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Ira Cooke

@iracooke.bsky.social
626 followers 250 following 9 posts

Evolutionary biologist at James Cook University. Mostly working on genomics of corals and other marine animals. www.marine-omics.net

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Reposted by Ira Cooke
Jan Strugnell @janstrugnell.bsky.social · 09/12/2025
Check out our new paper 'Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments' led by the fabulous Nadja Schneller @marine-omics.bsky.social @iracooke.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments
Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe ...
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METR @metr.org · 10/07/2025
We ran a randomized controlled trial to see how much AI coding tools speed up experienced open-source developers. The results surprised us: Developers thought they were 20% faster with AI tools, but they were actually 19% slower when they had access to AI than when they didn't.
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Matt Quin @mattquin.bsky.social · 25/06/2025
Ever wondered how DNA metabarcoding compares to traditional methods for assessing diet? Curious whether these techniques could help inform the management of introduced deer in Australia? Then our latest research is for you! @janstrugnell.bsky.social @coatiben.bsky.social doi.org/10.1002/ecs2...
doi.org
DNA metabarcoding provides new insight into the diet of invasive chital deer (Axis axis) in a tropical savanna landscape
The introduction of non-native species into new environments can cause significant ecological harm and is considered a major conservation threat. As populations of invasive species continue to establ....
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Jan Strugnell @janstrugnell.bsky.social · 21/05/2025
@zoologistedel.bsky.social wowing the crowd about her genomic research on Heard and McDonald Islands #pintofscience
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Jan Strugnell @janstrugnell.bsky.social · 30/05/2025
Joe Perkins entertaining the audience in his precompletion PhD seminar on Ecology, detection, and impacts of benthic toxic dinoflagellates in Qld: a focus on #ciguatera poisoning. @marine-omics.bsky.social 🧬
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Ryan Wick @rrwick.bsky.social · 27/05/2025
New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...
rrwick.github.io
Dorado v1.0.0 and the v5.2.0 basecalling models
a blog for miscellaneous bioinformatics stuff
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Jan Strugnell @janstrugnell.bsky.social · 14/05/2025
Is there a core response to heat stress in #abalone? You bet there is. Check out this fantastic new meta-analysis of heat stress studies across abalone led by Roy Barkan. @marine-omics.bsky.social @iracooke.bsky.social 🧬🧬 rdcu.be/elVL2
rdcu.be
Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis)
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Ira Cooke @iracooke.bsky.social · 09/05/2025
Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments. New @marine-omics.bsky.social paper by Nadja Schneller with @janstrugnell.bsky.social, @mattfield100.bsky.social and Kerstin Johannesson out today doi.org/10.1111/mec....
doi.org
Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments
Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe ....
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Reposted by Ira Cooke
Jan Strugnell @janstrugnell.bsky.social · 07/05/2025
Big thanks to the fabulous crew, deck officers and all the expeditioners onboard RSV #Nuyina on our voyage to the Denman Glacier, East #Antarctica. @arcsaef.bsky.social @jcuofficial.bsky.social @marine-omics.bsky.social @lausally.bsky.social 🐙🇦🇶🧬 www.youtube.com/watch?v=KAhD...
youtube.com
Our seafloor history teachers
YouTube video by SAEF - Securing Antarctica's Environmental Future
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Ira Cooke @iracooke.bsky.social · 02/05/2025
We @marine-omics.bsky.social are hiring. We're looking for a postdoc in population genomics. @janstrugnell.bsky.social careers.jcu.edu.au/jobs/postdoc...
careers.jcu.edu.au
Postdoctoral Research Fellow, Population Genomics - Townsville, QLD, Australia
James Cook University (JCU) is creating a brighter future for life in the Tropics and beyond, through education and research that makes a difference locally and globally.  We now have an opportunity a...
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David Grinspoon @drfunkyspoon.bsky.social · 08/03/2025
Raise a test tube for the brilliant, courageous young scientists who organized today’s #standupforscience rallies. You are my heroes. Well done! @standupforscience.bsky.social 🧪
Hands raising a toast with test tubes.A crowd at the Lincoln Memorial in DC with signs, including “Defend Science like lives depend on it. (They do)”
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Flora Vincent @floravincent.bsky.social · 16/01/2025
Still time to submit an Abstract for the @embl.org symposium on the Wild Frontiers of Model Systems ! If you’re into unconventional, non model systems, bringing more ecology in our understanding of biological processes, Lab-field interface this is for you. www.embl.org/about/info/c... #protistsonsky
embl.org
Wild frontiers of model organisms
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Yi-Jyun Luo @yjluo.bsky.social · 07/01/2025
To support genome structure studies in non-model systems, we developed SyntenyFinder, a synteny analysis pipeline combining OrthoFinder and RIdeogram. Learn more on our GitHub: github.com/symgenoevola...
github.com
GitHub - symgenoevolab/SyntenyFinder: SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-lev...
SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI. - s...
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Reposted by Ira Cooke
Claus Wilke @clauswilke.com · 08/01/2025
Some years ago I wrote a simple R app to explore colors in HCL space. While it's clunky, it still is my preferred way of selecting colors, because it offers features other color selectors don't normally have. Today, thanks to shinylive, the app is available standalone. 🧵
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Marine-Omics @marine-omics.bsky.social · 30/12/2024
A great year for Marine Omics! www.marine-omics.net
marine-omics.net
Marine Omics – Marine Molecular Biology and Genetics
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Luke Rendell @lrendell.bsky.social · 21/12/2024
🤯 "perhaps most great whales have an unrecognized potential for great longevity that has been masked by the demographic disruptions of industrial whaling. This unrecognized longevity has profound implication for basic biology and conservation of whales." Astonishing stuff.
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Anthony M. Bonacolta @ambonacolta.bsky.social · 03/12/2024
🚨New Preprint🚨: A Single-cell Atlas of Coral Bleaching! 🪸🦠🔥. We show the microbial ecology of coral bleaching from the gene expression of host and symbiont cells to the shifts in the bacterial and protist communities within the holobiont! #ProtistsOnSky #SymbioSky #MicroSky 🧪
researchsquare.com
A Single-Cell Atlas of Coral Bleaching
The symbiosis between corals and dinoflagellate algae is disrupted by heat stress, leading to bleaching. Recurring bleaching events, driven by the climate crisis, are causing massive coral mortality a...
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Michael Friendly @datavisfriendly.bsky.social · 05/12/2024
Lot's of neat tricks here 👏
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Liam Lachs @liamlachs.bsky.social · 29/11/2024
📢New Paper Alert📢 on corals and climate change in Science Adaptation via natural selection could determine whether Acropora corals persist under expected levels of global warming Hyperlinks & explainer thread below ⬇️ (1/12)
credit: Liam Lachs
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/11/2024
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics www.biorxiv.org/content/10.1101/202…
biorxiv.org
Divergent reference genomes compromise the reconstruction of demographic histories, selection scans, and population genetic summary statistics https://www.biorxiv.org/content/10.1101/2024.11.26.625554v1
Characterizing genetic variation in natural populations is central to evolutionary biology. However,
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Marine-Omics @marine-omics.bsky.social · 28/11/2024
New publication from the amazing Joe Perkins explores #dinoflagellate abundance & diversity in Hervey Bay, Qld using #DNAmetabarcoding. First-time identification of some #toxin-producing species in Australia!🧬 www.sciencedirect.com/science/arti...
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Paul Harrison @paulfharrison.bsky.social · 27/11/2024
I just ran my 1.5 hour HTML+SVG+JavaScript+D3 workshop at ResBaz Victoria 2024. Touched on hopefully most of the important ideas needed for an interactive web-based data visualization. #resbaz #resbazvic #resbazvic2024 pfh.github.io/jsfoot/
pfh.github.io
HTML, Javascript, SVG, D3: a foot in the door
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Philipp Bayer @philippbayer.bsky.social · 27/11/2024
Very timely!! #Pangenome construction from short-read sequences: benchmarking for population and conservation genomics www.authorea.com/users/616600...
authorea.com
Pangenome construction from short-read sequences: benchmarking for population and conservation genomics
As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches develop...
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The Shovel @theshovel.bsky.social · 25/11/2024
Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton
theshovel.com.au
Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton — The Shovel
Speaking from a prison cell in Brisbane, Mr Dutton – a former sex worker and director of adult films – said the laws were not necessary and that regulators should not be the arbiters of truth.
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Arthur Gessler @arthurobuntspecht.bsky.social · 25/11/2024
looks like it’s time for altimetric to skip twitter and include Bluesky or maybe even better just add Bluesky - would be nice to see where more science dissemination occurs!
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Altmetric @altmetric.com · 18/11/2024
We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics
docs.bsky.app
Action Intent Links | Bluesky
Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...
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Ira Cooke @iracooke.bsky.social · 24/11/2024
Prepping an EOI for DP 2025 without knowing the 2024 outcome. RMS is warning me that I will be over the grant limit if I am successful and asks me to nominate a grant that I would withdraw from. I don't want 3 grants. I just want to reapply for the one I might not get. @arc-tracker.bsky.social
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Kevin Bairos-Novak @ecolology.bsky.social · 14/11/2024
Many coral 'species' may, in fact, be separate 'cryptic' species! We found that up to 68% of #popgen studies in corals had putative cryptic taxa!! Check out the ms in Peer Community Journal! @peercommunityin.bsky.social #corals #crypticspecies peercommunityjournal.org/articles/10....
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Marine-Omics @marine-omics.bsky.social · 23/11/2024
Top work Nikki Rodewald taking hope the best poster prize at the Australian Antarctic Research Conference #AARC2024 for her PhD research on #Labidiaster ⭐🧬🇦🇶
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AC @andrewcalcino.bsky.social · 21/11/2024
First post and a new paper. The importance of genomics to the future of life in the tropics with @iracooke.bsky.social @mattfield100.bsky.social and a bunch of others who aren't here yet. globalizationandhealth.biomedcentral.com/articles/10....
globalizationandhealth.biomedcentral.com
Harnessing genomic technologies for one health solutions in the tropics - Globalization and Health
Background The targeted application of cutting-edge high-throughput molecular data technologies provides an enormous opportunity to address key health, economic and environmental issues in the tropics...
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Jan Strugnell @janstrugnell.bsky.social · 14/11/2024
Maybe the ARC could just let those of us that definitely didn’t get DPs know the outcome? Would sure be good to know outcomes before writing again…… @arc-tracker.bsky.social
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mr dog @firstdogonthemoon.bsky.social · 15/11/2024
BLUESKY! Twitter is awful and so is social media - what can everyone do instead? www.theguardian.com/commentisfre...
theguardian.com
Leaving Twitter? Here are some alternatives to checking an online Nazi bot sewer every 20 minutes | First Dog on the Moon
Plant a tomato bush then lecture it on how it should grow tomatoes
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Jonathan Eisen @phylogenomics.bsky.social · 09/11/2024
Refs this paper www.nature.com/articles/s41... which describes new mycoplasma-related symbionts of coral with strange, reduced genomes
nature.com
Discovery of deep-sea coral symbionts from a novel clade of marine bacteria with severely reduced genomes - Nature Communications
Corals and other marine invertebrates host diverse microbes that remain poorly characterized, especially in the deep sea. Here the authors discover a new clade of bacteria with uniquely streamlined ge...
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Jan Strugnell @janstrugnell.bsky.social · 10/11/2024
Great new review by Joe Perkins on ecology & detection of the #dinoflagellates that cause #ciguatera @marine-omics.bsky.social 🐠 🐟 🧬 🎣 www.sciencedirect.com/science/arti...
sciencedirect.com
Ciguatera poisoning: A review of the ecology and detection methods for Gambierdiscus and Fukuyoa species
Ciguatera poisoning is the most prevalent non-bacterial seafood illness globally, with an estimated 10,000 to 50,000 human cases reported annually. Wh…
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Marine-Omics @marine-omics.bsky.social · 10/11/2024
Unveiling the First Tropical #Abalone #Genome: chromosome level! 🧬🧬🧬 Top work by Roy Barkan communities.springernature.com/posts/unveil...
communities.springernature.com
Unveiling the First Tropical Abalone Genome: A Milestone in Abalone Genomics
The first chromosome-scale abalone genome assembly is now available, combining various sequencing techniques and bioinformatics tools to provide a high-quality, annotated reference genome for the stud...
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David N. Thomas @dnthomas01.bsky.social · 08/11/2024
Great to see so many marine scientists already on Bluesky - to help get you find some of them here is a starting list list of a few marine biologists If you want to be added (or deleted), or know other I have missed (many for sure) - just contact me and I'll sort it go.bsky.app/RS5zQHv
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Mónica Medina @momedinamunoz.bsky.social · 09/11/2024
Here is a coral reef science starter pack! go.bsky.app/Qo5Gh2H
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Ira Cooke @iracooke.bsky.social · 24/07/2024
Our paper on chromosomal inversions in the coral Acropora kenti is out today in Molecular Ecology. @janstrugnell.bsky.social @marine-omics.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef
The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to as...
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Paul Harrison @paulfharrison.bsky.social · 03/05/2024
Job offering at Monash University: Senior Lecturer in Bioinformatics careers.pageuppeople.com/513/cw/en/jo...
careers.pageuppeople.com
Job Search
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Jan Strugnell @janstrugnell.bsky.social · 04/04/2024
Well done Eva Paulus on a great PhD confirmation! Here espousing the benefits of Whole genome sequencing for investigating #dugong populations. @marine-omics.bsky.social @iracooke.bsky.social
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Thomas Lin Pedersen @thomasp85.com · 26/02/2024
One of the big improvements in the new version of #ggplot2 are related to legends. Teun van den Brand lays out all the detail in this blog post. Get ready for the legend extension extravaganza #stats
tidyverse.org
ggplot2 3.5.0: Legends - Tidyverse
The 3.5.0 version of ggplot2 comes with an overhaul of the guide system. Read here what is new for legends.
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Ira Cooke @iracooke.bsky.social · 24/02/2024
Inversions are likely to be common in corals as they are in many taxa but have mostly been overlooked so far because they can be challenging to find. Our work highlights the need to improve our understanding of SVs as a component of genetic variation, and hence adaptive capacity🧵3️⃣
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Ira Cooke @iracooke.bsky.social · 24/02/2024
We found five large inversions in this species on the GBR, and rates of potentially deleterious mutations were higher within inversions than in the genomic background. 🧵2️⃣
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Ira Cooke @iracooke.bsky.social · 24/02/2024
Our preprint on chromosomal inversions in Acropora kenti is finally out. Work with @janstrugnell.bsky.social, many others not on BlueSky, and of course Jia Zhang who did the majority of analyses. www.biorxiv.org/content/10.1... 🧵 1️⃣
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Sally Lau @lausally.bsky.social · 22/12/2023
New paper out now in Science! 🐙🧬 Historic animal migrations as paleoproxy indicating Last Interglacial West Antarctic Ice Sheet collapse, when temp was +0.5-1.5°C than preindustrial with @janstrugnell.bsky.social @iracooke.bsky.social @nick-golledge.bsky.social www.science.org/doi/10.1126/...
science.org
Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial
Genetic analyses of a type of octopus found around Antarctica show that the West Antarctic Ice Sheet collapsed during the last interglacial period.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 11/10/2023
Analyses of allele age and impact reveal human beneficial alleles are older than neutral controls www.biorxiv.org/content/10.1101/202…
biorxiv.org
Analyses of allele age and impact reveal human beneficial alleles are older than neutral controls https://www.biorxiv.org/content/10.1101/2023.10.09.561569v1
A classic population genetic prediction is that alleles experiencing directional selection should sw
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 14/10/2023
Decrypting corals: Does regulatory evolution underlie environmental specialization of coral cryptic lineages? www.biorxiv.org/content/10.1101/202…
biorxiv.org
Decrypting corals: Does regulatory evolution underlie environmental specialization of coral cryptic lineages? https://www.biorxiv.org/content/10.1101/2023.10.11.561896v1
A recent study has shown that two common Caribbean corals, Montastrea cavernosa and Siderastrea side
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Jan Strugnell @janstrugnell.bsky.social · 14/10/2023
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