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Kristina Gagalova, Bioinformatics scientist

@kgagalova.bsky.social
250 followers 469 following 65 posts

Evolutionary genomics enthusiast, plant genomics researcher, #NextflowAmbassador, my views; Works on: 🧬 Genome Science and Algorithms | 💻 Software Development | 👽 AI dev

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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 19/03/2026
Ourt super star, Pavel, is giving the first PhD Milestone. Looking forward to hear more about AI applied to protein-protein interactions
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Reposted by Kristina Gagalova, Bioinformatics scientist
Centre for Crop and Disease Management @theccdm.bsky.social · 04/03/2026
As 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
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Reposted by Kristina Gagalova, Bioinformatics scientist
Philipp Bayer @philippbayer.bsky.social · 26/02/2026
We (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! #biostatistics
seek.com.au
Technical Lead Biostatistics Job in Nedlands, Perth WA - SEEK
Life-changing science is our focus; we start there, and everything else follows
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/02/2026
kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations www.biorxiv.org/content/10.64898/20…
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 07/02/2026
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
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 01/02/2026
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
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Reposted by Kristina Gagalova, Bioinformatics scientist
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
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...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Sina Majidian @sinamajidian.bsky.social · 15/01/2026
Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly doi.org/10.1101/2025...
Figure 1. Workflow of fDOG-Assembly. (A) fDA starts its ortholog search from a pre- computed core ortholog group together with a multiple sequence alignment (MSA) of the corresponding amino acid sequences, and a profile Hidden Markov Model (pHMM) trained with the MSA. A consensus sequence is computed from the pHMM, and the MSA is used to produce a block profile. (B) A tblastn search with the consensus sequence as query identifies candidate regions in the target genome assembly that may harbour an ortholog. (C) Each candidate region from (B) serves as input for a gene prediction. fDOG-Assembly provides two alternative ways for gene prediction, Augustus in combination with the pre-computed block profile or MetaEuk in combination with a reference database. (D) To verify the ortholog candidates resulting from (C), the amino acid sequences of the predicted genes (ortholog candidates) are used as queries in a reverse blastp search in the protein set of a user-specified reference species. If two or more candidate orthologs are verified, only those are accepted as co-orthologs whose pair-wise distance is smaller than their respective distances to the reference protein. Otherwise, the candidate with the smaller distance is chosen. See main text for further information on the candidate verification. An assessment of the feature architecture similarities of the identified orthologs and the seed gene concludes the ortholog search.
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pierreatlas.bsky.social @pierreatlas.bsky.social · 30/04/2025
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
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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
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 07/01/2026
rformassspectrometry.github.io/Metabonaut/
rformassspectrometry.github.io
Exploring and Analyzing LC-MS Data
This resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages.
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Burstein lab @bursteinlab.bsky.social · 07/01/2026
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...
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Sina Majidian @sinamajidian.bsky.social · 01/01/2026
ntSynt: multi-genome synteny detection using minimizer graph mappings doi.org/10.1186/s129...
https://doi.org/10.1186/s12915-025-02455-whttps://doi.org/10.1186/s12915-025-02455-w
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 04/01/2026
Benchmarking
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Genome 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...
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Bruce S. Lieberman @bruceslieberman.bsky.social · 11/11/2025
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.
digitalatlasofancientlife.org
2.1 Reading Trees
Chapter 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...
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Admirable Women @admirablewomen.bsky.social · 26/12/2025
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."
An oil portrait painting of Mary Somerville, the renowned 19th-century Scottish mathematician, astronomer, and science writer, by Thomas Phillips (1834). She is depicted as a poised woman in her fifties, facing slightly to the left with a calm, intelligent expression. Her dark hair is elegantly styled, parted in the center and drawn up into intricate braids with soft ringlets framing each side of her face. She wears a formal dark blue or black off-the-shoulder gown with puffed sleeves, draped in a luxurious brown fur stole over her shoulders. A wide, elaborate white lace ruff collar frames her neck, and at the center of her chest is a prominent emerald-green brooch set in gold, fastened to the gathered fabric. The background is a dramatic, dark gradient with subtle warm highlights, employing chiaroscuro lighting to emphasize her serene face and the textures of lace, fur, and fabric, evoking a sense of dignified intellect and refinement typical of Regency-era portraiture.
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 26/12/2025
Bookmarking
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 09/12/2025
Bookmarking 🔖
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Francois Sabot @francoissabot.bsky.social · 03/12/2025
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
The GraSuite Logo a suite and a tie showing a graph, with a double strand DNA symbolized on the right
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 30/11/2025
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
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Nextflow @nextflow.io · 20/11/2025
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
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 25/10/2025
Jarritos gummies? Yeah
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Clara Jeffery @clarajeffery.bsky.social · 01/10/2025
RIP to Jane Goodall, who opened the world's eyes to our closest relatives. (Photo by NatGeo's Hugo Van Lawick)
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 01/10/2025
Not far from reality 😂
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Christian Hertig @chertig.bsky.social · 26/09/2025
The unraveling of purple grains caused by ANT2 in barley. A new story from PRB group @ @leibnizipk.bsky.social doi.org/10.1021/acs....
doi.org
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...
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 22/09/2025
👇🧠
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 17/09/2025
So cool!
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 10/09/2025
Laying the groundwork for more Australia-Europe cooperation in the life sciences www.embl.org/news/embl-an...
embl.org
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.
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Reposted by Kristina Gagalova, Bioinformatics scientist
Javier Santoyo @jsantoyo.bsky.social · 08/09/2025
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...
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Centre 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
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KC👨‍🔬🌾🍄🇦🇺 @karchuntan.bsky.social · 19/08/2025
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!
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Javier Santoyo @jsantoyo.bsky.social · 18/08/2025
Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv-genomic.bsky.social www.biorxiv.org/content/10.1...
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 18/08/2025
Interesting concepts, to further explore. Bookmarking
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 16/08/2025
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
github.com
[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: ...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 05/08/2025
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... & 🐍
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 12/07/2025
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
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Centre for Crop and Disease Management @theccdm.bsky.social · 07/07/2025
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 👩💻
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KC👨‍🔬🌾🍄🇦🇺 @karchuntan.bsky.social · 05/07/2025
Revolutionary propagandas are making their way around the @theccdm.bsky.social after @ShotaMorikawa69 PhD exit seminar. Dissidents 🤔must be reported @kgagalova.bsky.social! 🤣🤣🤣
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/07/2025
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
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/07/2025
Very interesting short paper about the evolution of scientific projects, dead branches are normal!
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 29/06/2025
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.
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Javier Santoyo @jsantoyo.bsky.social · 24/11/2024
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...
cell.com
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...
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Stephen Turner @stephenturner.us · 17/06/2025
Improving spliced alignment by modeling splice sites with deep learning arxiv.org/abs/2506.12986 minisplice github.com/lh3/minisplice 🧬🖥️🧪
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Javier Santoyo @jsantoyo.bsky.social · 05/06/2025
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...
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Gabriele Corso @gcorso.bsky.social · 06/06/2025
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… 🤗🚀
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AI x Bio Discovery @aixbiobot.bsky.social · 07/06/2025
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.
Benchmarking Docking Tools on Experimental and Artificial Intelligence-Predicted Protein StructuresFigure 2Figure 4Table I
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Stephen Turner @stephenturner.us · 06/06/2025
Flexible parsing, interpretation, and editing of technical sequences with splitcode academic.oup.com/bioinformati... 🧬🖥️ github.com/pachterlab/s...
academic.oup.com
Flexible parsing, interpretation, and editing of technical sequences with splitcode
AbstractMotivation. Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and uniq
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AI x Bio Discovery @aixbiobot.bsky.social · 06/06/2025
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.
Figure 1Figure 2Figure 3Figure 4
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Kristina Gagalova, Bioinformatics scientist @kgagalova.bsky.social · 03/06/2025
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.
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