SHE reconstructs eukaryotic evolution using structural comparisons across 1542 proteomes. It reveals a rigid Strict Core supporting a flexible translational Operational Engine, detects lineagespecific accelerations, and uses structural topology to see proteome quality and guide model organism choice

Dayhoff Atlas release is a big step for protein language models and generative protein design. By opening up massive protein datasets + pretrained models, it lowers the barrier for researchers to predict mutation effects, and generate functional sequences #ProteinAI #ProteinDesign #MicrosoftResearch

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly doi.org/10.1101/2025...

Fifty years ago today: the Fall of Saigon, April 30, 1975. I remember seeing these images on TV as if it was yesterday. #VietnamWar #Saigon

📚 On my 2026 reading bucket list. The "Quiet American" by Graham Greene, set in 1950s Saigon, at the end of French colonial rule and the start of U.S. involvement in Vietnam. A sharp, unsettling look at good intentions and their consequences. #ReadingBucketList #Saigon #HoChiMinhCity #BookBucketList

1/4 Ever wanted to predict bacterial protein-protein interactions (PPI) on a large scale? We wanted to, but realized there’s no such algorithm that is both rapid and optimized for bacterial protein analysis. This led our ⭐️Chen Agassy⭐️ to develop B-PPI: doi.org/10.64898/202...

ntSynt: multi-genome synteny detection using minimizer graph mappings doi.org/10.1186/s129...

Benchmarking

#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...

If you're a #teacher interested in a great #openaccess write up on reading #phylogenetic trees, check out www.digitalatlasofancientlife.org/learn/system... created by @jonhendricks.bsky.social and Elizabeth Hermsen.

Scottish mathematician, astronomer & polymath Mary Somerville was born #OTD in 1780. #WomenInSTEM William Whewell coined the term "scientist" in a review of Somerville's book, 𝘖𝘯 𝘵𝘩𝘦 𝘊𝘰𝘯𝘯𝘦𝘹𝘪𝘰𝘯 𝘰𝘧 𝘵𝘩𝘦 𝘗𝘩𝘺𝘴𝘪𝘤𝘢𝘭 𝘚𝘤𝘪𝘦𝘯𝘤𝘦𝘴. Used as gender-neutral term as the common term at the time was "man of science."

Bookmarking

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....

👇🧠

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