Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 19/03/2026Ourt super star, Pavel, is giving the first PhD Milestone. Looking forward to hear more about AI applied to protein-protein interactions 040
Reposted by Kristina Gagalova, Bioinformatics scientistCentre for Crop and Disease Management @theccdm.bsky.social · 04/03/2026As we lead up to #IWD2026, we’re celebrating Kristina Gagalova, Bioinformatics Scientist and part of AGGI, whose work bridges cutting‑edge genomics with real‑world agricultural impact. @curtinuniversity.bsky.social, #GRDC 062
Reposted by Kristina Gagalova, Bioinformatics scientistPhilipp Bayer @philippbayer.bsky.social · 26/02/2026We (PYC Therapeutics) are hiring two biostatisticians, one senior, one junior www.seek.com.au/job/90561321... and www.seek.com.au/job/90560959... We need people who can give us confidence in rare disease diagnostics with small n! #biostatisticsseek.com.auTechnical Lead Biostatistics Job in Nedlands, Perth WA - SEEKLife-changing science is our focus; we start there, and everything else follows 132
Reposted by Kristina Gagalova, Bioinformatics scientistbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/02/2026kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations www.biorxiv.org/content/10.64898/20… 0107
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 07/02/2026SHE 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 200
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 01/02/2026Dayhoff 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 111
Reposted by Kristina Gagalova, Bioinformatics scientistMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026FoldMason 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...science.orgMultiple protein structure alignment at scale with FoldMasonProtein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou... 4302147
Reposted by Kristina Gagalova, Bioinformatics scientistSina Majidian @sinamajidian.bsky.social · 15/01/2026Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly doi.org/10.1101/2025... 021
Reposted by Kristina Gagalova, Bioinformatics scientistpierreatlas.bsky.social @pierreatlas.bsky.social · 30/04/2025Fifty years ago today: the Fall of Saigon, April 30, 1975. I remember seeing these images on TV as if it was yesterday. #VietnamWar #Saigon 121
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 09/01/2026📚 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 030
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 07/01/2026rformassspectrometry.github.io/Metabonaut/rformassspectrometry.github.ioExploring and Analyzing LC-MS DataThis resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages. 032
Reposted by Kristina Gagalova, Bioinformatics scientistBurstein lab @bursteinlab.bsky.social · 07/01/20261/4 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... 153
Reposted by Kristina Gagalova, Bioinformatics scientistSina Majidian @sinamajidian.bsky.social · 01/01/2026ntSynt: multi-genome synteny detection using minimizer graph mappings doi.org/10.1186/s129... 0335
Reposted by Kristina Gagalova, Bioinformatics scientistGenome Research @genomeresearch.bsky.social · 07/11/2025#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... 0105
Reposted by Kristina Gagalova, Bioinformatics scientistBruce S. Lieberman @bruceslieberman.bsky.social · 11/11/2025If 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.digitalatlasofancientlife.org2.1 Reading TreesChapter contents: Systematics — 1. Taxonomy — 2. Phylogenetics —— 2.1 Reading trees ← —— 2.2 Building trees —— 2.3 Character mapping —— 2.4 Phylogenetic trees and classificationParts of a tree A phylo... 04118
Reposted by Kristina Gagalova, Bioinformatics scientistAdmirable Women @admirablewomen.bsky.social · 26/12/2025Scottish 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." 120891
Reposted by Kristina Gagalova, Bioinformatics scientistFrancois Sabot @francoissabot.bsky.social · 03/12/2025In 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 111
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 30/11/2025This 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 02712
Reposted by Kristina Gagalova, Bioinformatics scientistNextflow @nextflow.io · 20/11/2025Ready 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 164
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 25/10/2025Jarritos gummies? Yeah 030
Reposted by Kristina Gagalova, Bioinformatics scientistClara Jeffery @clarajeffery.bsky.social · 01/10/2025RIP to Jane Goodall, who opened the world's eyes to our closest relatives. (Photo by NatGeo's Hugo Van Lawick) 204108921931
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 01/10/2025Not far from reality 😂 030
Reposted by Kristina Gagalova, Bioinformatics scientistChristian Hertig @chertig.bsky.social · 26/09/2025The unraveling of purple grains caused by ANT2 in barley. A new story from PRB group @ @leibnizipk.bsky.social doi.org/10.1021/acs....doi.orgAnalysis of Anthocyanin-Less 2 Diversity in Barley Reveals a Specific Allele to Cause Purple-Colored GrainsThe 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... 064
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 10/09/2025Laying the groundwork for more Australia-Europe cooperation in the life sciences www.embl.org/news/embl-an...embl.orgLaying the groundwork for more Australia-Europe cooperation in the life sciences | EMBLAustralian BioCommons, Bioplatforms Australia, and EMBL have signed a formal agreement to encourage collaboration in bioinformatics. 031
Reposted by Kristina Gagalova, Bioinformatics scientistJavier Santoyo @jsantoyo.bsky.social · 08/09/2025PG-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... 021
Reposted by Kristina Gagalova, Bioinformatics scientistCentre for Crop and Disease Management @theccdm.bsky.social · 08/09/2025🧠 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 143
Reposted by Kristina Gagalova, Bioinformatics scientistKC👨🔬🌾🍄🇦🇺 @karchuntan.bsky.social · 19/08/2025This 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! 061
Reposted by Kristina Gagalova, Bioinformatics scientistJavier Santoyo @jsantoyo.bsky.social · 18/08/2025Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv-genomic.bsky.social www.biorxiv.org/content/10.1... 041
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 18/08/2025Interesting concepts, to further explore. Bookmarking 000
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 16/08/2025Call 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/jossreviewgithub.com[PRE REVIEW]: Taming your metabolic datasets with MeDUSA · Issue #6892 · openjournals/joss-reviewsSubmitting 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: ... 000
Reposted by Kristina Gagalova, Bioinformatics scientistMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 05/08/2025MMseqs2 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... & 🐍 06417
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 12/07/2025CASP 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 100
Reposted by Kristina Gagalova, Bioinformatics scientistCentre for Crop and Disease Management @theccdm.bsky.social · 07/07/2025Make 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 👩💻 001
Reposted by Kristina Gagalova, Bioinformatics scientistKC👨🔬🌾🍄🇦🇺 @karchuntan.bsky.social · 05/07/2025Revolutionary propagandas are making their way around the @theccdm.bsky.social after @ShotaMorikawa69 PhD exit seminar. Dissidents 🤔must be reported @kgagalova.bsky.social! 🤣🤣🤣 231
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/07/2025Well... 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 000
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/07/2025Very interesting short paper about the evolution of scientific projects, dead branches are normal! 022
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 29/06/2025Shackleton 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. 040
Reposted by Kristina Gagalova, Bioinformatics scientistJavier Santoyo @jsantoyo.bsky.social · 24/11/2024Pangenome 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...cell.comPangenome and pantranscriptome as the new reference for gene family characterisation – a case study of basic helix-loop-helix (bHLH) genes in barleyShort 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... 0146
Reposted by Kristina Gagalova, Bioinformatics scientistStephen Turner @stephenturner.us · 17/06/2025Improving spliced alignment by modeling splice sites with deep learning arxiv.org/abs/2506.12986 minisplice github.com/lh3/minisplice 🧬🖥️🧪 041
Reposted by Kristina Gagalova, Bioinformatics scientistJavier Santoyo @jsantoyo.bsky.social · 05/06/2025A 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... 063
Reposted by Kristina Gagalova, Bioinformatics scientistGabriele Corso @gcorso.bsky.social · 06/06/2025Excited 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… 🤗🚀 1021391
Reposted by Kristina Gagalova, Bioinformatics scientistAI x Bio Discovery @aixbiobot.bsky.social · 07/06/2025Benchmarking 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. 021
Reposted by Kristina Gagalova, Bioinformatics scientistStephen Turner @stephenturner.us · 06/06/2025Flexible parsing, interpretation, and editing of technical sequences with splitcode academic.oup.com/bioinformati... 🧬🖥️ github.com/pachterlab/s...academic.oup.comFlexible parsing, interpretation, and editing of technical sequences with splitcodeAbstractMotivation. Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and uniq 0145
Reposted by Kristina Gagalova, Bioinformatics scientistAI x Bio Discovery @aixbiobot.bsky.social · 06/06/2025Limitations 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. 021
Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/06/2025I’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. 220