📢 Hiring several postdocs in AI for RNA! Topics: - Explainable RNA LLMs - Optimising coding & non-coding parts of mRNA sequences - RNA 3D structure prediction - RNA–small molecule binding - Agents for RNA biology Strong AI track record needed; biology background a plus, not a must. Please RT 🔁

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

🧬 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

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

🙌 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

HERRO has been published in @nature.com nature.com/articles/s41.... This achievement is a result of the great work by Dominik Stanojevic, with contributions from Dehui Lin, @sergeynurk.bsky.social, and Paola Florez de Sessions Welcome to the era of high-quality genome assemblies supported by AI.

Happy to see MADRe published!! MADRe: Strain-level Metagenomic Classification academic.oup.com/gigascience/... Great work @jlipovac.bsky.social

Following up on this - MADRe is now officially published 🎉 Very grateful for the guidance of @msikic.bsky.social @rvicedomini.bsky.social and Kresimir Krizanovic 🔗 academic.oup.com/gigascience/...

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

Hiring a PhD student in AI × RNA 🧬 • Predict, generate and optimise RNA 3D structure 📍 Zagreb (EU hub, great quality of life) 🌍 Team across Zagreb & Singapore (visit SG possible) 🧠 CS/math/physics + strong AI (not just prompting) 🧪 Real wet-lab validation of models DM if interested. Share 🙏 1/

Martin Schmitz makes history in the lab! He successfully defended his PhD thesis, "Geometric Deep Learning for Diploid De Novo Genome Assembly," at the National University of Singapore, becoming the very first lab member to complete his doctorate there. Congratulations, Martin!!

Science Has a Major Fraud Problem 'For decades, scientists were above reproach. Not any more. Joe Nocera investigates the murky world of fraudulent research, and the sleuths exposing dishonest science.' @thefp.com www.thefp.com/p/science-ha...

This is an important step in the right direction. The methods are improving to start collectively thinking about how we should analyze raw nanopore signals for various new applications that are not possible without signal analysis. Congratulations to the authors!

1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed. link.springer.com/article/10.1...

Transformer-based AI has boosted @nanoporetech.com sequencing accuracy, but at a cost to portability due to GPU demands. Our new work, spearheaded by Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

🧬 Hiring Postdocs at @astar_gis ! We need Computer Scientists and Computational Biologists to develop novel algorithms for de novo assembly of cancer genomes or to help us reconstruct them. Experience in sequence alignment/assembly algorithms or assembly of complex genomes required Please RT! 🔄

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!

We are hiring a PhD student at the University of Zagreb, FER for a project aimed at developing AI models to predict RNA structure and generate new RNA molecules. We are looking for outstanding undergraduates in computer science, physics, or mathematics with demonstrated experience in AI. 1/n

1/ We’re hiring PIs in AI × Biology The @astar-gis.bsky.social Genome Institute of Singapore (GIS) is expanding its AI & Computation domain and recruiting junior & senior PIs.

1/ In an excellent Nature Methods editorial, Lin Tang outlines the future of AI agents in biology. www.nature.com/articles/s41...

When you train your AI on genomes (ie. genome language models), what is the best split for train/validation/test? Most people split chromosomes, but is that the best way? 1/3

I’m recruiting a postdoc to work on algorithms for cancer genome reconstruction. We have access to a rich set of tumour samples sequenced across multiple technologies. If interested, feel free to DM. Please share.

On my way to @neuripsconf.bsky.social in San Diego ✈️ Really excited that Joel Bonnie and Tin Vlasic will present on Dec 7 at the ML4LS workshop: “From Base Pairs to Functions: Rich RNA Representations via Multimodal Language Modeling.” 🔗 neurips.cc/virtual/2025... 1/4

AI-for-biology is becoming one of the toughest places to publish. Output in mainstream ML is exploding, but biology-focused AI moves slower—and students feel the pressure first. 1/12

🚀🧬 Beyond Structure-based Biomolecule Design Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry. So what are the next scientific problems academia could be thinking about? chaitjo.substack.com/p/beyond-str...

Well deserved. Richard is a giant in the fields of bioinformatics and computational biology.

Saturday mornings are ideal for contemplating AI in biology. It’s one of the most important frontiers for AI—but we can’t just copy what works for text or images. Biology speaks a different language. Right now, two major directions are emerging... 1/8

#GI2025 Mile Sikic @msikic.bsky.social presents "Geometric deep learning framework for de novo genome assembly" Now published in GenomeResearch @genomeresearch.bsky.social Full text here ➡️ tinyurl.com/Genome-Res-2...

Mile Sikic @msikic.bsky.social presents "AI for genomes—Rethinking de novo assembly" genome.cshlp.org/content/35/4/839 They devised a bidirectional message-passing procedure in GNN for the problem of genome assembly

Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment https://www.biorxiv.org/content/10.1101/2025.10.31.685625v1

Cool paper new paper from Lorién López-Villellas, @santiagomarco.bsky.social and others! Super cute and simple idea: In Gotoh's affine-cost alignment, only the M matrix is needed during tracing: we can just search for a gap-length x such that M[i][j] = M[i-x][j]+o+x*e or M[i][j] = M[i][j-x]+o+x*e.

🚀 Looking for talented PhD students! Join us in 🇸🇬 Singapore for 1-2 years to push the frontiers of AI for Genomics. Work on: 🧬 Cancer genome reconstruction 🧫 Cancer genome & cell foundation models 💊 RNA drug & mRNA therapeutic design #AI #Genomics #PhD 1/5

A popular humorous quote in the bioinfo community "About ten years ago, some computer scientists came by and said they heard we have some really cool problems. They showed that the problems are NP-complete and went away!” Now is the time for ML experts. 1/2

🚨New preprint out! 🧬Short reads can now decode centromeres. 🌍We reveal population-scale centromere haplogroups and their links to disease. biorxiv.org/content/10.1... (1/n)

🚀 AI + Genomics in Singapore! The AI Visiting Professorship at GIS invites world-class AI researchers (academia/industry, outside SG) to spend 20% of their time on AI–genomics projects. 💰 Up to 4M SGD (~3.1M USD) over 3 yrs. 📩 DM me if interested! #AI #Genomics #Research

Happy to present the first complete genome of an Indian individual biorxiv.org/content/10.1.... Joint effort by @astar-gis.bsky.social, FER, and partners, with support from the Singapore NPM programme! Joint effort with JJ Liu Lab! Prasad Sarashetti and @jlipovac.bsky.social as co-first authors.

Our RiNALMo RNA language model has been published in Nat Comm nature.com/articles/s41... Great work by Rafael Josip Penic and Tin Vlasic, with support and patience in teaching us RNA biology from Roland G Huber and Wan Yue RiNALMo is already an SOTA and a benchmark for RNA LLMs.

Seeking potential PhD students - Developing novel RNA therapeutics using AI-driven approaches - Decoding cancer genomics using LLMs and GNNs Deadline 1/6/2025. Contact me directly! a-star.edu.sg/Scholarships...

Work with @msikic.bsky.social, @rvicedomini.bsky.social, Kresimir Krizanovic MADRe is open-source, modular, and ready to use. Check it out: 🔗 github.com/lbcb-sci/MADRe 9/9

Join us at our GIS Seminar by Dr Marcin Magnus, Harvard University on OpenRNAFold: an end-to-end approach for RNA 3D structure prediction. Date: 29 April, 2PM Venue: GIS, Level 2 Host: Ivona MARTINOVIC @msikic.bsky.social @lvrcek.bsky.social

Join us at Genome Institute of Singapore! Great environment, stable funding!!

Apply now and be part of a team that values innovation, collaboration, and excellence! Check out www.linkedin.com/jobs/view/42... for more details. Find out more about the exciting work we do by our team – @jonathangoeke.bsky.social, @msikic.bsky.social

The first Singapore Long-Reads Symposium was a success! A massive thanks to the speakers: Keynote Heng Li, Ken Sung @jonathangoeke.bsky.social , @msikic.bsky.social & industrial partners @nanoporetech.com , @pacbio.bsky.social , @awscloud.bsky.social MGI_Technology Next Level Genomics & NovogeneAIT

GENOME: THE GIS SPEAKER SERIES Join us at our next seminar by Dr. Heng Li, Harvard Medical School & Dana-Farber Cancer Institute on Wed 12 March, 9.30am (SGT, GMT +8). Host: @msikic.bsky.social Webinar ID: 985 9424 0029 Participant ID: 371683 Passcode: 993251 #GISSPEAKERSERIES #genomics

We are organising ai4na-workshop.github.io at#ICLR2025. Topics: RNA, DNA and cell LLMs, structure, modifications, correction, variant calling... Deadline: Feb 10th 2025 Time for revision: 1 month Accepted papers - the opportunity to be invited by Nature Methods for submission

🚨Exciting news! We're partnering with @naturemethods.bsky.social 🧬High-quality submissions to the AI4NA workshop on @iclr-conf.bsky.social can also be considered for publication in the journal! 🌟 👉More details on our web page (link in comments) #AI4NA #ICLR2025

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio. www.nature.com/articles/s41...

🚨 1 month to go! 🚨 The submission deadline for the AI4NA workshop at @iclr-conf.bsky.social is fast approaching! 🧬 ✨ Submissions on OpenReview will open soon—stay tuned! ✨ 🔗 Learn more on our web page (link below 👇) #AI4NA #ICLR2025

Verkko2 paper is finally on the biorxiv www.biorxiv.org/content/10.1...

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references. #GenomeAssembly #HaplotypeResolved #Pangenomes #Genomics #GenomeBiology 🧬 🖥️ genomebiology.biomedcentral.com/articles/10....