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Reposted by Mile Sikic

Yuichi Shiraishi @friend1ws.bsky.social · Jul 30

🚨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)

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...

biorxiv.org

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Mile Sikic @msikic.bsky.social · Aug 9

🚀 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 · Jul 19

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.

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...

biorxiv.org

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Mile Sikic @msikic.bsky.social · Jul 7

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.

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...

nature.com

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Mile Sikic @msikic.bsky.social · May 17

Ideal Candidates:
- Demonstrate strong expertise in AI/machine learning
- Passion for interdisciplinary research
- Thrive in solving complex biological challenges
- Possess resilience and scientific curiosity

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Mile Sikic @msikic.bsky.social · May 17

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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Reposted by Mile Sikic

Josipa Lipovac @jlipovac.bsky.social · May 16

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
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GitHub - lbcb-sci/MADRe: Strain-level metagenomic classification with Metagenome Assembly driven Database Reduction approach

Strain-level metagenomic classification with Metagenome Assembly driven Database Reduction approach - lbcb-sci/MADRe

github.com

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Reposted by Mile Sikic

A*STAR Genome Institute of Singapore (A*STAR GIS) @astar-gis.bsky.social · Apr 28

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

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Mile Sikic @msikic.bsky.social · Apr 14

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

A*STAR Genome Institute of Singapore (A*STAR GIS) @astar-gis.bsky.social · Apr 14

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

A*STAR - Agency for Science, Technology and Research hiring Principal Investigators (GIS) in Singapore, Singapore | LinkedIn

Posted 11:59:37 AM. The Genome Institute of Singapore (GIS) is Singapore"s flagship institute for the genomic sciences.…See this and similar jobs on LinkedIn.

www.linkedin.com

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Reposted by Mile Sikic

A*STAR Genome Institute of Singapore (A*STAR GIS) @astar-gis.bsky.social · Apr 14

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

A*STAR - Agency for Science, Technology and Research hiring Principal Investigators (GIS) in Singapore, Singapore | LinkedIn

Posted 11:59:37 AM. The Genome Institute of Singapore (GIS) is Singapore"s flagship institute for the genomic sciences.…See this and similar jobs on LinkedIn.

www.linkedin.com

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Reposted by Mile Sikic

Alvin Wei Tian Ng @alvinwtng.bsky.social · Mar 17

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

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Reposted by Mile Sikic

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

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

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Mile Sikic @msikic.bsky.social · Mar 2

Our characters are not easy to handle 😅

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Mile Sikic @msikic.bsky.social · Feb 4

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

AI4NA

AI4NA Workshop @ ICLR'25

ai4na-workshop.github.io

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Reposted by Mile Sikic

ICLR Nucleic Acids Workshop @ai4na-workshop.bsky.social · Jan 23

🚨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

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Reposted by Mile Sikic

Jacob Schreiber @jmschreiber91.bsky.social · Jan 15

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.

www.nature.com/articles/s41...

De novo designed proteins neutralize lethal snake venom toxins - Nature

Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

www.nature.com

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Reposted by Mile Sikic

ICLR Nucleic Acids Workshop @ai4na-workshop.bsky.social · Jan 3

🚨 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

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Reposted by Mile Sikic

Dmitry Antipov @dantipov.bsky.social · Dec 27

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

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semi-manual combination of lo...

www.biorxiv.org

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Mile Sikic @msikic.bsky.social · Dec 22

Thanks. Sorry I didn't get about size. 1 percent of reads are longer than 100 k or 99%. How much HMW DNA is required? I see, there is a need to develop algorithms from the scratch. Yes that might be interesting. Actually, for de novo assembly only overlap needs to be re-done

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Mile Sikic @msikic.bsky.social · Dec 22

Interesting. Is there a distribution or read lengths, and is it possible to use them beyond mapping strategies, i.e. de novo assembly?

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Reposted by Mile Sikic

Javier Santoyo @jsantoyo.bsky.social · Dec 19

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

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references - Genome Biology

Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ult...

genomebiology.biomedcentral.com

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Mile Sikic @msikic.bsky.social · Dec 19

Looking ahead, the prospects are exciting. We anticipate that soon we will be able to resolve complete human genomes, from telomere to telomere, on a personal scale. Additionally, accurate cancer genome assemblies are on the horizon. Stay tuned :) 3/3

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Mile Sikic @msikic.bsky.social · Dec 19

The paper explores more details about the coverages required.
This project extends the work we began in 2016 - when we were among the first to demonstrate that nanopore can produce decent assembly academic.oup.com/bioinformati... 2/3

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

Abstract. Motivation : Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how e

academic.oup.com

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Mile Sikic @msikic.bsky.social · Dec 19

Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.... great collaborative effort with Prasad Sarashetti, @jlipovac.bsky.social, Filip Tomas and JJ Liu.
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references - Genome Biology

Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ult...

genomebiology.biomedcentral.com

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Mile Sikic @msikic.bsky.social · Dec 14

A comparative approach that predicts any modifications in RNA (or DNA) using raw @nanopore signals. Although simple, It outperforms the current SOTA.

academic.oup.com/nar/advance-...

w/ IvanVujaklija, Siniša Biđin, Marin Volarić, Sara Bakic, Zhe Li, Jianjun Liu and Roger Foo

Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering

Abstract. To date, over 40 epigenetic and 300 epitranscriptomic modifications have been identified. However, current short-read sequencing-based experiment

academic.oup.com

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