Real-time feature importance analysis

Kate from Kharkiv@kateinkharkiv.bsky.social · 2w ago

Zelenskyy: "When our strikes reached Yandex data centers, it suddenly became little easier to breathe on many social media platforms. Many people noticed it. There was less hate, less division, fewer provocations because there were fewer bots. It's pretty clear where those bots were coming from.

Very interesting indeed, and so many questions to follow up on. As the relative abundances of RNA species don't seem to change, do overall protein concentrations decrease? Rates of cellular processes? Is the number game why expression variability of individual genes seems to increase with age?

Erik van Nimwegen@erikvannimwegen.bsky.social · 2mo ago

Very interesting. Unless I’m missing something, this also seems to imply protein production is mRNA limited.

For folks interested in isoform variation in human disease, a new doctoral network will be kicking off in 2027! Check out available positions: euraxess.ec.europa.eu/jobs/461377

EUROPE: 15 PhD positions in the MSCA Doctoral Network DECODES: Deciphering the Splicing Code in Human Disease

EUROPE: 15 PhD positions in the MSCA Doctoral Network DECODES: Deciphering the Splicing Code in Human Disease Grant Agreement No. 101312753

euraxess.ec.europa.eu

Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n

Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology

High-dimensional data are visualized through representation on tree structures.

nature.com

Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

How do you visualize highly complex data without losing important information? Prof. Erik van Nimwegen’s team developed a new tool, Bonsai, that provides a faithful picture of the structure in the data. @erikvannimwegen.bsky.social @unibas.ch @dhdegroot.bsky.social @imbavienna.bsky.social

Seeing the Unseen: A new tool for exploring complex biological data

Modern biology research can now generate valuable data on an unprecedented scale. But there is one major obstacle: making sense of these complex high-dimensional datasets. Prof. Erik van Nimwegen’s te...

biozentrum.unibas.ch

🚀 New preprint 🥳 Fantastic work by our recent PhD graduate Daan ! How are mRNPs remodeled as they exit the nucleus? We identify PAIP1 as a factor that promotes exchange of the nuclear poly(A)-binding protein PABPN1 for cytoplasmic PABPC1, coupling mRNA export to cytoplasmic mRNP maturation.

bioRxiv Molecular Biology@biorxiv-molbio.bsky.social · 3mo ago

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis https://www.biorxiv.org/content/10.64898/2026.07.31.742013v1

Today (May 15) is the last day to get your special edition @rnacanada.ca RNEh? tshirts to celebrate your Canadian RNA pride at #RNA2026 @rnasociety.bsky.social. Order here: gametime.gearware.com/stores/rna! Delivery ONLY to RNA2026 in MTL/no shipping. Image design by Jasmine Tsang.

RNA Canada ARN is excited to be at the 2026 RNA Society Meeting. We will be set up at a table in the exhibition hall! Stop by to talk with RNA Canada members, grab some free swag, and sign up to renew your membership. !

The small GTPase Arf1 regulates TORC1 in two different ways! Great work by Ludovic Enkler and a great collaboration with @mihaelazavolan.bsky.social . Check out our preprint! www.biorxiv.org/content/10.6...

And there's more meetings.embo.org/event/26-gen...

Lots of things RNA going on early summer 2026 and I'm looking forward to Montreal! www2.rnasociety.org

How does a major liver function, protein synthesis, change when the organ can't cope anymore with challenges and cancer develops? Here's what we found: www.biorxiv.org/content/10.6... Another productive collaboration with Salvatore Piscuoglio. Thanks to my great team - Asier, Meric, Aleksei & co!

Context: Gene expression noise has been observed to decrease with growth rate in E. coli. journals.plos.org/plosbiology/... Consequently, fast growing cells are more phenotypically stable, and this has major implications for phenotypic adaptation www.pnas.org/doi/10.1073/... 2/n

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

Genome-wide flow cytometry measurements reveal that gene expression noise in bacteria is highly condition-dependent; while absolute noise levels of all genes decrease with growth-rate, theoretical mod...

journals.plos.org

What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases. www.biorxiv.org/content/10.6... 1/n

Sad day... way too soon

SIB Swiss Institute of Bioinformatics@sib.swiss · 11mo ago

We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We honour his legacy by continuing to build the future of bioinformatics.

Is this f*g real? The comedic tragedy we're living in.

Aaron Rupar@atrupar.com · last yr.

"Don't take Tylenol!" -- Trump has said this about a dozen times during this press conference

Are you excited to pursue your own research interests and contribute to our group’s experimental research in the quantitative biology of microbes? We have an opening for a potentially permanent position as research associate. Please repost and notify potential candidates!

Biozentrum, University of Basel@biozentrum.unibas.ch · last yr.

Research Associate (100%) Starting from 1 November 2025 or as per agreement Group @erikvannimwegen.bsky.social @biozentrum.unibas.ch @unibas.ch www.biozentrum.unibas.ch/open-positio... #job #research #biology #microbiology #science #basel #recruiting #career

What novel biological dynamics might be hiding under the measurement noise of your time-lapse fluorescence microscopy data? Try our new RealTrace tool to find out! Fantastic work by Bjoern Kscheschinski and others. Tweetorial follows. 1/n www.biorxiv.org/content/10.1...

RealTrace: Uncovering biological dynamics hidden under measurement noise in time-lapse microscopy data

One of the most powerful approaches for identifying the mechanisms underlying complex biological phenomena is not just to measure bulk populations, or even take single-cell snapshots, but to directly ...

biorxiv.org

Publication by the Becskei & Zavolan labs w/ co-1st authors Asier González, Muskan Pandey & Niels Schlusser "Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines" in Scientific Data buff.ly/WYwzw5V @mihaelazavolan.bsky.social @biozentrum.unibas.ch

Hey there, #mRNAtranslation buffs! Our latest multi-faceted dataset from liver cancer cell lines is out in #ScientificData: RNA-seq, ribosome run-off/ribo-seq, polysome-seq, pSILAC. rdcu.be/eC86H. Great team effort spearheaded by Asier Gonzalez Sevine and Niels Schlusser. Happy data crunching!

Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines

Scientific Data - Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines

rdcu.be

Spread the word - we at @stanford-chemh.bsky.social are searching to fill a new junior faculty at the interface of molecular and computational science. See link below!

Sarafan ChEM-H@stanford-chemh.bsky.social · last yr.

Open faculty position! We're seeking applicants for a tenure-track faculty position at the junior level (Assistant or untenured Associate Professor) with research programs that exist at the interface between molecular science and computation. Apply here: stanford.io/45MF3Qa

🤔 Can migrating cells 'remember' their past trajectories? In collab w/ @sgabriele.bsky.social & @kyohalie.bsky.social, we address this question: Confined cells undergo geometry-sensitive morphology switches, and these switches depend on the past migration history! www.nature.com/articles/s41...

The actin cortex acts as a mechanical memory of morphology in confined migrating cells - Nature Physics

Cells often navigate through confined spaces. Now it is shown that cells retain a mechanical memory of previous confinement events, which makes them more efficient at migrating through narrow microenv...

nature.com

The key point here is rather "who would your rather trust"? Because what is offered is not for anyone to decide for themselves, but rather one is coerced to go along with decisions made by few. People are expected to follow the orders of someone who understands nothing.

Carl T. Bergstrom@carlbergstrom.com · last yr.

1. "'Trusting the experts is not a feature of either a science or democracy," Kennedy said." It's literally a vital feature of both science and of representative democracy. I've written a fair bit about trust in expertise as a vital mechanism in the collective epistemology of science.

OTD in 1949 Soviets forcibly deported 30,000 people from Moldova, after we had "liberated them from fascism". Imagine mass deportations happening today...

Right! Maybe these folks who like to push others into various spheres of influence should try living there.

The Kyiv Independent@kyivindependent.com · last yr.

⚡️NATO expansion 'fair' concern for Putin, Kellogg says.

Really nice to see some fresh initiatives on the Romanian science scene 1health.ro/biotech-boot... kudos to the biomentorhub.ro and all those who made this possible.

Biotech Bootcamp 2025 – One Health Incubator

1health.ro

Back to reality www.brainonllm.com. Now imagine the cognitive debt on stuff that involves some abstraction...

Your Brain on ChatGPT: Accumulation of Cognitive Debt when Using an AI Assistant for Essay Writing Task

Your Brain on ChatGPT: Accumulation of Cognitive Debt when Using an AI Assistant for Essay Writing Task

brainonllm.com

RNase L cleaves most tRNAs in the anticodon loops into various tRNA-derived RNAs (tDRs) including 5'-tDRAla that shows a translation inhibitory effect. Some tRNAs are also cleaved in variable loops bit.ly/3YTwlNq

'Data analysed by the BBC show that Ukraine's Western allies have paid Russia more for its hydrocarbons than they have given Ukraine in aid.' What a bleak set of statistics.

How the West is helping Russia to fund its war on Ukraine

Data shows that Russian fossil fuel revenues are three times higher than aid allocated to Ukraine.

bbc.co.uk

It's really happening: AI-enabled noise injection in scientific information, from which models are trained, for more automated noisy inferences... journals.plos.org/plosbiology/...