The 2nd Workshop of the Human RNome Project Consortium took place last week in sunny Toronto 🇨🇦 ☀️, and @clare-r.bsky.social from our team had the pleasure of attending and hearing about the fantastic work happening all over the globe on #RNA modifications.

I'm very happy to be a recipient of the 2026 NRF Investigatorship grant from the National Research Foundation Singapore. We will develop new computational methods that use long read sequencing data to study genetic diseases in the Asian population. github.com/GoekeLab

Göke Lab

Computational Transcriptomics - Third Generation Sequencing - Göke Lab

github.com

Congratulations to Dr @jonathangoeke.bsky.social on being awarded the National Research Foundation (NRF) Investigatorship 2026! Presented by NRF Singapore, the award supports outstanding scientists and researchers in pursuing groundbreaking, high-risk research. @goekelab.bsky.social

Fantastic #longtrac meeting in Valencia, very happy to participate in the @nanoporetech.com workshop describing the recent updates in the cDNA protocol that doubles read length Postdoc positions available @goekelab.bsky.social to work on long read RNA seq (and Bambu)! github.com/GoekeLab

New in Bambu-Pipe: batch effect correction now integrated into clustering for long-read single-cell & spatial RNA-seq Integrate samples across ONT & PacBio, combine 10x 3'/5' chemistries, and get clusters that reflect biology, not technical artifacts. github.com/GoekeLab/bambu-pipe

The 2026 Rousseeuw Prize for Statistics has been awarded to the R Project. #RStats www.rousseeuwprize.org/2026

The 2nd Singapore RNA Salon is just 2 days away! We'll have talks from Early Career Researchers, snacks for networking and a *shuttle bus* to help transport attendees from NUS & A*STAR to NTU! Make sure to register to secure your spot (and receive the bus details!): form.gov.sg/69c0965ce982...

Applications are open for the Singapore Open Research Awards 2026. The awards recognise researchers for open, transparent, and reusable research with meaningful impact. Nominate someone or apply here libguides.ntu.edu.sg/SGORawards2026

We'll be at the NIRBA RNA Science Conference 2026! 🧬 🗓️ 22–23 Oct 2026 | 📍 Singapore Our lab is part of @NIRBA_sg Cluster 2 — RNA modifications & host immunity. Looking forward to the science and the community! #RNAScience #NIRBA #SaveTheDate

Nanopore sequencing provides not just long reads, but the the raw signal data can also be used to identify RNA and DNA modifications. This repository (and the associated review) lists some of the great tools that have been developed www.cell.com/trends/genet...

Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data

Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome t...

cell.com

Goeke Lab@goekelab.bsky.social · 2mo ago

We’ve updated our awesome-nanopore list! The list is a community-curated list of ONT software tools, please feel free to check it out & contribute: github.com/GoekeLab/awesome-nanopore #Nanopore #Bioinformatics #LongReadSequencing

2 weeks until the 2nd Singapore RNA Salon! Abstracts for the talks are below ⬇️ The event is open to everyone, from undergrads to PIs, hope to see you there! Registration: form.gov.sg/69c0965ce982...

Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...

AI is changing how science (& genomics!) gets done. 🧬 Check out our new "awesome" repo - a curated list of skills, MCP servers & benchmarks for AI agents in bioinformatics. Open source & open for contributions! github.com/GoekeLab/awe...

GitHub - GoekeLab/awesome-genomic-skills: A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc

A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc - GoekeLab/awesome-genomic-skills

github.com

Learn more about the latest long read cDNA sequencing upgrade by ONT and bambu-pipe for analysing single cell and spatial long read RNA-Seq data, presentation by @suiyue-0823.bsky.social @goekelab.bsky.social #RNA26 github.com/GoekeLab/bam...

GitHub - GoekeLab/bambu-pipe: Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu

Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu - GoekeLab/bambu-pipe

github.com

RNA Society@rnasociety.bsky.social · 3mo ago

Hey RNA Researchers! Are you arriving in Montreal for #RNA26 a bit early and looking for something to fill the time? Come learn about @nanoporetech.com Long Read RNA sequencing capabilities at a pre-conference workshop from 1:30-4:30pm!

🙌 Excited to share Bambu and our findings on the new long-read cDNA kit from Oxford Nanopore Technologies — featured at London Calling 2026. Full story at the RNA 2026 Pre-Meeting Workshop, Montreal! 🇨🇦 @nanoporetech.com @rnasociety.bsky.social #RNA2026 #OxfordNanopore #Bambu

The new long read cDNA kit by @nanoporetech.com is a major upgrade (and improvement!), substantially increasing read length, with a strong impact on transcript discovery and quantification. We @goekelab.bsky.social have tested this in the beta release, more updates soon #nanoporeconf

🧬 Join us for the 2nd Singapore RNA Salon! 📅 June 18th, 4–6 PM📍 NTU 3 talks from ECRs covering mitochondrial dsRNA & inflammation, engineered CasRx RNA editing and long-read single-cell & spatial RNA-seq followed by snacks and networking, all are welcome! ⭐ Link & more info in comments

Registration: Singapore RNA Salon: 18th June 16:00 - 18:00, NTU, School of Biological Sciences

form.gov.sg

Great trip to Fukuoka with PacBio! 🚀 Sui Yue is on-site, presenting bambu and representing the lab. Hands-on feedback always welcome — let’s discuss!💡 🔗 GitHub: github.com/GoekeLab/bambu 🔗 GitHub: github.com/GoekeLab/bambu-pipe 📄 Preprint: doi.org/10.1101/2024.12.30.630828

We are thrilled to release Bambu-pipe 🧬 🚀 A Nextflow pipeline built for speed, scalability, and precision — unlocking isoform-level insights from long-read single-cell and spatial RNA-seq data💡 🔗 GitHub: github.com/GoekeLab/bambu-pipe 📄 Preprint: doi.org/10.1101/2024.12.30.630828

GitHub - GoekeLab/bambu-pipe: Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu

Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu - GoekeLab/bambu-pipe

github.com

our first lab hackathon! lot's of updates and improvements coming to github.com/GoekeLab

Göke Lab

Computational Transcriptomics - Third Generation Sequencing - Göke Lab

github.com

Goeke Lab@goekelab.bsky.social · 4mo ago

🚀 1 Hackathon. 3 days! A ton of fun and brain-storming! Huge thanks to the team! 💻✨ Check out our GitHub page for the tools we developed: 🔗 github.com/GoekeLab And the lab website for the team: 🌐 jglab.org #ScienceSky #Hackathon #OpenSource #ResearchComputing🚀💻

Join us this week for the RNA Salon at the Genome Institute of Singapore! Speakers from @boxiangliu.bsky.social (NUS) Dahai Luo and @msikic.bsky.social labs. Thanks for support by @rnasociety.bsky.social!

A*STAR Genome Institute of Singapore (A*STAR GIS)@astar-gis.bsky.social · 6mo ago

RNA Salon Events 🧬 Join us for our first RNA Salon on February 12th, 2026, 4-6pm at the Genome Institute of Singapore. For more information, please refer to www.a-star.edu.sg/gis/news-eve... For registration: form.gov.sg/695dc837c1a7... #Genomics #RNA #Genomics #RNA

🧪Happy to share our latest paper in Genome Biology. We profiled #RNA isoforms from 31 neuropsychiatric risk genes in the human brain using long-read sequencing. Unannotated isoforms commonly made up a significant proportion of a gene's expression. genomebiology.biomedcentral.com/articles/10....

Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain - Genome Biology

Background Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Results Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain. Conclusions Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.

genomebiology.biomedcentral.com

📢📢📢 The #AsiaRNA2025 abstract deadline has been extended to September 5th!!! Join us at the inaugural Asia RNA Club Symposium 2025 🗓️ Nov 3-5, 2025 📍Seoul National University, Seoul, 🇰🇷 Register by Oct 10th More info: asiarnaclub.org #RNASky @rnasociety.bsky.social 🔄🙏🏽

The Asia RNA Club Symposium will be happening in Seoul in Nov 3-5, bringing together RNA scientists from the Asia-Pacific region. Excellent speakers and a great opportunity to connect! Abstract submission by Sept 5 asiarnaclub.org

Our paper using Oxford #Nanopore direct RNA sequencing to identify m6A modifications on RNA isoforms in human brain is now out in Science Advances. 🧪 www.science.org/doi/10.1126/...

Isoform-level profiling of m6A epitranscriptomic signatures in human brain

Direct RNA-seq in brain reveals RNA isoform and region-specific m6A modifications, highlighting their role in gene regulation.

science.org

🎉GIS turns 25! Join us in celebrating 25 years of innovation at #GIS25: Genome Innovation and Precision Medicine Conference, happening 11–12 September at Matrix, Biopolis, Singapore! 📅 Save the date and register now! Limited seats left! 👉 a-star.edu.sg/gis/news-eve... #Genomics #PrecisionMedicine

I am not sure how to do Bluesky yet, but I want to tell the world about our neighborhood NMF method. First of many collaborations with the Pelka Lab!!

Engelhardt Research Group@thebeehive.bsky.social · last yr.

Super excited to tell you about our preprint on Neighborhood Nonnegative Matrix Factorization (NNMF) for spatially-aware dimension reduction in spatial transcriptomics, led by Ragnhild Laursen in collaboration with Karin Pelka @pelkalab.bsky.social and her lab! www.biorxiv.org/content/10.1...

One of the gems from the last @genomeresearch.bsky.social #long-reads special issue, Part II. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resol… pubmed.ncbi.nlm.nih.gov/40086881/

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution - PubMed

Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding th...

pubmed.ncbi.nlm.nih.gov

New preprint from Ajay Nadig @nadigajay.bsky.social in Luke O'Connor's lab, with "a suite of statistical tools for formally modeling distributions of DE effects from RNA-seq experiments, including Perturb-seq" www.biorxiv.org/content/10.1...

Transcriptome-wide characterization of genetic perturbations

Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical ...

biorxiv.org

Scientists at A*STAR GIS have unveiled SG-NEx, one of the world's largest long-read RNA sequencing datasets! 🌍🔬 With 750M long RNA reads, it enhances detection of complex RNA features, aiding disease research and precision medicine. Available via AWS Open Data Registry. #Genomics #PrecisionMedicine

SINGAPORE SCIENTISTS UNVEIL ONE OF WORLD’S LARGEST LONG-READ RNA SEQUENCING DATASETS TO ADVANCE DISEASE RESEARCH

a-star.edu.sg