Ira Cooke is a senior lecturer in bioinformatics and co-director of the Centre for Tropical Bioinformatics and Molecular Biology. He uses a range of high throughput (big data) molecular techniques to understand the evolution, molecular biology and ecology of marine organisms. 

Ira’s research uses population genomics to understand local adaptation in the marine environment by connecting recent biogeographical events with evolutionary processes on specific genes and genomic regions. One of the major goals of this work is to improve our understanding of the basic molecular biology of marine taxa (ie what genes do and how they are regulated).  To further this goal Ira often works collaboratively, providing bioinformatic expertise to projects combining evo-devo, physiological and comparative genomic approaches. 

Ira also develops analytical tools that facilitate research on the molecular biology of marine taxa. These tools are typically targeted at specific questions, relevant to biology-focussed projects. For example his research group developed a tool for classifying antimicrobial peptides from protein sequences (ampir) to facilitate work on coral-microbe interactions. In the past he has worked on tools to simplify working with mass-spectrometry-based proteomics data. 

Ira completed his BSc (hons) at JCU in marine biology and chemistry, followed by a PhD in physics at Australian National University.  He then completed a postdoc with Prof. Markus Deserno at the Max Planck institute for polymer physics in Germany where he developed 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.  Ira returned to Australia in 2010 to take up a role as bioinformatician in the La Trobe University mass spectrometry facility. In 2016 he moved to James Cook University.

  • BC2023: Molecular Genetics (Level 2; TSV)
  • BC3101: Genes, Genomes and Development (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5101: Advanced Genes, Genomes and Development (Level 5; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
  • Population genetics of marine organisms
  • Evolution of cephalopod toxicity
  • Software for antimicrobial peptide discovery
  • Bioinformatics
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

ResearchOnline@JCU stores 59+ research outputs authored by A/Prof Ira Cooke from 2011 onwards.

Current Funding

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

Wet Tropics Management Authority - Contract Research

Genomic tools for monitoring yellow crazy ants.

Indicative Funding
$16,295 over 2 years
This project will establish protocols and baseline data for ddRAD-seq based sequencing of yellow crazy ants. In this phase of the project, we will sequence 200 individuals from historical infestations and develop tools to assess genetic relatedness among infestations. Baseline data established in this project will be used to help trace the origin of future infestations as well as improve our understanding of genetic diversity and gene flow in yellow crazy ants in Queensland.
Matt Field, Megan Higgie, Ira Cooke and Lori Lach (College of Public Health, Medical & Vet Sciences and College of Science & Engineering)
Yellow Crazy Ants; Invasive Species Monitoring; Anoplolepis gracilipes; Genomics; Genetic relatedness; biosecurity

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 and University of Technology Sydney)
Acropora tenuis (Family Acroporidae); Gene expression; RNASeq; Thermal tolerance; Bioinformatics; Coral

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)
  • Drivers of Biodiversity on Coral Reefs - the role of Antipatharians Supporting Species Richness and Abundance on Shallow and Mesophotic Reefs (PhD , Secondary Advisor/AM)
  • Structural Variant analysis in Coral Populations of A. tenuis and A. digitifera and their role in Gene Flow, Adaptive Evolution and Diversification (Masters , Primary Advisor)
  • Genomic Prediction of Heat Tolerance in Selectively-bred Corals (PhD , Primary Advisor/AM/Adv)
  • Population genomics of dugongs (Dugong dugon) in northern Australia (PhD , Secondary Advisor)
  • Characterization of the CpG methylation distribution and patterns in the mushroom coral Heliofungia actiniformis (PhD , Secondary Advisor)
  • Combating summer mortality in abalone: Can a little bit of stress be beneficial? (PhD , Secondary Advisor)
  • Insights into the molecular bases of coral-specific traits (PhD , Secondary Advisor)
  • Unravelling genomic patterns of population structure and fitness in the Australian koala (Phascolarctos cinereus) (PhD , Secondary Advisor)
  • Coral and Microbial Interactions during Progression of Black Band Disease (BBD) (PhD , Secondary Advisor)
  • The molecular bases of regeneration and the heat shock response that underlines coral bleaching (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)

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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