Anniina Vihervaara

Figure from the paper illustrating sequence–ensemble–function relationships for disordered proteins. ML prediction (black) and design (orange) approaches are highlighted on the connecting arrows. Prediction of properties/functions from sequence (or vice versa, design) can include biophysics approaches via structural ensembles, or bioinformatics approaches via other hetero- geneous sources. The lower panels show examples of properties and functions of IDRs for predictions or design targets. ML, machine learning; IDRs, intrinsically disordered proteins and regions.

Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB

authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei

Challenge.Gov Challenge.Gov is the official GSA government website supporting prize challenges and prize competitions that are sponsored by the US federal government. Here federal agencies provide prize awards to ...

NINDS just launched a $50K prize competition for early-career scientists championing research rigor beyond their normal duties. Do you organize workshops, journal clubs, or do work to try and shift culture? This could be you.
www.challenge.gov?challenge=ni...

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/

www.encodeproject.org/single-cell/...

Dynamic regulation of RNA Polymerase III transcription in mouse embryonic stem cells during heat shock stress Cells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation ...

🎉Excited to share our new preprint on Biorxiv 🥳
We uncover how RNA Polymerase III (Pol3) dynamically regulates tRNA transcription during heat shock (HS) stress!
So what did we find? 🧵

www.biorxiv.org/content/10.1...

We are happy to report that our journals and community sites now have Bluesky accounts. Follow them at:
@dev-journal.bsky.social
@jcellsci.bsky.social
@jexpbiol.bsky.social
@dmmjournal.bsky.social
@biologyopen.bsky.social
@the-node.bsky.social
@prelights.bsky.social
@focalplane.bsky.social

Look who's here
@pnas.org ✔️
@science.org ✔️
@naturecellbiology.bsky.social ✔️
@natrevgenet.bsky.social ✔️
@naturebiotech.bsky.social ✔️
@naturemicrobiol.bsky.social ✔️
@naturechemistry.bsky.social ✔️
@genesdev.bsky.social ✔️
@cellchembiol.bsky.social ✔️
@genomeresearch.bsky.social ✔️
@jcellbiol.bsky.social ✔️

Hey @biorxivpreprint.bsky.social, I think you need to add another icon here 🦋

Author link to the preview, freely accessible until Jan 10th, 2025: authors.elsevier.com/a/1k8Md3vVUP...

The original study by the Singer lab: doi.org/10.1016/j.mo...

Schematic representation of JNK-mediated phosphorylation of BRD4, which converts BRD4 from a chromatin remodeller (1. at the left part of the figure) to an activator of RNA Polymerase II pause-release (2. at the early gene body). BRD4 is dephosphorylated by PP4 (3b.) The image is cropped from the Figure 1 of the linked article.

Fascinated by molecular switches that transition cell states and coordinate transcription. Was a privilege to preview the Singer lab's latest in Molecular Cell, describing how the multitasker BRD4 transitions from a chromatin remodeler to a transcription activator. doi.org/10.1016/j.mo...

Thanks! Would be happy to be added.

Would be happy to be added.

Would be happy to be added to the list. We develop run-on techniques to track Pol II and its regulation.

Thank you for establishing. Could you add me to the list.

Thank you. I’d be happy to be added.

🙋🏻‍♀️

Oon nyt retuuttanut lelut ja rullannut matot… voisiks millään vaivautuu..?