iiinova — where your digital self keeps evolving

Reposted by Valentyn Bezshapkin 🇺🇦

Qiyun Zhu @zhuqiyun.bsky.social · 11/12/2025

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

nature.com

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 29/07/2025

My question is: How come we designed a system everyone currently tries to avoid with all possible shortcuts?

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Reposted by Valentyn Bezshapkin 🇺🇦

SIB Swiss Institute of Bioinformatics @sib.swiss · 31/03/2025

✔️The programme for the #bc2basel tutorials & workshops is out! From #geneexpression analysis to #machinelearning or #datavisualization, beginner or advanced: boost your #bioinformatics skills! 👉 Register to make sure to secure your spot (limited seats): bc2.ch/registration...

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Reposted by Valentyn Bezshapkin 🇺🇦

Fabian Theis @fabiantheis.bsky.social · 25/07/2025

Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future. Thanks to my amazing team and collaborators—this is our award! 🙌 📽️ Keynote: Atlases, AI & virtual cells 📝 doi.org/10.1093/bioi...

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 20/07/2025

The eagle has landed at #ISMBECCB2025 🦅 Interested in phages, metagenomics and protein language models? Catch me on 24th July, poster session D (D-295). See you on coffee breaks! ☕

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 19/06/2025

Congratulations @maksymuki.bsky.social and all the people involved. Very cool work! As a passionate photographer, would be cool to see new sensors in practice 📸

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 12/06/2025

Hello fellow Swiss scientists! 🇨🇭 An exciting opportunity from Pfizer Foundation: Got a project in immunology, oncology, or digital health? You could win CHF 20,000 in funding. DL: 31.07.2025 Apply here 👉 www.pfizerresearchprize.ch #ScienceFunding #Immunology #Oncology #DigitalHealth #Switzerland

pfizerresearchprize.ch

Pfizer Research Prize I Home

Outstanding Medical Research and Digital Innovation can receive the Pfizer Research Prize. Find out more here.

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Reposted by Valentyn Bezshapkin 🇺🇦

Department of Biology, ETH Zurich @eth-dbiol.bsky.social · 20/05/2025

For her innovative research on plant microbiomes paving the way for healthier crops and higher yields Julia Vorholt was awarded the Novonesis Biotechnology Prize 2025. Watch the video of the @novo-nordisk.bsky.social on Julia Vorholt's career and research: www.youtube.com/watch?v=LoXj...

youtube.com

Novonesis Biotechnology Prize 2025

YouTube video by Novo Nordisk Foundation

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 16/05/2025

Congratulations to the whole team! It is a great tool.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 16/05/2025

Waiting on my UK visa decision. Hopefully, see you there! 🤠

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 13/05/2025

Had a great fun at @rdrpsummit.bsky.social! The field of RNA virus discovery is gaining momentum and this community is in the forefront. New ideas and collaborative projects begin here, usually from a friendly conversation :)

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 08/05/2025

It would be useful to share evidence instead of rage baiting people.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 29/04/2025

That's what one can expect from people who tried to befriend putin, who did same to thousands of children.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 01/04/2025

Only 2 months to dismantle american national freedom myth.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 06/03/2025

Realistically, Zelenskyy doesn't have any opponents, even if they will have support. He is a juggernaut and he would have won evelections if they happened. That coming from me, a great sceptic of Zelenskyy becoming a president in 2019.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 15/02/2025

Yep, I guess freedom loving Americans turned out to be as cowardly as russians under regime pressure. Good game, well played.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 04/02/2025

Doechii is goated! Her Tiny Desk live is among the best ones from series.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 02/02/2025

I'm sorry. We're hanging here, a lot of humanitarian organisations left without grants, external policy is unclear. It might be the dawn, but we'll only learn when it's too late.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 22/01/2025

Very cool! I tried to do it once, but bwa code was not the easiest to bind :( Kudos!

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 15/12/2024

Fully adapted Obsidian and it does wonders for me. Graph tracing allows me to connect topics like never before.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 21/02/2024

I would say it's a problem with communication and delivery as well. The research should be digested and adequately prepared for public and their level of expertise.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 26/01/2024

Is there any good review on our current understanding of consciousness or theories explaining it?

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 22/01/2024

It is an interesting article, but possibility of such predictions concerns me a lot.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 22/01/2024

Which is not a bad thing, we need more methods to yield knowledge from these data.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 19/01/2024

And authorship is defined so easily, no hassle at all

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 19/01/2024

As a community, we should stop using "dark matter" trope in our presentations. merenlab.org/2017/06/22/m...

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Reposted by Valentyn Bezshapkin 🇺🇦

Laura Hug @lhug.bsky.social · 15/01/2024

Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min anonymous survey here: shorturl.at/NOUW2 Please RT!

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Reposted by Valentyn Bezshapkin 🇺🇦

Luis Pedro Coelho @luispedrocoelho.bsky.social · 15/01/2024

New experiment: I will work on a project (starting question: what antibiotic resistance genes co-occur in genomes/metagenomes and does it matter?) completely in the open Everyone is welcome!

youtu.be

Extremely Open Science Part 1 : introduction

#science #presentationLuis Pedro Coelho introduces the Extremely Open Science Project for 2024Links:- https://www.big-data-biology.org/extremely-open-science...

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 12/01/2024

I don't know if Polars is transition worth of spending time at the moment, if performance is not critical. API is very different, so there's a learning curve. And I still use setup.py, as it is more flexible in terms of building extensions and glueing soft together.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 11/01/2024

It's only cholesterol, there are much more happening to the organism! Kudos and carry on!

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 09/01/2024

Something I observed in conversation with my friends, I am opposed to existence of a free will, while they always try to debate me. However, I have a history of frequent stress-induced DP episodes, which luckily subsided with time. Now there is a paper for it!

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 05/01/2024

Embeddings are challengers to HMM-HMM comparisons, and in that category they seem to scale better. See Tab. 2 for data: academic.oup.com/bioinformati... Single pHMMs are hard to beat, especially in hyper optimized PyHMMER edition: github.com/althonos/pyh...

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 03/01/2024

Docking in general should be taken with a grain if salt, as currently used RMSD is just a bad metric for task evaluation: arxiv.org/abs/2308.05777

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 29/12/2023

It is a non-trivial task to create an unbiased testing set for such a task. Possibly there is some form of leakage happening, and high scores suggest it.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 18/12/2023

To be precise azithromycin has antiviral properties and was initially suggested as treatment for both MERS and SARS.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 10/12/2023

I remember talking to people from NLP research in 2019, where they said they discard clinical notes because of how inconsistent they're. If LLMs help to leverage these data, it's remarkable.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 09/12/2023

Exciting, this is a step in the right direction!

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 29/11/2023

To fully comprehend you need to become the one.

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 28/11/2023

Found original source of claim in Suttle 1994 link.springer.com/article/10.1...

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 28/11/2023

I am failing to keep up with the pace! 😃

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Valentyn Bezshapkin 🇺🇦 @valentynbez.bsky.social · 27/11/2023

This paper and the way authors handled it is going to cause so much damage 😓 The article is still in the Nature, completely invalid.

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