About

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.

Teaching
  • 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)
Interests
Research
  • Population genetics of marine organisms
  • Evolution of cephalopod toxicity
  • Software for antimicrobial peptide discovery
Teaching
  • Bioinformatics
Socio-Economic Objectives
Publications

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
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ResearchOnline@JCU stores 55+ 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)
Summary
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.
Investigators
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)
Keywords
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
Summary
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.
Investigators
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)
Keywords
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
Summary
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.
Investigators
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)
Keywords
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)
Summary
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.
Investigators
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)
Keywords
Coral; Acropora; stress-tolerance; Population Genomics; Biomarkers; Population Genetics
Supervision

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.

Current
  • Characterisation of PPDK and PEPS Regulation in Bacteria (PhD , Secondary Advisor/AM)
  • An anatomization of the molecular bases of regeneration and heat shock in corals (PhD , Secondary Advisor)
  • Genome wide analysis of natural selection in thermally tolerant coral communities from North Western Australia (PhD , Primary Advisor)
  • Investigating receptors and signalling pathways of coral settlement and metamorphosis using proteomics,transcriptomics and phylogenetics (PhD , Secondary 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)
  • 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)
  • Unravelling genomic patterns of population structure and fitness in the Australian koala (Phascolarctos cinereus) (PhD , Secondary Advisor)
  • Insights into the molecular bases of coral-specific traits (PhD , Secondary Advisor)
Completed
Collaboration

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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jcu.me/ira.cooke

Email
Phone
Location
  • 20.022, Molecular Genetics Laboratory (Townsville campus)
Advisory Accreditation
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