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.

  • AQ2002: Aquaculture of Tropical Species (Level 2; TSV)
  • AQ3007: Aquatic Animal Ecophysiology (Level 3; TSV)
  • AQ5007: Aquatic Animal Ecophysiology (Level 5; TSV)
  • AQ5009: Aquaculture of Tropical Species (Level 5; TSV)
  • BC2023: Molecular Genetics (Level 2; TSV)
  • BC3101: Genes, Genomes and Development (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5001: Advanced Readings in Molecular and Cell Biology (Level 5; TSV)
  • BC5002: Advanced Research in Molecular and Cell Biology 1 of 2 (Level 5; TSV)
  • BC5003: Advanced Research in Molecular and Cell Biology 2 of 2 (Level 5; 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
Research Disciplines
Socio-Economic Objectives

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
Conference Papers

ResearchOnline@JCU stores 38+ 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 - 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 and WA Department of Parks and Wildlife)
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)
  • 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)
  • Studying Stress Impacts Using the Mushroom Coral Heliofungia (PhD , Secondary Advisor)
  • Coral Mediation of Associated Microbial Community (PhD , Secondary Advisor)
  • Gene Expression of Sex Change in Ctenactis Echinatar and Fungia Fungites Corals (PhD , Secondary Advisor)
  • The Function and Ligands of G-Protein Coupled Receptors (GPCRs) in Coral Larvae Settlement (PhD , Secondary Advisor)
  • Venom evolution in the blue-ringed octopus (Hapalochlaena) species complex (PhD , Secondary Advisor)
  • Genome-wide assessments of thermal plasticity and theshold performance in corals across the Great Barrier Reef (PhD , Secondary Advisor)
  • Genome wide analysis of natural selection in thermally tolerant coral communities from North Western Australia (PhD , Primary Advisor)
  • Genome wide detection and evolutionary analysis of antimicrobial peptide repertoires in corals (PhD , Primary Advisor)
  • A new target mediating cell death in liver cancer. (Masters , 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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