As a bioinformatician I can combine my dual interests in molecular biology and computational tools.  My career reflects this crossing of disciplinary boundaries.  After completing my undergraduate studies at JCU in marine biology and chemistry I pursued a PhD in physics at ANU.  After that I worked with Markus Deserno at the Max Planck institute for polymer physics in Germany where I helped develop a model for simulating large scale lipid self assembly.  This was followed by several years in the UK working on economic and ecological models of farmland with Prof. Bill Sutherland.  I returned to Australia in 2010 where I started working as a bioinformatician with the La Trobe University mass spectrometry facility.  I soon realised that bioinformatics was the ideal way for me to combine my various computational and biological interests.  In 2016 I moved to James Cook University where I teach bioinformatics and use bioinformatic tools to answer a wide range of research questions related to molecular biology of marine organisms and tropical diseases.

I am interested in the analysis of large genomic, transcriptomic and proteomic datasets.  I use and develop computational tools that take advantage of this data to discover the role that genomic sequences play in cellular and whole organism biology.  I work on a wide variety of research questions including many related to human and veterinary health as well as aquaculture, coral biology and cephalopod toxins.

  • BC2023: Molecular Genetics (Level 2; TSV)
  • BC3101: Genes, Genomes and Development (Level 3; TSV)
  • BC3202: Special Topics in Biochemistry and Molecular Biology (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5101: Advanced Genes, Genomes and Development (Level 5; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
  • Coral genomics and transcriptomics
  • Evolution of cephalopod toxicity
  • Software for antimicrobial peptide discovery
  • Statistical analysis of gene and/or protein expression data

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles

ResearchOnline@JCU stores 50+ research outputs authored by Dr Ira Cooke from 2011 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

Australian Research Council - Linkage - Industrial Transformation Research Hubs

ARC Research Hub for Supercharging Tropical Aquaculture Through Genetic Solutions

Indicative Funding
$4,996,503 over 4 years, in partnership with Australian Genome Research Facility ($150,000); Cygnet Bay Pearls PL ($500,000); Mainstream Aquaculture ($500,000); Sea Forest Pty Ltd ($500,000) and THE COMPANY ONE PTY LTD ($500,000)
This project aims to integrate cutting edge genetic and genomic approaches into innovative aquaculture enterprises that farm in tropical northern Australia. It will deliver the requisite genetic knowledge to instigate world-leading and highly productive breeding programs for five species (barramundi, pearl oyster, prawn, grouper and marine seaweed), along with a novel understanding of the genetic basis of disease resistance and how the production environment interfaces with the bacterial microbiome, pathogens and water quality to cause disease. It will increase Australia's capacity to deliver advanced genetics outcomes to the aquaculture sector, while increasing productivity, international competitiveness, and lowered risk due to disease.
Dean Jerry, Kyall Zenger, Benjamin Hayes, Rocky de Nys, David Bourne, Andreas Lopata, Ron White, Jan Strugnell, Chaoshu Zeng, Kelly Condon, Mostafa Rahimi Azghadi, Ira Cooke, Leo Nankervis and Carla Ewels (College of Science & Engineering, The University of Queensland, College of Public Health and Medical & Vet Sciences)
Selective Breeding; Genomics; Aquaculture

Tropical Australian Academic Health Centre Limited - Research Seed Grants

Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North QLD Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North Using portable long-read sequencing to diagnose Chronic Kidney Disease

Indicative Funding
$50,000 over 2 years
This project addresses the early diagnosis of genetic predispositions for Chronic Kidney Disease (CKD), which poses an increasing burden on the North Queensland population and unequally affects the Indigenous Australian peoples. We will develop a mobile diagnostic pipeline that allows a rapid and cost-efficient screening for genetic CKD predispositions and circulating biomarkers using a targeted, DNA/RNA long-read sequencing approach.
Ulf Schmitz, Andrew Mallett, Matt Field, Paul Horwood, Helen Wright, Chirag Patel, Ira Cooke and Ben Lundie (College of Public Health, Medical & Vet Sciences, College of Medicine & Dentistry, College of Healthcare Sciences, Queensland Clinical Genetics Service and Pathology Queensland)
long-read sequencing; Nanopore; Chronic Kidney Disease; Genetic Testing; targeted sequencing; transcriptomic complexity

PADI Foundation - Research Grant

Using baseline gene expression of corals as a predictor of susceptibility to heat stress on the Great Barrier Reef

Indicative Funding
$10,670 over 1 year
My work explores the patterns of local thermal adaptation in multiple coral species across the GBR. I will investigate genetic changes responsible for differential thermal resilience within populations. This project will identify genes which are upregulated in more tolerant individuals, making these genes potential candidates for genetic markers of coral thermal tolerance. Such transcriptional markers will allow us to explore rapidly quantifiable metrics of thermal tolerance. Specific objectives are outlined below. ? Identify differentially expressed genes in susceptible and resistant individuals. ? Develop gene markers to predict coral heat stress responses to be deployed on large spatial scales.
Josephine Nielsen, Ira Cooke, Jan Strugnell, Line Bay, D Suggett and Kate Quigley (College of Public Health, Medical & Vet Sciences, College of Science & Engineering, Australian Institute of Marine Science, University of Technology and Sydney)
Acropora tenuis (Family Acroporidae); Gene expression; RNASeq; Thermal tolerance; Bioinformatics; Coral

Australian Research Council - Linkage - Projects

Coral resilience and the optimal management of biodiversity

Indicative Funding
$35,760 over 3 years (administered by Curtin University of Technology)
One of the most pressing questions facing coral reef managers is "Will reef-building corals survive climate change?" To answer this, managers need to know how coral biodiversity responds to climatic disturbances; the potential for acclimation and adaptation; and the best ways to monitor, manage and restore biodiversity. This project will examine the resilience of coral biodiversity to disturbances and build on recently developed genomic resources to explore the genotypic traits that confer thermal tolerance. Working with government, regulatory sectors and an industry group, we aim to generate tangible outcomes and strategies to optimise the management of Australia?s coral biodiversity while engaging the public through museum-based outreach.
Zoe Richards, Michael Bunce, David Miller, Ira Cooke and Michael Stat in collaboration with Jim Underwood, Nerida Wilson, James Gilmour and Andrew Halford (Curtin University of Technology, College of Public Health, Medical & Vet Sciences, Australian Institute of Marine Science, Western Australian Museum, WA Department of Biodiversity and Conservation and Attractions)
Coral; Acropora; stress-tolerance; Population Genomics; Biomarkers; Population Genetics

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

  • Characterisation of PPDK and PEPS Regulation in Bacteria (PhD , Secondary Advisor/AM)
  • A comparrison of the molecular bases of regeneration and development in corals (PhD , Secondary Advisor)
  • Genome wide analysis of natural selection in thermally tolerant coral communities from North Western Australia (PhD , Primary Advisor)
  • Impact of Water Quality on Physiological Performance of the Coral Acropora Millepora (PhD , Secondary Advisor)
  • Genomic Prediction of Heat Tolerance in Selectively-bred Corals (PhD , Secondary Advisor)
  • Population Connectivity of Antarctic Marine Invertebrates (PhD , Secondary Advisor)
  • Combating Summer Mortality in Abalone: Can a little bit of Stress be Beneficial? (PhD , Secondary Advisor)
  • Unravelling genomic patterns of population structure and fitness in the Australian koala (Phascolarctos cinereus) (PhD , Secondary Advisor)
  • Genome-wide assessments of thermal plasticity and theshold performance in corals across the Great Barrier Reef (PhD , Secondary Advisor)
  • Drivers of Biodiversity on Coral Reefs - the role of Antipatharians Supporting Species Richness and Abundance on Shallow and Mesophotic Reefs (PhD , Secondary Advisor)
  • Effects of Reef Restoration Techniques (Macroalgal Removal combined with Larval Capture and Release) on the Genetic Diversity and Connectivity in Scleratinian Populations of Magnetic Island, Australia (PhD , Secondary Advisor)
  • Utilising Bioinformatics Tools to Improve the Diagnosis of Crustacean and Fish Allergy (PhD , Secondary Advisor)
  • Understanding a new regulator of skeletal muscle myogenesis (PhD , Secondary Advisor)
  • Coral and Microbial Interactions during Progression of Black Band Disease (BBD) (PhD , Secondary Advisor)
  • The Function and Ligands of G-Protein Coupled Receptors (GPCRs) in Coral Larvae Settlement (PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

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