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Igor Martayan

@imartayan.bsky.social

PhD student in algorithmic bioinformatics at @bonsaiseqbioinfo.bsky.social. Interested in space-efficient data structures, sketching algorithms & high-performance computing https://igor.martayan.org

87 Posts821 Follower363 Folgt
Vikram Shivakumar@vikramshivakumar.bsky.social · 3w ago

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Navigating the pangenome coordinate system with Shredtools

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

biorxiv.org

Ragnar {Groot Koerkamp}@curiouscoding.nl · 4w ago

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 · 4w ago

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

Ragnar {Groot Koerkamp}@curiouscoding.nl · last mo.

In other news: Great SEA talk by Nathaniel Brown on Orbit, an efficient implementation of the move structure for run-length encoded permutations. Also, congrats on winning a best paper award with this work!

Nathaniel standing in front of his title slide at the start of the presentation.
Ben Langmead@benlangmead.bsky.social · last mo.

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)

Ragnar {Groot Koerkamp}@curiouscoding.nl · 2mo ago

Now also on arxiv arxiv.org/abs/2606.01190

The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme

In recent years, there has been a renewed interest in the search for low density minimizer schemes. These schemes take a window of $w$ consecutive $k$-mers, and sample one of them: the smallest under ...

arxiv.org

Ragnar {Groot Koerkamp}@curiouscoding.nl · 3mo ago

My WABI submission: anti-lexicographic SUS-anchors. For sigma=4, this selection scheme (a k=1 sampling scheme) has density within 1% of the lower bound! The idea: find the smallest* substring that does not have a 2nd occurrence, and sample its start pos. curiouscoding.nl/posts/sus-an...

Plots with the density of the sus-anchor for sigma in 2, 4, 32 as a function of w. For sigma=4, they have an overhead over the lowerbound of <1%, while other schemes have >15% overhead.
Rob Patro@robp.bsky.social · 3mo ago

Is anyone attending #RECOMB2026 with a talk in the Sequencing 2 session who would be willing to switch slots with a talk in Sequencing 1 a day earlier? We’d be very grateful. Please reach out if you might be willing to do this!

Camille Marchet ⚡@camillemrcht.bsky.social · 3mo ago

More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social

Floris Barthel@florisbarthel.bsky.social · 3mo ago

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

KaryoScope karyotype of the HG002 diploid assembly. All 22 autosomes plus X and Y, each shown as paired haplotypes (h1, h2). Each chromosome has a full-length track colored by chromosome of origin, a centromere zoom panel showing satellite composition, and a subtelomere zoom panel. Legends map chromosomes, satellite families, and subtelomeric features to colors.
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Paul Medvedev @pashadag.bsky.social · 3mo ago

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

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.

doi.org

PPaul Medvedev @pashadag.bsky.social · last yr.

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

Ragnar {Groot Koerkamp}@curiouscoding.nl · 3mo ago

New preprint: The SimdQuickHeap is the fastest priority queue by far! 2x faster than a radix heap and up to 10x faster than binary heaps. arxiv.org/abs/2604.25681 with Marvin Williams and Johannes Breitling:

SimdQuickHeap: The QuickHeap Reconsidered

Priority queues are data structures that maintain a dynamic collection of elements and allow inserting new elements and removing the smallest element. The most widely known and used priority queue is ...

arxiv.org