Bookmarking 🔖

In conclusion, GraTools is a powerful too for a one-tool manipulation of GFA pangenome variation graphs! It is a member of the GraSuite, feel free to discover ! forge.ird.fr/diade/GraSuite

This year, we celebrate Margaret Dayhoff’s 100th birthday. She built the first protein database when computers filled entire rooms, introduced the amino acid code, and worked on substitution matrices we still rely on today. #Bioinformatics #WomenInSTEM #HistoryOfScience #SciencePioneer

Ready to take your involvement with the Nextflow community to the next level?⬆️ Apply to become a Nextflow Ambassador by Dec 20, 2025!🧵 📚 Learn more: hubs.la/Q03V9PSs0 🔗 Apply here: hubs.la/Q03V9PQQ0 #Bioinformatics #DataScience

Jarritos gummies? Yeah

RIP to Jane Goodall, who opened the world's eyes to our closest relatives. (Photo by NatGeo's Hugo Van Lawick)

Not far from reality 😂

The unraveling of purple grains caused by ANT2 in barley. A new story from PRB group @ @leibnizipk.bsky.social doi.org/10.1021/acs....

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So cool!

Laying the groundwork for more Australia-Europe cooperation in the life sciences www.embl.org/news/embl-an...

PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers.#PangenomeGraphs #Kmers #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

🧠 Can AI help us understand how fungal pathogens infect plants? A new review says yes. AI tools show promise in modelling effector–plant protein interactions to fight crop disease🌾 📖 doi.org/10.1016/j.cs... #GRDC #CurtinUni @callumverdonk.bsky.social @kgagalova.bsky.social @mcderbyshire.bsky.social

This is shaping out to be a very good presentation by Leon on the interplay between tan/yellow leaf spot and septoria nodorum blotch of wheat. @theccdm.bsky.social collab with @DPIRDbroadacre and @agtbreeding @dionbenAGT If you are in town this Friday, please join us at Curtin!

Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv-genomic.bsky.social www.biorxiv.org/content/10.1...

Interesting concepts, to further explore. Bookmarking

Call for a JOSS Reviewer! I’m reviewing a submission for the Journal of Open Source Software, and we need one more reviewer. Reviews are open on GitHub, checklist-based, and collaborative. Interested? DM me, or join here: 🔗 tinyurl.com/jossreview

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

CASP is at risk, and the structural biology community must act. Without it, we lose the only independent benchmark driving real progress in the field. We need support to preserve and evolve CASP, ensuring transparency, fairness and innovation in protein science. #CASP #ProteinScience #OpenScience

Make sure to add this week's CCDM talk to your calendar 📆 If you're on #CurtinUni campus Friday 11 July, come hear from CCDM's @kgagalova.bsky.social as she explores what's new in Nextflow: from monoliths to modular workflows 👩💻

Revolutionary propagandas are making their way around the @theccdm.bsky.social after @ShotaMorikawa69 PhD exit seminar. Dissidents 🤔must be reported @kgagalova.bsky.social! 🤣🤣🤣

Well... I should either find a way or make a new one... Hannibal crossing the Alps with elephants... Sometimes, the most epic journeys begin with: "Well, this might be crazy, but..." #MakeYoueOwnWay

Very interesting short paper about the evolution of scientific projects, dead branches are normal!

Shackleton led the Trans-Antarctic (Endurance) expedition that, although unsuccessful, became famous as a tale of remarkable perseverance and survival... The expedition didn’t make it across Antarctica, but it made it into every leadership seminar since 1916. Call that a win.

Pangenome and pantranscriptome as the new reference for gene family characterisation – a case study of basic helix-loop-helix (bHLH) genes in barley. #Pangenome #Pantranscriptome #PlantCommunications 🧬🖥️ www.cell.com/plant-commun...

Improving spliced alignment by modeling splice sites with deep learning arxiv.org/abs/2506.12986 minisplice github.com/lh3/minisplice 🧬🖥️🧪

A new compression strategy to reduce the size of nanopore sequencing data. #DataCompression #Nanopore #SequenceData #Bioinformatics #Genomics @nanoporetech.com @genomeresearch.bsky.social‬ 🧬 🖥️ genome.cshlp.org/content/earl...

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Benchmarking Docking Tools on Experimental and Artificial Intelligence-Predicted Protein Structures [new] Evaluates docking tools on AI-predicted protein structures vs. experimental structures using known protein-ligand complexes.

Flexible parsing, interpretation, and editing of technical sequences with splitcode academic.oup.com/bioinformati... 🧬🖥️ github.com/pachterlab/s...

Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins [updated] ML models struggle w/ novel enzymatic function prediction for unknown proteins; lack sci. reasoning.

I’m not really used to writing posts like this, but today I had the chance to visit my old university, where it all began. Thank you, #UniBo, for being my home for five years and for setting my journey in academia. Like millions of others, I owe a lot to this place.

Expand your Bluesky network with R: Find people followed by the people you follow, but who you don't follow, using R and the atrrr package blog.stephenturner.us/p/expand-you... #Rstats

Do protein language models store different structural elements in factorizable subnetworks? To find out, we masked out PLM weights to suppress performance on CATH subcategories or secondary structure elements while maintaining performance on other sequences or residues.

Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER www.nature.com/articles/s41... #jcampubs

Random pic on campus, thinking of my Ukrainian friends... #slavaUkraini #russianInvasion

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!

This is how AI is evolving now, launched by a 23 year old with a fund raising of 5.3M. cluely.com #aicheating #blackmirrorinreallife #ai

This exciting opportunity to connect 🇦🇺 grains researchers and International collaborators has been extended to applicants with a Masters degree (not limited to PhDs). 👏🌾 Please share with your network, closes 12 June grdc.com.au/research/par...

IFLRC submission deadline is on the 11th of April! Almost there

PRİSENCÓLİNENSİNÁİNCIÚSOL, song from 1972, the lyrics are gibberish but they intend to sound like American English. That's a pure genius! 😂 #firstrap #firstto makeagif.com/i/8BwgHV

Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations. Thanks @jjimenezluna.bsky.social for the help! 🌐 colab.research.google.com/github/sokry... 📄 www.biorxiv.org/content/10.1...

A good start for a literature review on pangenomes. Next step: tools testing 🔥 #pangenomes #graph-pangenomes github.com/colindaven/a...

DeePhy: A Deep Learning Model to Reconstruct Phylogenetic Tree from Unaligned Nucleotide Sequences https://www.biorxiv.org/content/10.1101/2025.03.09.642239v1

I quite like coolors.co/generate. Add the hex code for one or more colours, click the padlock to lock it in and then press space until you get a palette you like. It likely won't be colour-blind safe/follow good rules on relative brightness etc though, so use with caution!

Pirates in town Ale STORM

#BOSC2025 is now accepting abstract submissions for talks and posters about #OpenSource #bioinformatics or #OpenScience 🍐 #BOSC2025 will include a joint session with the Bio-Ontologies and Knowledge Representation COSI, @bokr.bsky.social Submissions close April 17: www.open-bio.org/events/bosc-...

Reflecting on our time at TU Braunschweig as it comes to an end, we are proud to share some milestones from the past three years. Here is one of them: our review on flavonoid transport doi.org/10.3390/plan... #PlantScience #Flavonoids @bpucker.bsky.social 1/🧵

panHiTE: a comprehensive and accurate pipeline for TE detection in large-scale population genomes https://www.biorxiv.org/content/10.1101/2025.02.15.638472v1 🧬🖥️🧪 nextflow: https://github.com/CSU-KangHu/HiTE tutorial https://github.com/CSU-KangHu/HiTE/wiki/panHiTE-tutorial

🎤 Catch us at #GRDCUpdates on Monday! Don't miss CCDM's students Mohitul Hossain, Viet-Cuong Han, Anjana Sharma & Varthini Govindaraju Punithan presenting in the New Researchers session. 📅 Mon, 24 Feb | ⏰ 1:40 PM | 📍 Session 8 #GRDC #CurtinUni