Systems Biology, Bioinformatics and other fun things🥃 Mastodon: @aln@genomic.social
Ukraine
Joined December 2013
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aln🇺🇦 retweeted
Kyiv. Civilians try to escape the fire after a Russian drone struck the National Academy of Sciences.
The drone that carried out the strike was built mostly from Chinese components.
Meanwhile, the EU is lifting sanctions on Russian oligarchs.
The US President is asking that Russian oil refineries not be attacked.
The world has gone mad.
And soon this hell will come to other countries too. Because unpunished evil always grows.
aln🇺🇦 retweeted
Select your cell: I'm prototyping an interactive sc RNA-seq portal where the UMAP is dynamically linked to morphing 3D artistic renders of each cell type. You can play with the initial build below.
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We often talk about pangenome reference but what does "reference" mean? If it means the whole graph, what is a variant? My collaborators Pouria and Luke give a clean answer: the reference is a spanning tree including GRCh38 and variants are leftover edges. See preprint for more.
New preprint on a surprising question - with a pangenome reference, *what is a genetic variant?*
biorxiv.org/content/10.1101/…
With Pouria Salehi Nowbandani, Shenghan Zhang, Haoyang Hu, and Heng Li @lh3lh3
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The 19th International Conference on Data and Text Mining in Biomedical Informatics,
15-18 December 2025 (Muju, Republic of Korea)
I will be a speaker!
dtmbio.net/
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Latest preprint from the lab (and the last chapter from Shaojun Pan's PhD thesis)
Making strobealign nimbler and faster!
biorxiv.org/content/10.1101/…
aln🇺🇦 retweeted
Russia killed 31 people in Kyiv yesterday night. Among them were five children.
The youngest victim was just two years old.
159 people were injured, including 16 children.
🕯️
aln🇺🇦 retweeted
The death toll from yesterday's barbaric russian attack on Kyiv has risen to 31 — including five children.
aln🇺🇦 retweeted
Re-reading an old grant proposal (from 2023) and marveling that we used to write these without LLMs
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And the #CAMDA25 team continues with the celebration (including a visit to the super lambanana), wishing them all the best and looking forward to seeing you next year in the #ISMBECCB2025
aln🇺🇦 retweeted
А порадьте якийсь хороший наукпоп (можна англійською) на фізичну тематику, щоб позакривати в голові різні прогалини, які лишилися зі школи
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Kinga Zielińska (Jagiellonian Univ.) opens the #CAMDA25, #ISMBECCB2025 the Gut Microbiota Challenge: Can we build a better microbiome health index? With 4,398 samples & taxonomic + functional data, participants are encouraged to go beyond GMHI & hiPCA
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David Danko (Biotia Inc.) presents BIOTIA-DX Resistance at #CAMDA25, #ISMBECCB2025, a clinically validated metagenomic workflow adapted for AMR prediction. With curated global data and stringent preprocessing, the tool reached an F1 score of 84 on the challenge test set
aln🇺🇦 retweeted
Owen Visser (Univ. of Florida) presents an ensemble ML model for AMR prediction at #CAMDA25, #ISMBECCB2025. Trained on strain-specific markers & AMR gene classes, achieving up to 98.2% accuracy (A. baumannii). Permutation analysis reveals key resistance genes in diverse pathogens
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Now, Alper Yurtseven (Helmholtz Institute) tackles #AMR at #CAMDA25, #ISMBECCB2025 by predicting resistance across 9 key bacterial species using machine learning. With a focus on scalable, cross-species models in the fight against antimicrobial resistance.
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🔬 Ever wonder how your immune system ages?
📊 We used single-cell multi-omics (RNA + ATAC) + bulk ATAC on PBMCs to build a cell-by-cell map of aging.
🧠 Find out which genes fade, which chromatin gates close and why some immune systems age slower.
👉 Poster C-482 #ISMBECCB2025
aln🇺🇦 retweeted
Honored to open day two of #BOSC2025 and BOKR joint session at #ISMBECCB2025 introducing @chrismungall opening keynote: Open Knowledge Bases in the Age of Generative AI
