Sergey Nurk
@sergeynurk.bsky.social
Principal Bionformatician @nanopore. Ex: Postdoctoral fellow @ NIH; Researcher @ CAB. Views are my own; #StandWithUkraine Support Ukraine!
Mojo 1.0 is out! www.modular.com/blog/modular... Compiler open sourcing still looks on track for sometime in the next few months.
Modular: Modular 26.5: Mojo 1.0 is here!
Today, the Mojo language officially reaches 1.0: a milestone the language has been building toward since its first release in 2023. Mojo has grown into a general-purpose language with a vibrant develo...
modular.com
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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 · last mo.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
minibwa-0.4 released with minor improvement and a few fixes to typos. Also a new blog post on "minibwa is the new bwa-mem": lh3.github.io/2026/07/04/m...
Minibwa is the new bwa-mem
lh3.github.io
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
Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...
Oxford Nanopore Technologies hiring Senior Bioinformatics Software Engineer, Applications in Oxfordshire, England, United Kingdom | LinkedIn
Posted 3:04:10 PM. Job DescriptionOur goal is to bring the widest benefits to society through enabling the analysis of…See this and similar jobs on LinkedIn.
linkedin.com
Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)
Validate User
academic.oup.com
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...
Release v4.0.0 · rust-bio/rust-bio
4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...
github.com
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
This blog shares some thoughts on protein and genome foundation models. The first part explains some of the concepts by training models for example tasks. The second part is opinion on the state of the field. andrewcarroll.github.io/2026/05/26/g...
🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries" Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social
Hash functions in nucleotide sequence analysis genome.cshlp.org/content/earl...
Hash functions in nucleotide sequence analysis
Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.
genome.cshlp.org
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.
Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads - Nature
Nature - Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads
nature.com
New blog post! I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed! igor.martayan.org/posts/breaki...
Breaking ntHash (to better fix it)
NtHash is a popular method for hashing k-mers in bioinformatics, yet it has some surprising flaws. In this post, I walk through a few of them, and show that they can arise naturally, without an advers...
igor.martayan.org
Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University genomeinformatics.github.io/movingday/
We're moving!
Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed one hour north on I-95 to set up shop at Johns Hopkins University. This is a very bittersweet move for me, as NHGRI has prov...
genomeinformatics.github.io
This is the ultimate test for a constitutional order. Either constitutional mechanisms are used to check and balance this, and remove him from office, or they are not. For there can be no greater test for any constitution.
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 · last yr.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
A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers doi.org/10.64898/202...
More acrocentric investigations, this one led by @arhie.bsky.social 🕵🏻♀️ “Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes” 🧵[1/8] 📄 www.biorxiv.org/content/10.6...
biorxiv.org
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
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.
rdcu.be
Nature Biotechnology@natbiotech.nature.com · 5mo agoHigh-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
LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel. Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Nature Methods - In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.
rdcu.be
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
embl.org
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
employment.utah.edu
⚡️Fully funded #PhD position in my lab at Stockholm University / SciLifeLab! If you’re interested in #lichens, #symbiosis, fungal biology, or meta-omics, please apply. Deadline Feb 1. Read more here: su.varbi.com/en/what:job/...
If you’ve heard me talk in the past ~5 years, you will know I have developed an obsession with acrocentric chromosomes. This is all of that, condensed into one paper. I will do a full thread in the new year, but for those that want something to read over the holidays, have at it. Such a cool story!
bioRxiv Genomics@biorxiv-genomic.bsky.social · 8mo agoOrigin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from @martinsteinegger.bsky.social andco
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 8mo agoAccelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
1/9 Just out: k-mer indexes are the backbone of fast search in genomic data, but many degrade under small k, subsampling, or high diversity. With Ondřej Sladký and @pavelvesely.bsky.social we asked: can we build one that works efficiently for any k-mer set?
Bioinformatics Advances@bioinfoadv.bsky.social · 8mo ago🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)” Full article available: https://doi.org/10.1093/bioadv/vbaf290 Authors include: @pavelvesely.bsky.social, @brinda.eu
This package to decompose weighted graphs into weighted paths by @alextomescu.bsky.social is going to be very useful. Can't wait to try it out in my viral metagenomic tools. 🤩🧬🖥️ #bioinformatics #graphs #graph-algorithms #flow-decomposition #integer-linear-programming github.com/algbio/flowp...
GitHub - algbio/flowpaths: A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.
A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models. - algbio/flowpaths
github.com
Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software
agtools: a software framework to manipulate assembly graphs
Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...
biorxiv.org