Kristina Gagalova, Bioinformatics scientist

I recently damaged an entire repo trying to remove a large file I added 2 commits ago... "I don't know what I did" moment

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 😂

Analysis of Anthocyanin-Less 2 Diversity in Barley Reveals a Specific Allele to Cause Purple-Colored Grains The purple color of the barley (Hordeum vulgare L.) grain is attributed to anthocyanins which are beneficial for human health. Synthesis of these pigments in both grain and vegetative tissues is contr...

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 | EMBL Australian BioCommons, Bioplatforms Australia, and EMBL have signed a formal agreement to encourage collaboration in bioinformatics.

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

Bologna?

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

[PRE REVIEW]: Taming your metabolic datasets with MeDUSA · Issue #6892 · openjournals/joss-reviews Submitting author: @laura-hetzel (Laura Ann Hetzel) Repository: https://github.com/laura-hetzel/MeDUSA Branch with paper.md (empty if default branch): Version: v1.0 Editor: @jromanowska Reviewers: ...

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... & 🐍

Exclusive: Famed protein structure competition nears end as NIH grant money runs out Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

Here is the full article
www.science.org/content/arti...

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 👩💻

Memes co-author @callumverdonk.bsky.social

Glad to see my memes are getting peer-reviewed now. Waiting on journal acceptance... 😄

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.

What is the main difference with minimap?

Pangenome and pantranscriptome as the new reference for gene family characterisation – a case study of basic helix-loop-helix (bHLH) genes in barley Short Summary: Traditional gene family analyses were limited and biased toward gene content in a single reference genome, which failed to account for the gene presence/absence variations (gPAVs) in th...

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

Figure 2

Figure 4

Table I

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.