aln🇺🇦

Systems Biology, Bioinformatics and other fun things🥃
Mastodon: @[email protected]

[aln🇺🇦 @systemnaBio]

First keynote at #ISMBECCB2025 #Liverpool #deepmind #alphafold!

[aln🇺🇦 @systemnaBio]

@tkhir_pivnyk Я не впевнена, що пан володів мовою, можливо, вивчив конкретні фрази. Але вимова була ідеальна. Якось мене це розчулило. Українська і японська фонетично схожі, як на мене. Хоч і географічно ми далеко.

[aln🇺🇦 @systemnaBio]

@tkhir_pivnyk Їхала з ними в потязі. Останню евакуацію сиділи в підвалі вокзалу одного містечка. Була незрозуміла ситуація, бо хтось сказав, йти назад в потяг, а хтось сказав, що тривога триває. Один з делегатів підійшов до нас і запитав чистою українською "Загроза є?" 😳

[Serhii Sternenko @sternenko]

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🇺🇦 @systemnaBio]

@LabMutwil What did you use to implement the atlas? Is it WebGL based? Looks cool!

[Brad Krajina @BradKrajina]

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.

[Ihor Lachenkov @igorlachenkov]

Center of Kyiv, two Russian missiles hit a regular residential area

[scverse @scverse_team]

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!

[Heng Li @lh3lh3]

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.

[Luis Pedro Coelho @luispedrocoelho]

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!

https://t.co/hqF62ImHFZ

[Luis Pedro Coelho @luispedrocoelho]

Latest preprint from the lab (and the last chapter from Shaojun Pan's PhD thesis)

Making strobealign nimbler and faster!

https://t.co/JPRDRxgYke

[Maria Drutska 🇺🇦 @maria_drutska]

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.

🕯️

[Olena Halushka @OlenaHalushka]

The death toll from yesterday's barbaric russian attack on Kyiv has risen to 31 — including five children.

[Luis Pedro Coelho @luispedrocoelho]

Re-reading an old grant proposal (from 2023) and marveling that we used to write these without LLMs

[CAMDA 2025 @CAMDA_conf]

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

[Irina Kostyshina 🇺🇦 🩷💜💙 @irinikostyshina]

А порадьте якийсь хороший наукпоп (можна англійською) на фізичну тематику, щоб позакривати в голові різні прогалини, які лишилися зі школи

[Costa Lab - @costalab.bsky.social @vanvanka123]

Celebreting a busy & sucessfull #ISMBECCB2025

[CAMDA 2025 @CAMDA_conf]

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

[CAMDA 2025 @CAMDA_conf]

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

[CAMDA 2025 @CAMDA_conf]

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

[CAMDA 2025 @CAMDA_conf]

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.