Ira Cooke
@iracooke.bsky.social
Evolutionary biologist at James Cook University. Mostly working on genomics of corals and other marine animals.
https://www.marine-omics.net
https://www.marine-omics.net
Reposted by Ira Cooke
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.
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.
July 10, 2025 at 7:47 PM
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.
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.
Reposted by Ira Cooke
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...
@janstrugnell.bsky.social @coatiben.bsky.social
doi.org/10.1002/ecs2...
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....
doi.org
June 25, 2025 at 6:57 AM
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...
@janstrugnell.bsky.social @coatiben.bsky.social
doi.org/10.1002/ecs2...
Reposted by Ira Cooke
@zoologistedel.bsky.social wowing the crowd about her genomic research on Heard and McDonald Islands #pintofscience
May 21, 2025 at 8:46 AM
@zoologistedel.bsky.social wowing the crowd about her genomic research on Heard and McDonald Islands #pintofscience
Reposted by Ira Cooke
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 🧬
May 30, 2025 at 10:42 PM
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 🧬
Reposted by Ira Cooke
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...
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...
Dorado v1.0.0 and the v5.2.0 basecalling models
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
May 27, 2025 at 7:02 AM
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...
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...
Reposted by Ira Cooke
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
Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis)
rdcu.be
May 14, 2025 at 4:59 AM
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
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....
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 ....
doi.org
May 9, 2025 at 9:21 AM
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....
Reposted by Ira Cooke
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...
Our seafloor history teachers
YouTube video by SAEF - Securing Antarctica's Environmental Future
www.youtube.com
May 7, 2025 at 12:51 AM
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...
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...
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...
careers.jcu.edu.au
May 2, 2025 at 5:03 AM
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...
Reposted by Ira Cooke
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 🧪
You are my heroes. Well done! @standupforscience.bsky.social 🧪
March 8, 2025 at 3:52 AM
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 🧪
You are my heroes. Well done! @standupforscience.bsky.social 🧪
Reposted by Ira Cooke
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
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
Wild frontiers of model organisms
www.embl.org
January 16, 2025 at 6:48 PM
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
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
Reposted by Ira Cooke
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 - 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...
github.com
January 7, 2025 at 6:20 AM
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...
Reposted by Ira Cooke
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. 🧵
January 8, 2025 at 6:19 PM
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. 🧵
Reposted by Ira Cooke
A great year for Marine Omics! www.marine-omics.net
Marine Omics – Marine Molecular Biology and Genetics
www.marine-omics.net
December 30, 2024 at 12:11 AM
A great year for Marine Omics! www.marine-omics.net
Reposted by Ira Cooke
🤯 "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.
New paper alert
Extreme longevity may be the rule not the exception in Balaenid whales
by @alaskaraven.bsky.social , Els Vermeulen, and me.
2 messages:
♀Southern rights could live much longer than we thought (10% >130);
♀North Atlantic rights' lives are truncated (10%>47)
🐳🌍🦑
Extreme longevity may be the rule not the exception in Balaenid whales
by @alaskaraven.bsky.social , Els Vermeulen, and me.
2 messages:
♀Southern rights could live much longer than we thought (10% >130);
♀North Atlantic rights' lives are truncated (10%>47)
🐳🌍🦑
Extreme longevity may be the rule not the exception in Balaenid whales
Whale life spans have likely been greatly underestimated.
www.science.org
December 21, 2024 at 7:36 AM
🤯 "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.
Reposted by Ira Cooke
🚨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 🧪
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...
www.researchsquare.com
December 3, 2024 at 2:57 PM
🚨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 🧪
Reposted by Ira Cooke
Lot's of neat tricks here 👏
Can I tell you about the gospel of our lord and saviour `theme_set()`? github.com/teunbrand/gg...
GitHub - teunbrand/ggplot_tricks: Here, I collect some tricks I've learned about the {ggplot2} R package
Here, I collect some tricks I've learned about the {ggplot2} R package - teunbrand/ggplot_tricks
github.com
December 5, 2024 at 2:05 AM
Lot's of neat tricks here 👏
Reposted by Ira Cooke
📢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)
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)
November 29, 2024 at 10:11 PM
📢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)
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)
Reposted by Ira Cooke
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
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,
www.biorxiv.org
November 30, 2024 at 9:31 AM
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
Reposted by Ira Cooke
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...
www.sciencedirect.com/science/arti...
November 28, 2024 at 10:06 AM
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...
www.sciencedirect.com/science/arti...
Reposted by Ira Cooke
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/jsfoot/
HTML, Javascript, SVG, D3: a foot in the door
pfh.github.io
November 27, 2024 at 7:12 AM
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/jsfoot/
Reposted by Ira Cooke
Very timely!!
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics
www.authorea.com/users/616600...
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics
www.authorea.com/users/616600...
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...
www.authorea.com
November 27, 2024 at 10:19 AM
Very timely!!
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics
www.authorea.com/users/616600...
#Pangenome construction from short-read sequences: benchmarking for population and conservation genomics
www.authorea.com/users/616600...
Reposted by Ira Cooke
Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton
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.
theshovel.com.au
November 25, 2024 at 7:02 AM
Misinformation Laws Not Necessary, Says Meth Addict Peter Dutton
Reposted by Ira Cooke
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!
November 25, 2024 at 7:31 AM
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!
Reposted by Ira Cooke
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/docs/advance...
#AcademicSky #HigherEd #Altmetrics
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...
docs.bsky.app
November 18, 2024 at 2:48 PM
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/docs/advance...
#AcademicSky #HigherEd #Altmetrics