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)
• MB5370: Techniques in Marine Science 1 (Level 5; TSV)

Interests

Research

• Population genetics of marine organisms
• Evolution of cephalopod toxicity
• Software for antimicrobial peptide discovery

Teaching

• Bioinformatics

Research Disciplines

• Genetics (3105)
• Biochemistry and cell biology (3101)
• Evolutionary biology (3104)

Socio-Economic Objectives

• Expanding knowledge (2801)

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

• Matias A, Popovic I, Thia J, Cooke I, Torda G, Lukoschek V, Bay L, Kim S and Riginos C (2023) Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef. Evolutionary Applications, 16 (2). pp. 293-310
• Kuek F, Motti C, Zhang J, Cooke I, Todd J, Miller D, Bourne D and Raina J (2022) DMSP production by coral-associated bacteria. Frontiers in Marine Science, 9.
• Schmidt C, Cooke I, Wilson D, Miller D, Peigneur S, Tytgat J, Field M, Takjoo R, Smout M, Loukas A and Daly N (2022) Newly Discovered Peptides from the Coral Heliofungia actiniformis Show Structural and Functional Diversity. Journal of Natural Products, 85 (7). pp. 1789-1798
• Sidorczuk K, Gagat P, Pietluch F, Kala J, Rafacz D, Bakala L, Slowik J, Kolenda R, Rodiger S, Fingerhut L, Cooke I, Mackiewicz P and Burdukiewicz M (2022) Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data. Briefings in Bioinformatics, 23 (5).
• Thomas L, Underwood J, Rose N, Fuller Z, Richards Z, Dugal L, Grimaldi C, Cooke I, Palumbi S and Gilmour J (2022) Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia. Science Advances, 8 (17).
• Whitelaw B, Jones D, Guppy J, Morse P, Strugnell J, Cooke I and Zenger K (2022) High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa). Diversity, 14 (12).
• Zhang J, Richards Z, Adam A, Chan C, Shinzato C, Gilmour J, Thomas L, Strugnell J, Miller D and Cooke I (2022) Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum. Molecular Biology and Evolution, 39 (10).
• Andrade Rodriguez N, Moya A, Jones R, Miller D and Cooke I (2021) The significance of genotypic diversity in coral competitive interaction: a transcriptomic perspective. Frontiers in Ecology and Evolution, 9.
• Bongaerts P, Cooke I, Ying H, Wels D, den Haan S, Hernandez-Agreda A, Brunner C, Dove S, Englebert N, Eyal G, Foret S, Grinblat M, Hay K, Harii S, Hayward D, Lin Y, Morana M, Moya A, Muir P, Sinniger F, Smallhorn-West P, Torda G, Ragan M, van Oppen M and Hoegh-Guldberg O (2021) Morphological stasis masks ecologically divergent coral species on tropical reefs. Current Biology, 31 (11). pp. 2286-2298.e8
• Grinblat M, Cooke I, Shlesinger T, Ben-Zvi O, Loya Y, Miller D and Cowman P (2021) Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals). Molecular Phylogenetics and Evolution, 164.
• Mason B, Cooke I, Moya A, Augustin R, Lin M, Satoh N, Bosch T, Bourne D, Hayward D, Andrade N, Forêt S, Ying H, Ball E and Miller D (2021) AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones. Developmental and Comparative Immunology, 114.
• Caruana N, Strugnell J, Finn J, Faou P, Plummer K and Cooke I (2020) Quantitative proteomic analysis of the slime and ventral mantle glands of the Striped Pyjama squid (Sepioloidea lineolata). Journal of Proteome Research, 19. pp. 1491-1501

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

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)
• Drivers of Biodiversity on Coral Reefs - the role of Antipatharians Supporting Species Richness and Abundance on Shallow and Mesophotic Reefs (PhD , Secondary Advisor/AM)
• Exploiting whole-genome sequencing to understand the evolution of corals and their symbionts (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)
• 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)
• Natural variation in heat tolerance of corals on the Great Barrier Reef (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)
• An anatomization of the molecular bases of regeneration and heat shock in corals (PhD , Secondary Advisor)

Completed

• Biogeography, reproductive biology and early development in scleractinian corals (2022, PhD , Secondary Advisor)
• Investigating receptors and signalling pathways of coral settlement and metamorphosis using proteomics,transcriptomics and phylogenetics (2023, PhD , Secondary Advisor)
• Novel targets and strategies in the treatment of liver and oral pharyngeal cancer (2021, Masters , Secondary Advisor)
• The iridescent enigma: Genome evolution and species boundaries of the blue-ringed octopus species complex (Octopodidae: Hapalochlaena) (2021, PhD , Secondary Advisor)
• Characterizing the bacterial community associated with the model alcyoniid Lobophytum pauciflorum (2021, PhD , Secondary Advisor)
• Identifying antimicrobial peptides in genomes using machine learning (2022, PhD , Primary Advisor)
• Molecular insights into a novel coral model, Heliofungia actiniformis (2022, PhD , Secondary Advisor)
• Non-contact competition between soft and hard corals: a transcriptomic perspective (2018, PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
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