Publications by: Ira R. Cooke

Also publishes as (Ira Cooke, Ira Robin Cooke)

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Number of items: 33.

Caruana, Nikeisha J., Strugnell, Jan M., Faou, Pierre, Finn, Julian, and Cooke, Ira R. (2019) Comparative proteomic analysis of slime from the striped pyjama squid, Sepioloidea lineolata, and the southern bottletail squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). Journal of Proteome Research, 18 (3). pp. 890-899.

Whitelaw, Brooke L., Cooke, Ira R., Finn, Julian, Zenger, Kyall, and Strugnell, J.M. (2019) The evolution and origin of tetrodotoxin acquisition in the blue-ringed octopus (genus Hapalochlaena). Aquatic Toxicology, 206. pp. 114-122.

Ying, Hua, Cooke, Ira, Sprungala, Susanne, Wang, Weiwen, Hayward, David C., Tang, Yurong, Huttley, Gavin, Ball, Eldon E., Forêt, Sylvain, and Miller, David J. (2018) Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biology, 19. 175.

Nuez-Ortín, Waldo G., Carter, Chris G., Nichols, Peter D., Cooke, Ira R., and Wilson, Richard (2018) Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature. BMC Genomics, 19. 133.

Woodings, Laura N., Murphy, Nicholas P., Doyle, Stephen R., Hall, Nathan E., Robinson, Andrew J., Liggins, Geoffrey W., Green, Bridget S., Cooke, Ira R., Bell, James J., and Strugnell, Jan M. (2018) Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi. Marine Biology, 165 (12). 185.

Fingerhut, Legana C.H.W., Strugnell, Jan M., Faou, Pierre, Labiaga, Àlvaro Roura, Zhang, Jia, and Cooke, Ira R. (2018) Shotgun proteomics analysis of saliva and salivary gland tissue from the common octopus Octopus vulgaris. Journal of Proteome Research, 17 (11). pp. 3866-3876.

Shiel, Brett P., Cooke, Ira R., Hall, Nathan E., Robinson, Nicholas A., and Strugnell, Jan M. (2018) Summer mortality in molluscs: the genetic basis for resilience and susceptibility. In: Breeding Focus 2018. pp. 59-79. From: Breeding Focus 2018: reducing heat stress, 19-20 September 2018, Armidale, NSW, Australia.

Liu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J.H., Voolstra, Christian R., Ragan, Mark A., and Chan, Cheong Xin (2018) Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1. 95.

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A., Stone, David A.J., and Strugnell, Jan M. (2017) The effect of commercial, natural and grape seed extract supplemented diets on gene expression signatures and survival of greenlip abalone (Haliotis laevigata) during heat stress. Aquaculture, 479. pp. 798-807.

Cameron, Timothy C., Cooke, Ira, Faou, Pierre, Toet, Hayley, Piedrafita, David, Young, Neil, Rathinasamy, Vignesh, Beddoe, Travis, Anderson, Glenn, Dempster, Robert, and Spithill, Terry W. (2017) A novel ex vivo immunoproteomic approach characterising Fasciola hepatica tegumental antigens identified using immune antibody from resistant sheep. International Journal for Parasitology, 47 (9). pp. 555-567.

Lin, Mei-Fang, Moya, Aurelie, Ying, Hua, Chen, Chaolun Allen, Cooke, Ira, Ball, Eldon E., Forȇt, Sylvain, and Miller, David J. (2017) Analyses of corallimorpharian transcriptomes provide new perspectives on the evolution of calcification in the Scleractinia (corals). Genome Biology and Evolution, 9 (1). pp. 150-160.

Dagonnier, Marie, Cooke, Ira Robin, Faou, Pierre, Sidon, Tara Kate, Dewey, Helen Margaret, Donnan, Geoffrey Alan, and Howells, David William (2017) Discovery and longitudinal evaluation of candidate biomarkers for ischaemic stroke by mass spectrometry-based proteomics. Biomarker Insights, 12.

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A., and Strugnell, Jan M. (2017) Epipodial tentacle gene expression and predetermined resilience to summer mortality in the commercially important greenlip abalone, Haliotis laevigata. Marine Biotechnology, 19 (2). pp. 191-205.

Schneider, Maria Victoria, Griffin, Phillippa C., Tyagi, Sonika, Flannery, Madison, Dayalan, Saravanan, Gladman, Simon, Watson-Haigh, Nathan, Bayer, Philipp E., Charleston, Michael, Cooke, Ira, Cook, Rob, Edwards, Richard J., Edwards, David, Gorse, Dominique, McConville, Malcolm, Powell, David, Wilkins, Marc R., and Lonie, Andrew (2017) Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics, 2017.

Nuez-Ortin, Waldo G., Carter, Chris G., Wilson, Richard, Cooke, Ira R., Amoroso, Gianluca, Cobcroft, Jennifer M., and Nichols, Peter D. (2017) Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 22. pp. 67-77.

Chambers, Matthew C., Jagtop, Pratik D., Johnson, James E., McGowan, Thomas, Kumar, Praveen, Onsongo, Getiria, Guerrero, Candace R., Barsnes, Harald, Vaudel, Marc, Martens, Lennart, Grüning, Björn, Cooke, Ira, Heydarian, Mohammad, Reddy, Karen L., and Griffin, Timothy J. (2017) An accessible proteogenomics informatics resource for cancer researchers. Cancer Research, 77 (21). E43-E46.

Shafee, Thomas, and Cooke, Ira (2016) AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments. BMC Bioinformatics, 17 (1). pp. 1-6.

Whitelaw, Brooke Lauren, Strugnell, Jan M., Faou, Pierre, da Fonseca, Rute R., Hall, Nathan, Norman, Mark, Finn, Julian, and Cooke, Ira Robin (2016) Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus. Journal of Proteome Research, 15 (9). pp. 3284-3297.

Nuez Ortin, Waldo, Carter, Chris G., Wilson, Richard, Cooke, Ira, and Nichols, Peter D. (2016) Preliminary validation of a high docosahexaenoic acid (DHA) and -linolenic acid (ALA) dietary oil blend: tissue fatty acid composition and liver proteome response in Atlantic salmon (Salmo salar) smolts. PLoS ONE, 11 (8). e0161513. pp. 1-27.

Caruana, Nikeisha J., Cooke, Ira R., Faou, Pierre, Finn, Julian, Hall, Nathan E., Norman, Mark, Pineda, Sandy S., and Strugnell, Jan M. (2016) A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda). Journal of Proteomics, 148. pp. 170-182.

Robinson, Nick A., Hall, Nathan E., Ross, Elizabeth M., Cooke, Ira R., Shiel, Brett P., Robinson, Andrew J., and Strugnell, Jan M. (2016) The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing. Mitochondrial DNA Part A: DNA mapping, sequencing and analysis, 27. pp. 437-438.

Hall, Nathan E., Hanzak, Jan, Allcock, A. Louise, Cooke, Ira R., Ogura, Atsushi, and Strugnell, Jan M. (2016) The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae. Mitochondrial DNA Part A: DNA mapping, sequencing and analysis, 27 (1). pp. 5-6.

Nguyen, Vinh A., Carey, Leeanne M., Giummarra, Loretta, Faou, Pierre, Cooke, Ira, Howells, David W., Tse, Tamara, Macaulay, S. Lance, Ma, Henry, Davis, Stephen M., Donnan, Geoffrey A., and Crewther, Sheila G. (2016) A pathway proteomic profile of ischemic stroke survivors reveals innate immune dysfunction in association with mild symptoms of depression: a pilot study. Frontiers in Neurology, 7. 85. pp. 1-16.

Murugesan, Selvaraaju, Tay, David B.H., Cooke, Ira, and Faou, Pierre (2015) Application of dual tree complex wavelet transform in tandem mass spectrometry. Computers in Biology and Medicine, 63. pp. 36-41.

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A, and Strugnell, Jan M. (2015) De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family. Marine Biotechnology, 17. pp. 23-32.

Boekel, Jorrit, Chilton, John, Cooke, Ira, Horvatovich, Peter, Jagtap, Pratik, Kall, Lukas, Lehtiö, Janne, Lukasse, Pieter, Moerland, Perry, and Griffin, Timothy (2015) Multi-omic data analysis using Galaxy. Nature Biotechnology, 33. pp. 137-139.

Cooke, Ira R., Whitelaw, Brooke, Norman, Mark, Caruana, Nikeisha, and Strugnell, Jan (2015) Toxicity in cephalopods. In: Gopalakrishnakone, P., and Malhotra, Anita, (eds.) Evolution of Venomous Animals and Their Toxins. Toxinology . Springer, Leiden, The Netherlands, pp. 1-15.

Cooke, Ira R, Jones, Dan, Bowen, Joanna K, Deng, Cecilia, Faou, Pierre, Hall, Nathan E, Jayachandran, Vignesh, Liem, Michael, Taranto, Adam P, Plummer, Kim M, and Mathivanan, Suresh (2014) Proteogenomic analysis of the Venturia pirina (pear scab fungus) secretome reveals potential effectors. Journal of Proteome Research, 13 (8). pp. 3635-3644.

Cooke, Ira R., Mattison, Elizabeth H.A., Audsley, Eric, Bailey, Alison P., Freckleton, Robert P., Graves, Anil R., Morris, Joe, Queenborough, Simon A., Sandars, Daniel L., Siriwardena, Gavin M., Trawick, Paul, Watkinson, Andrew R., and Sutherland, William J. (2013) Empirical test of an agricultural landscape model: the importance of farmer preference for risk aversion and crop complexity. SAGE Open, 3. pp. 1-16.

Robinson, Nick, Smith, Ben, Cooke, Ira, and Strugnell, Jan (2013) A snail's pace: a preliminary analysis of the effects of stress and genetics on movement of Haliotis. Aquaculture, 376-379. pp. 25-35.

Appleby, Sarah L., Cockshell, Michaelia P., Pippal, Jyotsna B., Thompson, Emma J., Barrett, Jeffrey M., Tooley, Katie, Sen, Shaundeep, Sun, Wai Yan, Grose, Randall, Nicholson, Ian, Levina, Vitalina, Cooke, Ira, Talbo, Gert, Lopez, Angel F., and Bonder, Claudine S. (2012) Characterization of a distinct population of circulating human non-adherent endothelial forming cells and their recruitment via intercellular adhesion molecule-3. PLoS ONE, 7 (11). e46996.

Siriwardena, Gavin M., Cooke, Ira R., and Sutherland, William J. (2012) Landscape, cropping and field boundary influences on bird abundance. Ecography, 35 (2). pp. 162-173.

Allcock, A. Louise, Cooke, Ira R., and Strugnell, Jan M. (2011) What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda? Zoological Journal of the Linnean Society, 161 (3). pp. 573-586.

This list was generated on Wed Nov 13 04:49:32 2019 AEST.