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Mile Sikic

@msikic.bsky.social
173 followers 103 following 92 posts

AI in genomics

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Reposted by Mile Sikic
Adam Phillippy @aphillippy.bsky.social · 13/08/2026
"Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere" Brief commentary from me, @khmiga.bsky.social, @msikic.bsky.social, Yu Kang and Yafei Mao for the T2T special issue. Why do we need complete genomes? Check it out! www.cell.com/cell/fulltex...
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Goeke Lab @goekelab.bsky.social · 27/07/2026
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.
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Sina Majidian @sinamajidian.bsky.social · 26/07/2026
MADRe: Strain-level metagenomic classification through assembly-driven database reduction doi.org/10.1093/giga... Software: github.com/lbcb-sci/MADRe
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Mile Sikic @msikic.bsky.social · 25/07/2026
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.
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Elisabeth Bik @elisabethbik.bsky.social · 20/07/2026
Great video by Full Disclosure, where Loveena Kamath investigates how bad research enters legitimate systems. She even calls a paper mill to buy a scientific paper! With Achal Agrawal, PhD, and myself. "World’s Easiest Fraud, Apparently!" www.youtube.com/watch?v=bYTk...
youtube.com
I Read 126 Research Papers To Expose A Billion Dollar Fraud
YouTube video by Full Disclosure
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Mile Sikic @msikic.bsky.social · 15/07/2026
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!
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Mile Sikic @msikic.bsky.social · 11/07/2026
@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
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Sina Majidian @sinamajidian.bsky.social · 09/07/2026
JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/07/2026
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
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Randall Munroe @xkcd.com · 08/07/2026
Offside xkcd.com/3268/
Comic. [chessboard with red dotted line and flag at second line. Highlighted rook is positioned next to King behind the red line.]  [caption] I thought I had checkmate, but I didn’t realize my rook was offside.
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Igor Martayan @imartayan.bsky.social · 15/06/2026
Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone
phd.martayan.org
Algorithm design and implementation for the scale of sequencing data
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Mile Sikic @msikic.bsky.social · 27/06/2026
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.in
A*STAR - Agency for Science, Technology and Research hiring AI Scientist - Generative AI Models for the Creation of RNA-Based Drugs (GIS) in Singapore, Singapore | LinkedIn
Posted 9:30:08 AM. Project backgroundMessenger RNA (mRNA)-based therapeutics, including vaccines, represent a…See this and similar jobs on LinkedIn.
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Mile Sikic @msikic.bsky.social · 06/06/2026
📢 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 🔁
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Goeke Lab @goekelab.bsky.social · 13/05/2026
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
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Goeke Lab @goekelab.bsky.social · 21/05/2026
🧬 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
form.gov.sg
Registration: Singapore RNA Salon: 18th June 16:00 - 18:00, NTU, School of Biological Sciences
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Jonathan Göke @jonathangoeke.bsky.social · 22/05/2026
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
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Goeke Lab @goekelab.bsky.social · 25/05/2026
🙌 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
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Mile Sikic @msikic.bsky.social · 28/04/2026
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.com
Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads - Nature
Nature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads
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Mile Sikic @msikic.bsky.social · 07/04/2026
Happy to see MADRe published!! MADRe: Strain-level Metagenomic Classification academic.oup.com/gigascience/... Great work @jlipovac.bsky.social
academic.oup.com
Validate User
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Josipa Lipovac @jlipovac.bsky.social · 06/04/2026
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/...
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Jim Shaw @jimshaw.bsky.social · 27/03/2026
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.be
High-resolution metagenome assembly for modern long reads with myloasm
Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
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Mile Sikic @msikic.bsky.social · 28/03/2026
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/
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Mile Sikic @msikic.bsky.social · 11/03/2026
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!!
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Elisabeth Bik @elisabethbik.bsky.social · 10/03/2026
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.com
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.
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Can Firtina @firtinac.bsky.social · 10/03/2026
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!
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Kristoffer Sahlin @ksahlin.bsky.social · 09/03/2026
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.com
Multi-context seeds enable fast and high-accuracy read mapping - Genome Biology
A 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 ...
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Mile Sikic @msikic.bsky.social · 10/03/2026
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.com
Campolina: a deep neural framework for accurate segmentation of nanopore signals - Genome Biology
Nanopore 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...
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Mile Sikic @msikic.bsky.social · 14/02/2026
🧬 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! 🔄
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Jonathan Göke @jonathangoeke.bsky.social · 10/02/2026
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!
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Mile Sikic @msikic.bsky.social · 05/01/2026
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
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Mile Sikic @msikic.bsky.social · 21/12/2025
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.
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Mile Sikic @msikic.bsky.social · 12/12/2025
1/ In an excellent Nature Methods editorial, Lin Tang outlines the future of AI agents in biology. www.nature.com/articles/s41...
nature.com
Artificial intelligence agents for biology - Nature Methods
Artificial intelligence agents may have a transformative effect on how biological research is performed.
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Mile Sikic @msikic.bsky.social · 12/12/2025
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
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Mile Sikic @msikic.bsky.social · 11/12/2025
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.
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Mile Sikic @msikic.bsky.social · 02/12/2025
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
neurips.cc
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Mile Sikic @msikic.bsky.social · 26/11/2025
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
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/11/2025
🚀🧬 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...
chaitjo.substack.com
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
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Mile Sikic @msikic.bsky.social · 15/11/2025
Well deserved. Richard is a giant in the fields of bioinformatics and computational biology.
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Mile Sikic @msikic.bsky.social · 15/11/2025
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
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Genome Research @genomeresearch.bsky.social · 06/11/2025
#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...
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Sina Majidian @sinamajidian.bsky.social · 06/11/2025
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
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 03/11/2025
Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment www.biorxiv.org/content/10.1101/202…
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 04/11/2025
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.
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Mile Sikic @msikic.bsky.social · 04/11/2025
🚀 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
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Mile Sikic @msikic.bsky.social · 29/10/2025
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
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Yuichi Shiraishi @friend1ws.bsky.social · 30/07/2025
🚨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)
biorxiv.org
Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations
Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive α-satellite hi...
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Mile Sikic @msikic.bsky.social · 09/08/2025
🚀 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
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Mile Sikic @msikic.bsky.social · 19/07/2025
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.
biorxiv.org
A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population
Human reference genomes have been instrumental in advancing genomic and biomedical research, but South and Southeast Asian populations are underrepresented, despite accounting for a large proportion o...
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Mile Sikic @msikic.bsky.social · 07/07/2025
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.
nature.com
RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks - Nature Communications
RiNALMo, a large-scale RNA language model trained on non-coding RNA sequences, captures structural information and achieves state-of-the-art performance on multiple tasks, notably generalizing to unse...
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Mile Sikic @msikic.bsky.social · 17/05/2025
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...
a-star.edu.sg
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