable stable expression (PMID: 25342201 & 26729303). This lends itself to understanding how disease associated intergenic single nucleotide polymorphisms (SNPs) impact on the phenotype by regulating genes they spatially contact (PMID: 22688649, 29018042, 30518762, & 29081791).


We are currently working in two main areas: 1) developing approaches to convert population-based measures of genetic risk to understand the mechanisms that contribute to an individual’s risk of developing a disease. To do this we are using novel approaches to interrogate how single nucleotide polymorphisms work together to contribute to complex polygenic conditions (e.g. Parkinson's, Mood disorders, Auto-immunity, Asthma, type 1 and 2 diabetes, Neuromuscular disorders, Coronary artery disease, Pre-eclampsia, Juvenile Idiopathic Arthritis, Huntington’s disease, Autism Spectrum Disorder); 2) how the genomes of bacteria the microbes that live with us (our microbiome) contribute to our well-being, if we can manipulate this interaction and modify our health status.

Teaching, affiliations and collaborations

Honorary Professor, University of Southampton, UK. (2019-2022)

Visiting Scientist, Garvan Institute, Sydney, Australia (2021-present)               

Honorary Senior Lecturer in Molecular Biology, Massey University, Auckland, New Zealand. (2012-2020)

Dr O’Sullivan has collaborations with researchers in:

  • The University of Otago, NZ.
  • The University of Canterbury, NZ.
  • University of Southampton, UK.
  • Murdoch Childrens Research Institute, Melbourne, Aus.
  • Garvan Institute of Medical Research, Sydney, Aus.
  • NiH, Washington, USA
  • Icahn School of Medicine at Mount Sinai, New York, USA

Dr O’Sullivan has recently collaborated with researchers in:

  • Imperial College London, UK
  • Cold Spring Harbor Laboratory, USA
  • The National Cancer Institute, National Institutes of Health, USA
  • University of Edinburgh, UK
  • University of Oslo, Norway
  • The Murdoch Childrens Research Institute, Melbourne, Australia
  • The Garvan Instititute, Sydney, Australia

Research | Current

  • Understanding how genomes are organized in 3-dimensions and the role that epigenetics has in shaping and maintaining this organization. Studies are designed to advance our understanding of the complex inter-relationships between what a cell’s DNA codes for (the genotype), the epigenetic code, and the result of the genotype’s conditional expression (the phenotype). These projects include paractical wet-laboratory work/experiments...
  • Investigating these problems using a holistic systems biology approach to understand genome structure formation, function, and inheritance. This approach integrates methods and technologies from molecular biology, bioinformatics, and computational biology.
  • Investigating the inter-relationships between the microbiome and the host. Can the microbiome be changed and how does this alter host development and later life disease? We are using randomised controlled trials (i.e. fecal microbiome transfer and feeding strategies) to do this.These studies include clinical, wet-laboratory, and computational aspects.
  • Investigating how SNPs contribute to the development of disease through gene regulatory networks. Studies focus on integrating data to enable crossing levels of biological information from the population based genetic information to the tissue-specific biological pathways that are affected by these changes.
  • Using network-based approaches that incorporate machine learning to identify multimorbid diseases, the genetic variants that are associated with them, the mechanisms through which they work and the drugs that might be therapeutically useful. The approaches that are being developed and implemented represent a possible step-change in our ability to understand the comorbidity, development and therapeutic avenues for pathologically related disease.

Postgraduate supervision

Current Doctoral (as lead/co-supervisor)

  1. Daniel Ho (Converting population risk to individual risk. 2017-under examination)
  2. Githal Arachchige (Measuring lipid soluble vitamins in children; 2018-present)
  3. Sreemol Gokuladhas (Genetic variants in muscle disorders; 2018-present)
  4. Sophie Farrow (Genetic variants in Parkinson's disease, 2019-present)
  5. Rachel Jaros (CoVID-19 and the lung - precision genetics, 2020-present)
  6. Michele Zuppi (Co-supervisor with Tommi Vatanen, 2020-current) 
  7. Roan Zaied (Asthma - precision genetics , 2020-present)
  8. Nicholas Pudjihartono (Co-supervisor with Tayaza Fadason and Andreas Kempa-Liehr, 2021-present)
  9. Michael Pudjihartono (Co-supervisor with William Schierding, 2021-present)
  10. Frankie Day (Co-supervisor with Chris Pook, 2021-present)


Completed Doctoral 

  1. Denis Nyaga (Regulatory network for SNPs in Type 1 diabetes in children; lead supervisor, 2017-2020)
  2. Brooke Wilson (The human microbiome. 2018-2021) Dean's list    
  3. Clara Chong Yieh Lin (Role of smell and taste in feed tolerance in preterm babies; co-supervisor, 2017-2020, Bloomfield, Liggins UoA) Dean's List
  4. Evgeniia Golovina (Finessing predictors of obesity and cognition. 2017-2021).
  5. Sarah Mitchell (co-supervisor David Cameron-Smith) 2019..
  6. Lekha Jain (co-supervisor Jo Perry) 2020. 
  7. Stephanie Andraos (Measuring water soluble vitamins, one C metabolites and methylation profeiles in infants; 2017-2020).
  8. Tayaza Fadason (Modelling SNPs, genes and pathways to predict metabolic activity; lead supervisor, completed 2019) 
  9. Thilini Maddegoda Vidanelage (Role of gut microbiome on insulin resistance of children with early adverse life events; lead-supervisor; completed 2018)
  10. Elsie Jacobson (3D chromatin and immune cell activation: do physical constraints alter nuclear conformation, and does this change cell behaviour?; lead supervisor; completed 2019) Dean's List
  11. William Schierding (The third dimension of Genetics; co-supervisor; completed 2017)
  12. Dharani Sontam (Early-life high-fat diet and voluntary physical activity affect body composition, bone phenotype and gene expression in the male rat; lead supervisor; completed 2017)
  13. Malina Doynova (Linking genome organization to nuclear function in astrocytes and muscle cells; lead supervisor; completed 2017)
  14. Tatyana Pichugina (Unravelling genome structure and function through experimentally informed polymer models; lead supervisor; completed 2015)
  15. Inswasti Cahyani (Characterisation of the Role of the RPA135-IGS1 Interaction in the Stability of Ribosomal DNA I Saccharomyces cerevisiae; lead supervisor; completed 2015)
  16. Ralph Grand (Genomes in Space and Time; lead supervisor; completed 2014)
  17. Chris Rodley (Unravelling the genomic structure of Saccharomyces cerevisiae; lead supervisor; completed 2011)


Completed Masters


  1. Sara Ershadi (co-supervisor Thomas Lumley, 2020). 
  2. Sachin Jayan (Analysis of the metabolic profiles from faeces and plasma of children born very preterm; lead supervisor, 2015)
  3. Rachel Bowden (The 3D-structure of the Escherichia coli nucleoid through one division; lead supervisor; completed 2013)
  4. Steven Chou (lead supervisor; completed 2011)

Completed Honours

1.    Veronica Benton Guy (A metagenomic study of the microbial population at hot water beach, Coromandel; First class Honours, 2011)

2.    Ralph Grand (Implementation of a DNA enrichment step into the GCC protocol for the elucidation of human chromosome organisation. First class Honours, 2009)

3.    Chris Rodley (Searching for Inter- and Intra-chromosomal interactions within regulatory regions of loci associated with Leukaemia; First class Honours, 2007)


10/09/2016-5/9/2017    Convenor Epigenetics symposium QMB Research Week, 2017.

10/6/2016-current         Elected member of Long Bay College board of trustees.

21/1/2016                       Member of the Asian Conference on Transcription Scientific organizing committee for Penang, Malaysia (2017).

21/12/2015                    Member Mapnet symposium organizing committee for QMB 2016.

7/12/2015                       Invited speaker. The 4th International Symposium on the Mathematics on Chromatin Live Dynamics (4ISMCD): 7th- 9th December 2015, Hiroshima, Japan.

21/06/2015                    Invited speaker The 8th international fission yeast meeting: 21-26/6/15 Kobe, Japan.

23/10/14-current           Appointment to editorial board of Nutrients.

04/09/14                         Invited speaker. The 2016 FASEB Summer Research Conference on Yeast Chromosome Structure, Replication and Segregation.

28/8/14-current             Appointed to Metabolic Health Expert panel for High Value Nutrition National Science Challenge.

19/5/2013                       Invited speaker - 50th ICTP Advanced workshop on interdisciplinary views on chromosome structure and function: 15-19 September 2014, Trieste, Italy.

1/10/13-28/8/14             Convenor - QMB 2014 main meeting.

17/2/2013                       Invited speaker - Lorne Genomics 2013, Lorne, Australia.

1/9/12-1/10/13               Convenor - Epigenetics and chromatin symposium, QMB 2013.

2012-2016                     Associate Investigator in Gravida: National Centre for Growth and Development.

1/1/2011-1/10/2013      Panellist for the Cellular, Molecular and Physiological Biology panel - Marsden Fund, Royal Society of New Zealand.

1/9/10-1/9/11                 Convenor - Epigenetics and chromatin symposium, QMB 2011.

30/10/10-30/10/12        North Island representative - the Australian and New Zealand Society for Cell and Developmental Biology.

1/9/10                             2010 Life Technologies Life Science Award: for Emerging Excellence in Molecular biology in New Zealand.

3/6/10-current               Associate Investigator - Maurice Wilkins Centre for Molecular Biodiscovery.

06/2010-06/2016          Elected member of Long Bay Primary School board of trustees. Chairman (2012-2015).

1/1/09-current               Member of QMB organizing committee.

1/1/09-04/12/10             Member of organizing committee for NZMS/NZSBMB joint conference December 2010.

2005                               Massey University Early Career Research Medal.

1/1/05-2012                   Coordinator of the NZMS eukaryotic special interest group.



Deputy Director

Associate Director for Research

Areas of expertise

My research centres on the use of high throughput techniques in the meta-analyses of genomes. We specialise in the integration of novel experimental and computational techniques to answer biologically relevant questions, including what is the physical structure of a genome within a cell or what is the epigenetic structure of a genome within an environment? Our group also has considerable experience with genetic and biochemical manipulation, mostly in yeast, and increasingly in other organisms.

Committees/Professional groups/Services

28/8/14-current Appointed to Metabolic Health Expert panel for High Value Nutrition National Science Challenge.

01/10/13-28/8/14          Convenor QMB 2014 main meeting.

01/01/2011-01/10/2013 Panellist for the Cellular, Molecular and Physiological Biology panel, Marsden Fund, Royal Society of New Zealand.

01/09/12- 01/10/13       Organizer Epigenetics and chromatin symposium, QMB 2013.

01/09/10-09/11              Organizer Epigenetics and chromatin symposium, QMB 2011.

01/01/09-current Member of QMB organizing committee.

30/10/10-30/10/12        North Island representative; The Australian and New Zealand Society for Cell and Developmental Biology.

01/01/09-04/12/10        Member of organizing committee for NZMS/NZSBMB joint conference December 2010.

01/01/05-2012             Coordinator of the NZMS eukaryotic special interest group.

Selected publications and creative works (Research Outputs)

As of 29 October 2020 there will be no automatic updating of 'selected publications and creative works' from Research Outputs. Please continue to keep your Research Outputs profile up to date.
  • Schierding, W., Horsfield, J. A., & O'Sullivan JM (2020). Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways. Journal of medical genetics10.1136/jmedgenet-2020-107095
    Other University of Auckland co-authors: William Schierding
  • Davies, N., O'Sullivan JM, Plank, L. D., & Murphy, R. (2020). Gut Microbial Predictors of Type 2 Diabetes Remission Following Bariatric Surgery. Obesity surgery, 30 (9), 3536-3548. 10.1007/s11695-020-04684-0
    Other University of Auckland co-authors: Lindsay Plank, Rinki Murphy
  • Schierding, W., Farrow, S., Fadason, T., Graham, O. E. E., Pitcher, T. L., Qubisi, S., ... Kennedy, M. A. (2020). Common Variants Coregulate Expression of GBA and Modifier Genes to Delay Parkinson's Disease Onset. Movement disorders : official journal of the Movement Disorder Society, 35 (8), 1346-1356. 10.1002/mds.28144
    Other University of Auckland co-authors: Jo Perry, William Schierding, Tayaza Fadason, Alan Davidson
  • Butler ÉM, Chiavaroli, V., Derraik, J. G. B., Grigg, C. P., Wilson, B. C., Walker, N., ... Cutfield, W. S. (2020). Maternal bacteria to correct abnormal gut microbiota in babies born by C-section. Medicine, 99 (30)10.1097/md.0000000000021315
    Other University of Auckland co-authors: José Derraik
  • Andraos, S., Lange, K., Clifford, S. A., Jones, B., Thorstensen, E. B., Kerr, J. A., ... O'Sullivan JM (2020). Plasma Trimethylamine N-Oxide and Its Precursors: Population Epidemiology, Parent-Child Concordance, and Associations with Reported Dietary Intake in 11- to 12-Year-Old Children and Their Parents. Current developments in nutrition, 4 (7)10.1093/cdn/nzaa103
    Other University of Auckland co-authors: Melissa Wake
  • Leong, K. S. W., O'Sullivan JM, Derraik, J. G. B., & Cutfield, W. S. (2020). Gut microbiome transfer-Finding the perfect fit. Clinical endocrinology, 93 (1), 3-10. 10.1111/cen.14183
    Other University of Auckland co-authors: Karen Leong, José Derraik, Wayne Cutfield
  • Hibberd, R., Golovina, E., Farrow, S., & O'Sullivan JM (2020). Genetic variants associated with alcohol dependence co-ordinate regulation of ADH genes in gastrointestinal and adipose tissues. Scientific reports, 10 (1)10.1038/s41598-020-66048-z
  • Chong, C. Y. L., Vatanen, T., Oliver, M., Bloomfield, F. H., & O'Sullivan JM (2020). The microbial biogeography of the gastrointestinal tract of preterm and term lambs. Scientific Reports, 10 (9113)10.1038/s41598-020-66056-z
    Other University of Auckland co-authors: Tommi Vatanen, Mark Oliver, Frank Bloomfield