Eduardo Eyras

Eduardo Eyras appointed Director of Shine‑Dalgarno Centre for RNA Innovation | EMBL Australia From being recruited through a highly competitive international search to Centre Director, Professor Eduardo Eyras has charted an impressive journey at EMBL Australia. After joining the John Curtin Sc...

🔦 Spotlighting Prof @edueyras.bsky.social - EMBL Australia Group Leader & newly appointed Director of the Shine‑Dalgarno Centre for #RNA Innovation at ANU!

🔗 Read about his vision for the Centre:
www.emblaustralia.org/eduardo-eyra...

here is a better resolution image

Altogether, more than 130 different ONT experiments analysed, including IVTs, cell lines, and tissues. SWARM is open source, operates without a control sample & works with both ONT chemistries: github.com/comprna/SWARM
#RNA #Epitranscriptomics #Nanopore
6/6

We also discovered a new splicing-shaped Ψ deposition! TRUB1-mediated pseudouridylation near splice sites preferentially occurs after exon-exon ligation, consistent with local RNA structure stabilisation, which we validate via nascent RNA and in vitro experiments
5/6

Exploiting SWARM’s precision on data from 6 different tissues in 5 mammals (from Santos-Rodriguez, Srivastava et al www.biorxiv.org/content/10.1... ) yielded a couple of interesting findings. One is that we find no evidence of widespread m6A-Ψ interplay.
4/6

We benchmarked SWARM on synthetic RNAs & cell lines, showing unmatched precision vs. existing tools, and strong correlations with orthogonal methods like GLORI, BACS, & mass spec
3/6

SWARM is an AI framework for nanopore direct RNA sequencing that detects m6A, pseudouridine (Ψ), and m5C mods at single-nucleotide & single-molecule resolution.
Key innovation: Crosstalk-aware training with non-target mods & validated cellular signals to reduce false positives.
2/6

Excited to share our latest preprint: "SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications" www.biorxiv.org/content/10.6...
Led by Stefan Prodic #RNA #Epitranscriptomics #Nanopore 1/6

While AI Data Centres Boom, Public Research Hits a Wall For the last five years, the National Computational Merit Allocation Scheme (NCMAS) has functioned like a steady “electricity grid” for science: a somewhat predictable way to access national supercomp...

nathangarland.substack.com/p/while-ai-d...

Thrilled to announce that I've been appointed Director of the ANU Shine Dalgarno Centre for RNA Innovation. Honoured to work with a world-class team advancing RNA science. Stay tuned for more exciting updates 🚀 jcsmr.anu.edu.au/research/cen... #RNA #RNAInnovation #ANU

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

Very sad to hear about Peer Bork's passing. I met him as a very junior group leader in an early European network on splicing. He's been an inspiration for me since then. He visited us in Canberra ~2 years ago for my EMBL-A review. His legacy lives on www.embl.org/news/embl-an...

Thanks to our excellent team @edueyras.bsky.social and Stefan Prodic!

Resolving systematic bias in nanopore-based RNA modification detection Nanopore direct RNA sequencing has accelerated the growth of the epitranscriptomics field, yet nanopore-based RNA modification landscapes are generally unreliable due to the heuristic and unvalidated ...

New preprint 🚀 We uncover and correct systematic bias in nanopore-based RNA modification detection. ModkitOpt optimises pipelines using validated sites, increasing true positives while reducing unvalidated calls across contexts.
💻: github.com/comprna/modk...
📄: www.biorxiv.org/content/10.6...

SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications Nanopore direct RNA sequencing promises to decode the epitranscriptome by detecting multiple modifications on individual RNA molecules, but its potential for biological discovery is hampered by high f...

SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications
#RNAmods #epitranscriptomics #nanopore
github.com/comprna/SWARM
www.biorxiv.org/content/10.6...

And today:

🧬 Machine Learning in RNA Biology - with our very own Prof
@edueyras.bsky.social
🧪 Text Mining for data organisation & understanding - Prof Richi Nayak
🧠 Building a genomic language model from scratch - Dr Ke Ding

(4/5)

BenchMake: turn any scientific data set into a reproducible benchmark iopscience.iop.org/article/10.1... by Amanda Barnard pypi.org/project/benc...

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

Quantification of transcript isoforms at the single-cell level using SCALPEL nature.com/articles/s41... by @miriplass.bsky.social and her team

Free online event about CSIRO Industry PhD (iPhD) program. You will also hear from current iPhD students who will share their experiences and advice events.csiro.au/Events/2025/...

Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored an AI researcher going back to school for immunology

"a fascinating case study on the limits of AI in biology and the harms of current publishing incentives" rachel.fast.ai/posts/2025-0...

Postdoctoral Research Fellow, Bioinformatics - Cairns, QLD, Australia James Cook University (JCU) is creating a brighter future for life in the Tropics and beyond, through education and research that makes a difference locally and globally.  We now have an opportunity a...

An opportunity exists for an exceptional early career bioinformatician to join the Field lab in tropical Cairns Australia, home of the Great Barrier Reef. Job offered until Dec 2026 however extension possible. Internationals welcome to apply. Closes Mar 26th!
careers.jcu.edu.au/jobs/postdoc...

Prediction of molecular interactions with RNA using AI - CSIRO Industry PhD Program opportunities This Project will develop deep-learning models to predict interactions of ribonucleic acid (RNA) with other molecules. The expected outcomes are to improve prediction capabilities to decode RNA intera...

CSIRO Industry PhD position available in my group: Prediction of molecular interactions with RNA using AI research.csiro.au/iphd-opportu... #RNA #molecularinteractions #AI #academicjobs

Boarding an infinitely long plane 😊

Phage people: Rich Losick and I are combing the world looking for T4 rIIB mutant FC0 (also known as P13). FC0 was the starting point for Francis Crick's beautiful 1961 paper on the triplet nature of the genetic code. We want to sequence it. Anyone have it in an ancient stock collection?

Yes! I think so. Let's talk. Please find me during the poster session

Don't miss AJ's talk (T-93) on dFORCE this afternoon in the RNA processing session (Ballroom A) #RNA2025 #RNA25

GitHub - comprna/SWARM: Single-molecule Workflow for Analysing RNA Modifications Single-molecule Workflow for Analysing RNA Modifications - comprna/SWARM

SWARM (Single-molecule Workflow for Analysing RNA Modifications) detects pseudouridine, m6A, and m5C on individual molecules from direct RNA nanopore signals (in both chemistries RNA002 and RNA004) github.com/comprna/SWARM see more on poster P2-396 at #rna2025 #RNA25 #RNAmods

Design of an orally bioavailable small molecule that modulates the microtubule-associated protein tau’s pre-mRNA splicing Frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) is caused by the aberrant alternative pre-mRNA splicing of microtubule-associated protein tau ( MAPT ) exon 10, the inclusio...

Cool recent study:
www.biorxiv.org/content/10.1...

The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines RNA presents abundant opportunities as a drug target, offering significant potential for small molecule medicine development. The transcriptome, comprising both coding and noncoding RNAs, is a rich area for therapeutic innovation, yet challenges persist in targeting RNA with small molecules. RNA structure can be predicted with or without experimental data, but discrepancies with the actual biological structure can impede progress. Prioritizing RNA targets supported by genetic or evolutionary evidence enhances success. Further, small molecules must demonstrate binding to RNA in cells, not solely in vitro, to validate both the target and compound. Effective small molecule binders modulate functional sites that influence RNA biology, as binding to nonfunctional sites requires recruiting effector mechanisms, for example degradation, to achieve therapeutic outcomes. Addressing these challenges is critical to unlocking RNA’s vast potential for small molecule medicines, and a strategic framework is proposed to navigate this promising field, with a focus on targeting human RNAs.

pubs.acs.org/doi/10.1021/...