Stefan Köstler @stefankoestler@qoto.org

🤩
---
RT @SwuliusLab
We’re excited to share cryo-TomoSim (aka CTS), our #cryoET modeling and simulation software, in addition to our new preprint documenting its use in training regressive denoising and semantic segmentation U-Nets.

https://www.biorxiv.org/content/10.1101/2023.04.28.538636v1
https://twitter.com/SwuliusLab/status/1652884981289500672

Patrick Cramer & his lab (@CramerLab @mpi_nat) study the molecular mechanisms of gene transcription using integrative structural biology & systems biology approaches. The lecture “Gene transcription: from mechanisms to regulation” is now online: 📺https://www.youtube.com/watch?v=CWQtaWOG0yc

I really like the idea of microPublications. This one is an intriguing observation:

https://www.micropublication.org/journals/biology/micropub-biology-000737

I’m sure many labs have some interesting results tucked away that suit this format.

#CellBiology #MembraneTraffic #ScienceMastodon

I'm delighted to say our paper "Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization" has now been accepted by CurrentProtocols and you can read it there open access at the link below! If you've always wondered what you can actually do with all those measurements CellProfiler gives you, wonder no longer!

https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.713

Preprint thread in more detail here - https://fediscience.org/@bethcimini/109393739675866418

Should the UK made a deal with Springer Nature (SN)?

I argue that the UK should no longer support transformative deals; other forward-looking models are proposed.

1. Nature APCs are not justified.

2. Gold OA is not the only way forward.

3. Gold OA creates another paywall that prevents many authors from publishing.

4. SN refuse to recognise #RightsRetention for all authors.

5. SN have not met last year's targets for over half their transformative journals.

https://unlockingresearch-blog.lib.cam.ac.uk/?p=3494

And another workflow acquisition by one of the big four surveillance publishers:

https://group.springernature.com/gp/group/media/press-releases/springer-nature-acquires-researcher-created-writing-tool/24020648

Soon, there will be no escaping the surveilance...

#openscience #surveillance

As the pilot of the Open Peer Reviewers in Africa project comes to an end, AfricArXiv, Eider Africa, PREreview, the Training Centre in Communication Africa and we reflect on this collaborative effort to promote best open peer-review practices in Africa, and outline what comes next
https://elifesciences.org/inside-elife/55167fa5/open-peer-reviewers-in-africa-a-train-the-trainer-program-pilot-recap?utm_source=mastodon&utm_medium=social&utm_campaign=organic

Springer Nature will no longer help authors publishing via the subscription option to comply with the NIH PubMed Central mandate, shifting the burden back to them:
"We are getting in touch to let you know that Springer Nature will no longer be able to provide a manuscript deposition service via an automated feed for accepted manuscripts of journal articles published via the subscription route to PubMed Central (PMC) and Europe PubMed Central (EPMC)."

#OpenScience #PubMedCentral #SpringerNature

#GeneRegulation digest #4:

🧬 New role of histone tails in nucleosome remodelling https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad079/7034407

🧬 TFBSs under accelerated #evolution in primates https://www.nature.com/articles/s41467-023-36421-3

🧬 Review of IDRs in #transcription regulators https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(23)00008-7

🧬 CpG islands & protection of genes from premature transcription termination https://www.nature.com/articles/s41467-023-36236-2

🧬 Regulation of #enhancers by DNA #methylation https://www.sciencedirect.com/science/article/pii/S1097276523000400

🧬 H2A-H2B & short-term memory of #chromatin states https://www.sciencedirect.com/science/article/pii/S0092867423000077

We're hiring for our Postdoctoral Training Program in #BioimageAnalysis! Are you a wet lab biologist who wants to move into computational tools and workflows? Do you love collaborating with others & solving puzzles? Do you want a career-specific training program? Do you want to do all this in Cambridge, MA, USA, with awesome coworkers and collaborators? If so, check us out! If not, but you think this all sounds good, please boost! https://docs.google.com/document/d/1mcjHtTfIe3_LH4aHoly1sFIrRhS3GsOx2Yi6lnlQyZ0/preview

In this episode of the Epigenetics Podcast, we caught up with Karen Arndt from the University of Pittsburgh to talk about her work on transcription elongation control by the Paf1 complex. #epigenetics #chromatin #podcast #womeninstem @epigenetics

Listen here: https://activemotif.com/podcasts#karen-arndt

This new paper from Obashi and colleagues in the Taraska lab is very nice. It uses a FRET-CLEM approach to look at protein conformations in cells and tie those to ultrastructural correlates. Here they are looking at clathrin light chain dynamics relative to the clathrin cage during #endocytosis, but there are many other questions in cell biology where this could be applied.

https://doi.org/10.1038/s41467-023-36304-7

#CellBiology #StructuralBiology #ElectronMiscroscopy #MembraneTraffic

Non-profit journals as a solution to open science?

Publishers charge researchers incredible amounts to remove paywalls from their own papers...and make unbelievable profits from doing so. Several have an >30% profit margin.

Initiatives such as @PeerCommunityIn provide an alternative: open access, non-profit journals that are free to publish in.

https://peercommunityin.org/
https://peercommunityjournal.org/
#OpenScience #Science #AcademicChatter @academicchatter
Graph (2013): @alexh https://alexholcombe.wordpress.com/2013/01/09/scholarly-publishers-and-their-high-profits/

My lab has a #vacancy for a #PostDoc working on a #MembraneTraffic project. It will be of interest to #microscopy people with an interest in neuronal cell biology. Closing 12th Feb.
Boosts appreciated!

https://bit.ly/3GTORvi

https://www.linkedin.com/jobs/view/3433441743/

Petition: Remove academic age limits on ERC grants
https://chng.it/gGSycngtmg