Hey, if anyone is wrapping up their PhD and wants to apply for this with us, let us know! You would be working on our organoid screen for TDP-43! www.theaftd.org/wp-content/u...

Here's a really exciting #phd opportunity to work with us on non-coding #RNAs in Bladder Cancer as part of a collaboration with Dr Jon Griffin and @iansudbery.bsky.social -check it out! tinyurl.com/4rp9abxr

Developing a non-coding RNA predictive biomarker in bladder cancer at University of Sheffield on FindAPhD.com

PhD Project - Developing a non-coding RNA predictive biomarker in bladder cancer at University of Sheffield, listed on FindAPhD.com

tinyurl.com

Congratulations to Pietro Fratta on being elected as a Fellow of the Academy of Medical Sciences 😊- acmedsci.ac.uk/more/news/ac...

For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...

Check out the phenomenal PhD work by Katie Copley, a current postdoc in our lab @yaleneuro.bsky.social @yalerna.bsky.social. www.science.org/doi/10.1126/...

Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration

Aberrant aggregation of the prion-like RNA binding protein TDP-43 drives several fatal neurodegenerative proteinopathies, including amyotrophic lateral sclerosis (ALS). In this work, we define how sho...

science.org

If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.

I'm excited to share that my new lab at the University of Aberdeen is recruiting a PhD student. This fully funded project will use advanced hiPSC models to investigate how microglia, astrocytes, and motor neurons interact in ALS/FTD. For more details and to apply: www.findaphd.com/phds/project...

Dissecting Microglia–Astrocyte Crosstalk in Amyotrophic Lateral Sclerosis Using Human Stem Cell Models at University of Aberdeen on FindAPhD.com

PhD Project - Dissecting Microglia–Astrocyte Crosstalk in Amyotrophic Lateral Sclerosis Using Human Stem Cell Models at University of Aberdeen , listed on FindAPhD.com

findaphd.com

Join us! Research Fellow role at UCL @ukdri.ac.uk @uclqsion.bsky.social with me & @sj-marzi.bsky.social studying oligodendrocytes, genetics & epigenetics in ageing & neurodegeneration using multiomics/bioinformatics. Collaboration with Alexi Nott & @rikeshrajani.bsky.social Closing date: 2nd June

Dementia Researcher@dementiaresearcher.bsky.social · 3mo ago

Research Fellow role at UCL @ukdri.ac.uk with @dervissalih1.bsky.social studying oligodendrocytes, genetics and epigenetics in ageing and neurodegeneration using multiomics and bioinformatics. Closing date: 2nd June www.dementiaresearcher.nihr.ac.uk/job/research...

I'm excited to have new and streamlined instructions in tximport and tximeta about how to take output of those functions and move into edgeR / limma transcript-level analysis. Thanks to Pedro @plbaldoni.bsky.social and Gordon for making this connection so simple, through these new functions.

Congrats to Jobert, Anna-Leigh, and Kai on showing how #BDNF amplifies #transcription, coordinates #RNA dynamics, and spatially regulates the #phosphoproteome. Beautiful cover art too! @jamessleigh.bsky.social @frattalab.bsky.social @uclqsion.bsky.social

Brain-derived neurotrophic factor coordinates neuron-intrinsic programs to enhance axonal regeneration in human motor neurons

BDNF promotes axon-regenerative gene expression, RNA metabolism, and kinase signaling in motor neurons.

science.org

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

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e... This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

COMBINE-lab - The skeptic’s guide to generative AI assisted coding

An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

combine-lab.github.io

A new Agentic IDE for developers from google antigravity.google/product

Pyranges v1: a Python framework for ultrafast sequence interval operations www.biorxiv.org/content/10.6... 🧬🖥️🧪 Docs: pyranges1.readthedocs.io/en/latest/ Rust backend: github.com/pyranges/rur... 🦀

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

Hey, any #ALS researchers want to get together for a basic biology consortium (TALS has open proposals)? DM me if so - happy to do a bunch of cool stuff in our organoids!

a close up of a feather on a rock with the words `` hello '' written in white letters .

ALT: a close up of a feather on a rock with the words `` hello '' written in white letters .

media.tenor.com

@andreaserio.bsky.social and I are recruiting a postdoc to lead an exciting MNDA-funded project using multi-omics to study long axons in motor neurons and how they shape susceptibility to #ALS. Get in touch for any questions and apply by 2 December: my.corehr.com/pls/kclrecru...

Are you an Early Career Researcher in bioinformatics? Then this symposium is for you 💡 Join us for a day of talks, networking and career discussions. Present your work to get fresh new ideas and the chance to win prizes 💸 Featuring @avsecz.bsky.social of Google DeepMind as our keynote speaker⚡️

If you are looking for a PhD, are passionate about neurobiology and enjoy microscopy, come and join us for a PhD project on axonal pathophysiology in ALS! www.findaphd.com/phds/project... Applications close on Friday 4th July 2025 @mndassoc.bsky.social @uclqsion.bsky.social

Axonal pathophysiology in ALS: investigating the role of FUS-ALS mutations in axonal damage and regrowth at University College London on FindAPhD.com

PhD Project - Axonal pathophysiology in ALS: investigating the role of FUS-ALS mutations in axonal damage and regrowth at University College London, listed on FindAPhD.com

findaphd.com

Our new review on the challenges of modelling TDP-43 pathology in mice is just out: rdcu.be/ejZ5a As usual, together with Lizzy Fisher. Thanks to Jose Brito and @lucastaoro.bsky.social from the lab for putting the data together for the comprehensive tables.

New online! The regulation and function of post-transcriptional RNA splicing

The regulation and function of post-transcriptional RNA splicing

Nature Reviews Genetics, Published online: 11 April 2025; doi:10.1038/s41576-025-00836-zPost-transcriptional splicing has emerged as a key layer of gene expression regulation but is challenging to differentiate from co-transcriptional splicing. The authors review methodologies to detect post-transcriptional splicing, the mechanisms controlling splicing timing and how the temporal regulation of splicing affects gene expression.

nature.com

An Analysis presents benchmarking results from the Singapore Nanopore Expression consortium project, plus a valuable resource of datasets generated from various long-read and short-read RNA sequencing technologies. @jonathangoeke.bsky.social @astar-gis.bsky.social www.nature.com/articles/s41...

New in @naturecomms.bsky.social: I'm thrilled to share with you our latest work that applies #srRNAseq to understand splicing accuracy across human introns, tissues and in the context of ageing and neurodegeneration www.nature.com/articles/s41...

Splicing accuracy varies across human introns, tissues, age and disease - Nature Communications

Inaccuracies in RNA splicing may play a significant role in aging and disease. Here, the authors present a comprehensive characterization of splicing accuracy across over 14,000 human samples, offerin...

nature.com

Special Issue (Part 1) of @genomeresearch.bsky.social on #LongRead DNA #Sequencing Applications in Biology and Medicine by @anaconesa.bsky.social, @ahoischen.bsky.social and @sedlazeck.bsky.social genome.cshlp.org/content/34/1...

in this article we delve into the world of splicing models! i specifically focused on the latest omics technologies that will help us to interpret and train models, looking towards future opportunities. lots of biorxiv citations because the field is moving so fast!!! go.nature.com/4gPju63

From computational models of the splicing code to regulatory mechanisms and therapeutic implications - Nature Reviews Genetics

This Review describes how increasingly sophisticated omics data and computational models of the splicing code are paving the way to more accurate, context-specific splicing predictions, while also pro...

go.nature.com

Multicenter integrated analysis of noncoding CRISPRi screens www.nature.com/articles/s41...

Multicenter integrated analysis of noncoding CRISPRi screens - Nature Methods

This analysis provides 108 noncoding CRISPR screens collated by the ENCODE4 consortium and establishes experimental guidelines for future CRISPRi screens characterizing functional cis-regulatory eleme...

nature.com