Ok this is very good

Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪

Free and open-source images, icons, and tools for creating scientific illustrations

Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics

doi.org

The requirements for supplying source data for Nature journal family papers is out of control.

'Look, it's going to be an easy paper. Trust me. Six months. Tops'

Very pleased to say that the paper version of our study examining the role of de novo DNMTs in cancer-associated hypomethylation is now out in @plos.org Genetics 🎉: doi.org/10.1371/jour... You can read more on the previous thread but here is a summary of the main updates! #epigenetics 🧵 1/9

Duncan Sproul@sproullab.bsky.social · 2y ago

New pre-print alert 🚨 Interested in what @ikafetzo.bsky.social learned about DNA hypomethylation in cancer from investigating surprising gains DNA methylation in DNMT1 KO cells? Read all about it here: www.biorxiv.org/content/10.1... For a quick summary see this 🧵 1/8 #epigenetics

Join us this Wednesday to hear about fascinating research from @kashyapchhatbar.bsky.social and @a-radzisheuskaya.bsky.social! If you're not already registered, click here to sign up: us06web.zoom.us/webinar/regi... you can also join the conversation at our discord: discord.com/invite/dXqT89r

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/

Welcome to RustQC

Fast quality control tools for sequencing data, written in Rust.

seqeralabs.github.io

Antibodies don't work. NLRP3 is by far the most studied inflammasome — yet <30% of commercial antibodies were specific. Only 4 of 14 tested antibodies detected NLRP3 specifically. Antibodies must be validated before use. Full report by @ycharos.bsky.social : zenodo.org/records/1162...

If you work in AI for Science, take a moment to familiarize yourself with a common failure mode: paranormal citations (or paracites). Our paper describes them.

Lior Pachter@lpachter.bsky.social · 6mo ago

AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare. www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

An amazing experience to be a part of this multi-disciplinary project within the Bird Lab! 🐦✨ We brought together molecular biology🧩⛓️, genomics🧬🧶, and explainable machine learning📈🖥️🤖 to understand mechanisms of SALL4 function. So proud of this team effort! 🤝🙌 Check out the full breakdown below 🧵👇

Raphaël Pantier@r-pantier.bsky.social · 8mo ago

1/8🧵 Excited to share two studies in which I was involved within the Bird Lab📄📄 We have explored how the transcription factor SALL4 assembles and shapes chromatin in embryonic stem cells. @kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social

🚨 Multiple #PhD opportunities for lab or computational applicants. Do you want to understand the molecular basis of #epigenetic dysfunction in human disease? Come work with our group at the fantastic, collaborative @uoe-igc.bsky.social in a beautiful, liveable city. 🧵 1/4 Please repost 🙏

1/5 Glad to share our latest work with Ian Chambers’ lab published @embojournal.org in which we investigated the role of TET DNA de-methylases during cell fate transitions. Great team effort, many thanks to Sara Gonzalez Brito @ebarbieri.bsky.social @edinuni-irr.bsky.social doi.org/10.1038/s443...

TET knockout cells transit between pluripotent states and exhibit precocious germline entry | The EMBO Journal

imageimageThe roles of TET DNA demethylases during early development remain poorly defined. This work uncovers independence of early mouse embryonic stem cell (ESC) transitions from TET proteins but a...

embopress.org

Integrator and Restrictor act sequentially to control transcription! Great set of experiments to complement some of the Integrator-Restrictor overlap hypotheses proposed here doi.org/10.1371/jour...

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies

Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...

doi.org

Chris Estell@thequietscientist.bsky.social · 10mo ago

Ding ding! New Restrictor paper out showing that ZC3H4 affects transcription universally at a checkpoint downstream and distinct to Integrator! Sequential verification of transcription by Integrator and Restrictor: Molecular Cell www.cell.com/molecular-ce...

🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics doi.org/10.1371/jour... Let's break down what we found! 👇

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies

Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...

doi.org

Excited to share my latest preprint! 🚀 We infer regulatory relationships between chromatin-associated proteins and transcriptional control.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Unravelling epigenetic regulation of gene expression with explainable AI - a case study leveraging degron data https://www.biorxiv.org/content/10.1101/2025.01.30.635704v1

Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)

The PNUTS phosphatase complex controls transcription pause release

Kelley et al. discover that the PNUTS phosphatase complex plays an essential role in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves this through its TND, which recog...

cell.com

Looking forward to sharing a new publication from the lab tomorrow! Something a bit different from us this time around. Stay tuned….

Non-native English speakers need 50% more time to write a paper When they do, they face a 2.5 times higher chance of being rejected because of language journals.plos.org/plosbiology/...

Loved being back in Edinburgh. Such a beautiful city, such great science. Great to catch up with Adrian, @cathyabbott.bsky.social @cellysally.bsky.social @hannahlong.bsky.social @kashyapchhatbar.bsky.social @r-pantier.bsky.social et al. Thanks Cath+Adrian for the hospitality and Congrats Sara!