Joined December 2013
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139 Photos and videos
Pinned Tweet
20 Jul 2025
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aln🇺🇦 retweeted
2 Sep 2025
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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aln🇺🇦 retweeted
28 Aug 2025
Center of Kyiv, two Russian missiles hit a regular residential area
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aln🇺🇦 retweeted
11 Aug 2025
anndata 0.12 is out now! We have lots of great features that we hope address some persistent needs. Here are some of the highlights!
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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.
7 Aug 2025
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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aln🇺🇦 retweeted
5 Aug 2025
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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aln🇺🇦 retweeted
2 Aug 2025
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/…
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aln🇺🇦 retweeted
1 Aug 2025
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.
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aln🇺🇦 retweeted
1 Aug 2025
The death toll from yesterday's barbaric russian attack on Kyiv has risen to 31 — including five children.
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aln🇺🇦 retweeted
30 Jul 2025
Re-reading an old grant proposal (from 2023) and marveling that we used to write these without LLMs
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aln🇺🇦 retweeted
25 Jul 2025
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
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aln🇺🇦 retweeted
25 Jul 2025
А порадьте якийсь хороший наукпоп (можна англійською) на фізичну тематику, щоб позакривати в голові різні прогалини, які лишилися зі школи
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aln🇺🇦 retweeted
23 Jul 2025
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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aln🇺🇦 retweeted
23 Jul 2025
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
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aln🇺🇦 retweeted
23 Jul 2025
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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aln🇺🇦 retweeted
23 Jul 2025
Jack Vaska (Stony Brook Univ) applies LLMs to #AMR prediction at #CAMDA25: Fine-tuned DNABERT2 models DBGWAS identify resistance-linked sequences across 9 pathogens & 4 antibiotics. Results show high accuracy, showcasing the power of deep sequence context in AMR genomics.
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aln🇺🇦 retweeted
23 Jul 2025
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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aln🇺🇦 retweeted
🔬 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
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aln🇺🇦 retweeted
22 Jul 2025
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
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aln🇺🇦 retweeted
22 Jul 2025
A strong tour by @GiuliaCesaro4 on cell cell Communication and intra celular signaling at ISMB
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