Mile Sikic

Mile Sikic

@msikic.bsky.social

AI in genomics

173 followers103 following92 posts

Mile Sikic reposted

Goeke Lab
@goekelab.bsky.social

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.

Mile Sikic
@msikic.bsky.social

AI in biology must be experimentally verifiable, and that requires wet labs. @astar_gis is hiring pre- and postdocs with proven AI knowledge to build foundation models for RNA therapeutics: mRNA vaccines/drugs, gene editing, ribozymes and in vivo CAR-T. Singapore-based. DM me and please repost.

Mile Sikic
@msikic.bsky.social

Preferred candidates: - Experience with deep learning models or theoretical machine learning. Not looking for computational biologists for these positions - We are looking exclusively for those who are ready to come to Singapore - Those interested in creating biotech startups are more than welcome

Mile Sikic
@msikic.bsky.social

Singapore is funding a generous Visiting Professorship — I'm recruiting AI researchers (academia or industry, based outside SG) to join @astar-gis.bsky.social for 20% of their time. We're tightly integrating AI with wet-lab experiments for training + validation. Deadline soon. DM me. Please share!

Mile Sikic
@msikic.bsky.social

@anthropic.com c is betting biology is AI's next frontier. I agree—but there are two streams: building virtual bioinformaticians that combine existing knowledge & tools, or AI that discovers new biology in close collaboration with wet-lab scientists. Our focus is the latter. 1/3

Mile Sikic
@msikic.bsky.social

We're hiring interns, research officers & postdocs at the A*STAR Genome Institute of Singapore. Projects: • RNA therapeutics—optimizing mRNA for drugs & vaccines • RNA drugs—structure prediction & small-molecule binding • World models for biology • Read error correction for cancer genomes HERRO2 2/3

Mile Sikic
@msikic.bsky.social

Looking for candidates with a proven AI track record—papers at top AI conferences and in journals. If that's you, get in touch. Please share!! 🔁

Mile Sikic reposted

Ragnar {Groot Koerkamp}
@curiouscoding.nl

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

arXiv cs.DS Data Structures and Algorithms@csds-bot.bsky.social

Ragnar Groot Koerkamp, Stefan Hermann, Peter Sanders, Stefan Walzer: Non-minimal k-perfect hashing: Tight lower bounds and an application to fast static hash tables https://arxiv.org/abs/2607.07257 https://arxiv.org/pdf/2607.07257 https://arxiv.org/html/2607.07257

Mile Sikic
@msikic.bsky.social

Excited to apply AI to real-world biology problems (in vivo CAR-T therapy)? We’re hiring postdocs with strong AI expertise, ideally with publications in top AI conferences/journals. Work includes: • Next-generation RNA LLMs • Post-training methods Apply here: lnkd.in/d6Br2_he Please share!

lnkd.inA*STAR - Agency for Science, Technology and Research hiring AI Scientist - Generative AI Models for the Creation of RNA-Based Drugs (GIS) in Singapore, Singapore | LinkedInPosted 9:30:08 AM. Project backgroundMessenger RNA (mRNA)-based therapeutics, including vaccines, represent a…See this and similar jobs on LinkedIn.
Mile Sikic
@msikic.bsky.social

📢 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 🔁

Mile Sikic
@msikic.bsky.social

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.

nature.comTelomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads - NatureNature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads

Mile Sikic reposted

Josipa Lipovac
@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/...

Josipa Lipovac@jlipovac.bsky.social

I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification. 🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1 1/9

Mile Sikic reposted

Jim Shaw
@jimshaw.bsky.social

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

rdcu.beHigh-resolution metagenome assembly for modern long reads with myloasmNature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
Nature Biotechnology@natbiotech.nature.com

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

go.nature.comHigh-resolution metagenome assembly for modern long reads with myloasm - Nature BiotechnologyA long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
Mile Sikic
@msikic.bsky.social

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/

Mile Sikic
@msikic.bsky.social

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!!

Mile Sikic reposted

Elisabeth Bik
@elisabethbik.bsky.social

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...

thefp.comScience Has a Major Fraud ProblemFor decades, scientists were above reproach. Not any more. Joe Nocera investigates the murky world of fraudulent research, and the sleuths exposing dishonest science.

Mile Sikic reposted

Can Firtina
@firtinac.bsky.social

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!

Mile Sikic@msikic.bsky.social

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.

link.springer.comCampolina: a deep neural framework for accurate segmentation of nanopore signals - Genome BiologyNanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggl...

Mile Sikic reposted

Kristoffer Sahlin
@ksahlin.bsky.social

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...

link.springer.comMulti-context seeds enable fast and high-accuracy read mapping - Genome BiologyA key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but reduce sensitivity in ...
Mile Sikic
@msikic.bsky.social

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.

link.springer.comCampolina: a deep neural framework for accurate segmentation of nanopore signals - Genome BiologyNanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggl...
Mile Sikic
@msikic.bsky.social

🧬 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! 🔄

Mile Sikic reposted

Jonathan Göke
@jonathangoeke.bsky.social

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

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

Mile Sikic
@msikic.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

Mile Sikic
@msikic.bsky.social

The position offers close mentorship in a leading AI-for-RNA biology lab, access to substantial GPU resources, and full support to attend top international AI and ML conferences. There is also an opportunity to spend 1 to 2 years at @astar-gis.bsky.social. 2/n

View full thread
View full thread
Mile Sikic
@msikic.bsky.social

4/ At scale ⚙️ • Automated experimental platforms • Dedicated GPU clusters • Access to A*STAR & National Supercomputing Centre Singapore compute resources