Lightnews — Scholar-powered news

Reposted by Ira Cooke

METR @metr.org · Jul 10

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 · Jun 25

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...

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

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Jan Strugnell @janstrugnell.bsky.social · May 21

@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 · May 30

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 · May 27

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...

Dorado v1.0.0 and the v5.2.0 basecalling models

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Jan Strugnell @janstrugnell.bsky.social · May 14

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

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Ira Cooke @iracooke.bsky.social · May 9

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

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Jan Strugnell @janstrugnell.bsky.social · May 7

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

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Ira Cooke @iracooke.bsky.social · May 2

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

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David Grinspoon @drfunkyspoon.bsky.social · Mar 8

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 🧪

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 · Jan 16

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

Wild frontiers of model organisms

www.embl.org

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Yi-Jyun Luo @yjluo.bsky.social · Jan 7

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

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Claus Wilke @clauswilke.com · Jan 8

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 · Dec 30

A great year for Marine Omics! www.marine-omics.net

Marine Omics – Marine Molecular Biology and Genetics

www.marine-omics.net

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Luke Rendell @lrendell.bsky.social · Dec 21

🤯 "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.

Peter Corkeron @petercorkeron.bsky.social · Dec 20

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

Whale life spans have likely been greatly underestimated.

www.science.org

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Anthony M. Bonacolta @ambonacolta.bsky.social · Dec 3

🚨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

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Michael Friendly @datavisfriendly.bsky.social · Dec 5

Lot's of neat tricks here 👏

Teun van den Brand @teunbrand.bsky.social · Dec 4

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

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Liam Lachs @liamlachs.bsky.social · Nov 29

📢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)

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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Nov 30

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

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Marine-Omics @marine-omics.bsky.social · Nov 28

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 · Nov 27

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/

HTML, Javascript, SVG, D3: a foot in the door

pfh.github.io

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Philipp Bayer @philippbayer.bsky.social · Nov 27

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

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

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The Shovel @theshovel.bsky.social · Nov 25

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

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Arthur Gessler @arthurobuntspecht.bsky.social · Nov 25

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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Ira Cooke @iracooke.bsky.social · Nov 25

Hi Mel I am not sure to be honest. I had mine mostly complete. We will find out tomorrow now I hope

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