Reposted by Mile Sikic
🚀🧬 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...
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...
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
chaitjo.substack.com
November 15, 2025 at 9:39 AM
🚀🧬 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...
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.
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 15, 2025 at 6:00 AM
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
Right now, two major directions are emerging... 1/8
November 15, 2025 at 5:58 AM
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
Right now, two major directions are emerging... 1/8
Reposted by Mile Sikic
#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...
November 6, 2025 at 10:33 PM
#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...
Reposted by Mile Sikic
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
They devised a bidirectional message-passing procedure in GNN for the problem of genome assembly
November 6, 2025 at 4:22 PM
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
They devised a bidirectional message-passing procedure in GNN for the problem of genome assembly
Reposted by Mile Sikic
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
November 3, 2025 at 3:47 AM
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
Reposted by Mile Sikic
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.
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.
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
November 4, 2025 at 7:12 PM
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.
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.
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
"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
October 29, 2025 at 6:30 AM
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
"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
Reposted by Mile Sikic
🚨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)
🧬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
July 30, 2025 at 1:50 PM
🚨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)
🧬Short reads can now decode centromeres.
🌍We reveal population-scale centromere haplogroups and their links to disease.
biorxiv.org/content/10.1... (1/n)
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.
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
July 19, 2025 at 10:18 AM
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.
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.
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
July 7, 2025 at 4:52 PM
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.
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...
- 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
May 17, 2025 at 2:53 AM
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...
- 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...
Reposted by Mile Sikic
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
MADRe is open-source, modular, and ready to use.
Check it out:
🔗 github.com/lbcb-sci/MADRe
9/9
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
May 16, 2025 at 8:37 AM
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
MADRe is open-source, modular, and ready to use.
Check it out:
🔗 github.com/lbcb-sci/MADRe
9/9
Reposted by Mile Sikic
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
Date: 29 April, 2PM
Venue: GIS, Level 2
Host: Ivona MARTINOVIC
@msikic.bsky.social @lvrcek.bsky.social
April 28, 2025 at 10:28 AM
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
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
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
April 14, 2025 at 5:26 AM
Join us at Genome Institute of Singapore! Great environment, stable funding!!
Reposted by Mile Sikic
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
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
April 14, 2025 at 4:09 AM
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
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
Reposted by Mile Sikic
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
March 17, 2025 at 2:32 AM
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
Reposted by Mile Sikic
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
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
March 6, 2025 at 8:01 AM
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
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
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
February 4, 2025 at 10:46 AM
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
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
Reposted by Mile Sikic
🚨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
🧬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
January 23, 2025 at 10:52 AM
🚨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
🧬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
Reposted by Mile Sikic
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
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
January 15, 2025 at 8:25 PM
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mile Sikic
🚨 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
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
January 3, 2025 at 2:49 PM
🚨 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
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
Reposted by Mile Sikic
Verkko2 paper is finally on the biorxiv
www.biorxiv.org/content/10.1...
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
December 27, 2024 at 7:55 PM
Verkko2 paper is finally on the biorxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...