🧬 Preprint update with @worm-lab.bsky.social !
If you are aiming for a phased assembly, should you sequence @pacbio.bsky.social HiFi or @nanoporetech.com R10 reads? Whichever you have easier access to!
The real question is: which assembler should you use based on your data? (1/2)
#genomes
a simplified evolutionary tree of eukaryotes with pictures of various microbes
New #ISEPpapers #preprint by @deemteam.bsky.social: Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data www.biorxiv.org/content/10.6...
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
#ERGAReads | Cookbook for plant genome sequences 🌱 🌴 🌵 🌿 🌾 🌿 🍀
link.springer.com/article/10.1...
@bpucker.bsky.social @unibonn.bsky.social @puckerlab.bsky.social 🌱 🖥️
#Plant #genomes
Hiring a PhD student in AI × RNA 🧬
• Predict, generate and optimise RNA 3D structure
📍 Zagreb (EU hub, great quality of life)
🌍 Team across Zagreb & Singapore (visit SG possible)
🧠 CS/math/physics + strong AI (not just prompting)
🧪 Real wet-lab validation of models
DM if interested.
Share 🙏 1/
Transformer-based AI has boosted
@nanoporetech.com
sequencing accuracy, but at a cost to portability due to GPU demands.
Our new work, spearheaded by
Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.
Screenshot of peartree with a tree and a root-to-tip plot
New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest
We just published a review 🗞️😁:
‘The ecology of adaptive radiation’ revisited: A 25-year reflection
Dolph Schluter’s book inspired the interest in adaptive radiation, and we wanted to revisit it.
academic.oup.com/evolinnean/a...
1/5 🧵
Would you like to learn about how genetic differentiation and phenotypic plasticity shape a species' range expansion? Here is a new, comprehensive paper led by Monica Sheffer from my group - supported by wonderful colleagues.
"Formation and maintenance of genome gigantism"
by Yuan Huang & colleagues
FREE till May 15th at
authors.elsevier.com/a/1mqbK_3rsx...
Ever wondered about #specimen custody - where specimens are housed relative to where they were collected - in #natural #history museum collections across time?
A new study looked at 253,131 preserved specimen records. See the persistent geographic imbalances they found here 👇
@mystyn.bsky.social
AI-generated cartoon of a computational biologist and wet-lab biologist collaborating on a research project
✂️🧬preprint!
"Quantitative prediction of nonsense-mediated #mRNA decay across human genes by #genomic language #model & large-scale mutational scanning"
Fantastic teamwork by @IgnasiToledano 👨🔬and @MarcellVeiner👨💻. We combine massive experiment and sequence AI to elucidate NMD👇
Check out the newly discovered cave shrimp 𝘊𝘢𝘳𝘪𝘥𝘪𝘯𝘢 𝘵𝘢𝘴𝘩𝘢𝘯𝘪𝘤𝘢 from the Tashan Cave in Iran.
This discovery marks the first record of a #cave atyid #shrimp in Iran and the first documented occurrence of a Caridina species inhabiting sulphidic groundwater: doi.org/10.3897/subt...
#newspecies
📢📢REMINDER LinneSys applications close this Friday, March 27th at 23:59 GMT+1!!!📢📢
Apply now! systass.org/linnesys/
Do remember to join the @systassn.bsky.social or the @linneansociety.bsky.social as a member first!
Also, we only fund taxonomy and systematics related projects!
How do you turn many individual experiences, workflows, and challenges into something the whole community can use?
Watch Katja Reichel explaining the writing of doi.org/10.1111/1755...
Link: youtu.be/80cedW-Oc6c
#Genomics #Biodiversity #ReferenceGenomes #ERGA
What can spider names tell us about the tangled web of author inequalities?
A recent paper in @biojlinnsoc.bsky.social by Montana et al. looked at every spider described from the Americas in 1946-2021, analysing over 9,000 species and nearly 600 researchers.
Read more:
Calling all systematics and taxonomy researchers! Applications are now open for our Linnesys grants.
Run with the Systematics Association, the scheme supports small-scale research and education projects with grants of up to £1,500.
Find out more and apply by Friday 27 March
buff.ly/WrVmOnY
Preprint: Dishonesty can be based on honesty.
Increased pheromonal attractiveness despite reduced pheromone production in a aging female spider.
Senescent widow spiders are poor mates but remain attractive to mate-seeking males through deceptive signalling.
doi.org/10.64898/2026.03.04.709482
In @ecoevorxiv.bsky.social, we just released a open dataset on subterranean spiders, with >30000 georeferenced localities for >600 cave spider species:
doi.org/10.32942/X2M...
The kind of information we need to implement evidence-based subterranean conservation!
#Subterranean #habitats host unique species that remain largely under-explored.
New study on the endemic ground Trechus #beetles of Portugal, currently Red Listed as Endangered, revealed an interesting #evolutionary trajectory.
⬇️Uncover what the study found here: doi.org/10.3897/subt...
#ArticleIRBio
📄 chromosome-level genome assembly of the blind scorpion Belisarius xambeui Simon, the most singular scorpion in Europe
👥S.GuiraoRico, VA.Pisarenco, M.Domènech,ABellvert,SAdriánSerrano,ASánchezGracia,M.Arnedo, J.Rozas
📕 ERGA-BGE-CBP
🔗 open-research-europe.ec.europa.eu/articles/6-5...
Everything you always wanted to know about mushroom-forming fungi! Great collab with amazing mycologists. Thanks Laszlo Nagy for leading this effort!
www.nature.com/articles/s44...
So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).
Footage of the World Wide(st) Web - in a smelly cave in the Balkans.
🕷️🕸️
🧪
youtube.com/shorts/8yhOF...
The colonial spider web in Sulfur Cave, is home to a mixed colony of Tegenaria domestica and Prinerigone vagans. A. Side view; B. frontal view. The swarm of adult chironomids is visible near the cave stream. Photo A: Marek Audy.
Biggest spider web in the world: the area of a flat.
Found in a sulphur-smelling cave in the Balkans, this ~100m² spongy web is maintained by two species of solitary 🕷️. The 110K inhabitants feed on midges, probably because they can't see the other spiders.
🧪
subtbiol.pensoft.net/article/1623...
Read more about this Arachnopolis here: doi.org/10.3897/subt...
🧬 Hiring Postdocs at @astar_gis !
We need Computer Scientists and Computational Biologists to develop novel algorithms for de novo assembly of cancer genomes or to help us reconstruct them.
Experience in sequence alignment/assembly algorithms or assembly of complex genomes required
Please RT! 🔄
Let's look at some numbers
2022: 7 044 applications submitted. 17.9 % success rate
2023: 8 039 applications submitted. 15.8 % success rate
2024: 10 360 applications submitted. 16.6 % success rate
2025: 17 058 applications submitted (record high). 9.7% success rate (preliminary numbers).
Long-read sequencing can revolutionise the way we monitor #biodiversity.
A comprehensive guide for using #ONT & #PacBio for analysis of biodiversity through #eDNA, #metabarcoding, metagenomics
Just published in @methodsinecoevol.bsky.social
besjournals.onlinelibrary.wiley.com/doi/10.1111/...
Highlight of our review paper on long-read sequencing for biodiversity analysis by the EBP @ebpgenome.bsky.social
#BiodiversityGenomics #eDNA #Biodiversity
#PacBio #ONT
Read @methodsinecoevol.bsky.social doi.org/10.1111/2041...
Subterranean ecosystems are key to water, climate, biodiversity & culture. But to what extent?
As part of @biodiversa.eu DarCo we demonstrate that they contribute to 75% of classified ecosystem services. Read OA in Biol Rev:
doi.org/10.1002/brv....
Illustration @jmalumbresolarte.bsky.social