Eduardo Eyras

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/...

"Bullying is a means for mediocre scientists to rise to the top" … often supported by allies and networks. www.nature.com/articles/s41...

Still available: CSIRO industry PhD project - Prediction of molecular interactions with RNA using AI for basic research and therapeutic discovery - collaboration with CSIRO and RNAfold.ai science.anu.edu.au/study/resear...

🧬 Meet Dr. Liana Lareau, 2025 MTI Innovator Awardee!

Her lab is using CRISPR + machine learning to reprogram RNA and silence toxic genes - offering hope for retinitis pigmentosa & beyond.

A new era of mutation-agnostic therapeutics.

#MTI #CRISPR #RNA
moleculartherapeutics.org/2025-mti-inn...

CSIRO Industry PhD program: Prediction of molecular interactions with RNA using AI

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...

research.csiro.au/iphd-opportu...

"Psychological safety" was the #1 predictor of an effective team in a study by Google. 'In other words, for a diverse team to work to its fullest capacity, everyone on the team must feel that it is safe to voice his or her opinions without being ridiculed.' 🙏@virusesimmunity.bsky.social

If you want to know more, please have a look at the preprint or come to RNA2025 😉

dFORCE provides a revised timeline for mRNA synthesis wherein cleavage, termination, and m6A
deposition occur earlier than, or at least partially decoupled from, the bulk of splicing in thousands of genes

Our findings in human cells are recapitulated in mouse tissues, for which previous methods have been hindered by technical challenges.

We also identify recursive polyadenylation at hundreds of genes, and measured that transcription termination occurs closely after cleavage.

m6A methylation occurs extensively on unspliced pre-mRNA and it is not only gated by exon-junction complexes.

Some of the key findings: Splicing is largely delayed until after transcription and polyadenylation, with 20-30k introns remaining unspliced until RNA polymerase II has transcribed >10 kb beyond their boundaries.

We introduce dFORCE (direct fractionated observation of RNA coupled to elongation), a single-molecule approach capturing endogenous pre-mRNA processing without metabolic labelling or amplification. dFORCE separates elongating pre-mRNA from post-transcriptional pre-mRNA and catalytic intermediates

Single-molecule multimodal timing of in vivo mRNA synthesis mRNA synthesis requires extensive pre-mRNA maturation, the organisation of which remains unclear. Here, we directly sequence pre-mRNA without metabolic labelling or amplification to resolve transcript...

"Single-molecule multimodal timing of in vivo mRNA synthesis" a collaboration with Rippei Hayashi's lab, work led by AJ Sethi #RNA #pre-mRNA #splicing #RNAprocessing #m6A #polyadenylation
www.biorxiv.org/content/10.1...

Group photo of the conference participants taken in front of the EMBL Imagine Centre in Heidelberg.

How is AI transforming life sciences – and what’s holding it back?

Participants of the 5th EMBL Partnership Conference share insights on data challenges, validation hurdles, and why collaboration is key.

👉 www.embl.org/news/connect...

#EMBLAIOneHealth

Details : Lecturer / Senior Lecturer in Machine Learning in Omics : The University of Melbourne Careers at The University of Melbourne

Amazing opportunity: Lecturer / Senior Lecturer in Machine Learning in Omics at Melbourne Integrative Genomics and the School of Mathematics and Statistics, University of Melbourne, Australia. jobs.unimelb.edu.au/en/job/91945...

Great opportunity! PhD position in @mfeldbruegge.bsky.social lab #PhD #RNA