Search Results - "Cooke, Ira R"

Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials by Cooke, Ira R, Deserno, Markus

“…We present a simple and highly adaptable method for simulating coarse-grained lipid membranes without explicit solvent. Lipids are represented by one head bead…”
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Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature by Nuez-Ortín, Waldo G, Carter, Chris G, Nichols, Peter D, Cooke, Ira R, Wilson, Richard

“…Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can…”
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Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef by Matias, Ambrocio Melvin A., Popovic, Iva, Thia, Joshua A., Cooke, Ira R., Torda, Gergely, Lukoschek, Vimoksalehi, Bay, Line K., Kim, Sun W., Riginos, Cynthia

“…Genomic studies are uncovering extensive cryptic diversity within reef‐building corals, suggesting that evolutionarily and ecologically relevant diversity is…”
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The evolution and origin of tetrodotoxin acquisition in the blue-ringed octopus (genus Hapalochlaena) by Whitelaw, Brooke L., Cooke, Ira R., Finn, Julian, Zenger, Kyall, Strugnell, J.M.

“…Tetrodotoxin is a potent non-proteinaceous neurotoxin, which is commonly found in the marine environment. Synthesised by bacteria, tetrodotoxin has been…”
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High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa) by Whitelaw, Brooke L, Jones, David B, Guppy, Jarrod, Morse, Peter, Strugnell, Jan M, Cooke, Ira R, Zenger, Kyall

“…Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present…”
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Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus by Whitelaw, Brooke L, Strugnell, Jan M, Faou, Pierre, da Fonseca, Rute R, Hall, Nathan E, Norman, Mark, Finn, Julian, Cooke, Ira R

“…This study provides comprehensive proteomic profiles from the venom producing posterior salivary glands of octopus (superorder Octopodiformes) species. A…”
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Landscape, cropping and field boundary influences on bird abundance by Siriwardena, Gavin M., Cooke, Ira. R., Sutherland, William J.

“…Given likely dramatic land use changes in the UK, there is a need to predict their impact upon biodiversity. Such predictions require an understanding of the…”
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A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda) by Caruana, Nikeisha J., Cooke, Ira R., Faou, Pierre, Finn, Julian, Hall, Nathan E., Norman, Mark, Pineda, Sandy S., Strugnell, Jan M.

“…Sepiadarium austrinum, the southern bottletail squid, is a small squid that inhabits soft sediments along Australia's south-east coast. When provoked, it…”
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What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda? by ALLCOCK, A. LOUISE, COOKE, IRA R, STRUGNELL, JAN M

“…We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony…”
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Coupling between Lipid Shape and Membrane Curvature by Cooke, Ira R., Deserno, Markus

“…Using molecular dynamics simulations, we examine the behavior of lipids whose preferred curvature can be systematically varied. This curvature is imposed by…”
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ampir: an R package for fast genome-wide prediction of antimicrobial peptides by Fingerhut, Legana C H W, Miller, David J, Strugnell, Jan M, Daly, Norelle L, Cooke, Ira R

“…Abstract Summary Antimicrobial peptides (AMPs) are the key components of the innate immune system that protect against pathogens, regulate the microbiome and…”
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The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae by Hall, Nathan E, Hanzak, Jan, Allcock, A Louise, Cooke, Ira R, Ogura, Atsushi, Strugnell, Jan M

“…We report the first complete mitochondrial genome of the pygmy squid, Idiosepius, (Idiosepiidae). The mtDNA genome is 16,183 bp long with an AT content of…”
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Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods: Co-evolutionary Signatures Across Levels of Genome Organization May Shed Light on Functional Linkage and Origin of Cephalopod Novelties by Ritschard, Elena A, Whitelaw, Brooke, Albertin, Caroline B, Cooke, Ira R, Strugnell, Jan M, Simakov, Oleg

“…How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction…”
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Multi-omic data analysis using Galaxy by Boekel, Jorrit, Chilton, John M, Cooke, Ira R, Horvatovich, Peter L, Jagtap, Pratik D, Käll, Lukas, Lehtiö, Janne, Lukasse, Pieter, Moerland, Perry D, Griffin, Timothy J

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Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data by Sidorczuk, Katarzyna, Gagat, Przemysław, Pietluch, Filip, Kała, Jakub, Rafacz, Dominik, Bąkała, Laura, Słowik, Jadwiga, Kolenda, Rafał, Rödiger, Stefan, Fingerhut, Legana C H W, Cooke, Ira R, Mackiewicz, Paweł, Burdukiewicz, Michał

“…Abstract Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells…”
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Morphological stasis masks ecologically divergent coral species on tropical reefs by Bongaerts, Pim, Cooke, Ira R., Ying, Hua, Wels, Dagmar, den Haan, Stijn, Hernandez-Agreda, Alejandra, Brunner, Christopher A., Dove, Sophie, Englebert, Norbert, Eyal, Gal, Forêt, Sylvain, Grinblat, Mila, Hay, Kyra B., Harii, Saki, Hayward, David C., Lin, Yu, Mihaljević, Morana, Moya, Aurelie, Muir, Paul, Sinniger, Frederic, Smallhorn-West, Patrick, Torda, Gergely, Ragan, Mark A., van Oppen, Madeleine J.H., Hoegh-Guldberg, Ove

“…Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains…”
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SNP data reveals the complex and diverse evolutionary history of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) in the Asia-Pacific by Whitelaw, Brooke L., Finn, Julian K., Zenger, Kyall R., Cooke, Ira R., Morse, Peter, Strugnell, Jan M.

“…[Display omitted] •This investigation indicates substantially greater species diversity present within the genus Hapalochlaena than is currently described.•11…”
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Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial by Lau, Sally C Y, Wilson, Nerida G, Golledge, Nicholas R, Naish, Tim R, Watts, Phillip C, Silva, Catarina N S, Cooke, Ira R, Allcock, A Louise, Mark, Felix C, Linse, Katrin, Strugnell, Jan M

“…The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories, and its tipping point may…”
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Quantitative Proteomic Analysis of the Slime and Ventral Mantle Glands of the Striped Pyjama Squid (Sepioloidea lineolata) by Caruana, Nikeisha J, Strugnell, Jan M, Finn, Julian, Faou, Pierre, Plummer, Kim M, Cooke, Ira R

“…Cephalopods are known to produce an extensive range of secretions including ink, mucus, and venom. Sepiadariidae, a family of small, benthic bobtail squids,…”
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BioEssays 12/2019 by Ritschard, Elena A., Whitelaw, Brooke, Albertin, Caroline B., Cooke, Ira R., Strugnell, Jan M., Simakov, Oleg

“…Cephalopods provide a unique model system to investigate how organismal novelties evolve. In article number 1900073, Elena A. Ritschard et al. discuss how…”
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