imartayan.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

If you're interested in #ScientificComputing and/or #RustLang, you should come to #SciCompInRust25 next week. It's taking place virtually and is free to attend. Timetable at scientificcomputing.rs/2025/timetable. Register at scientificcomputing.rs/2025/register.

submitted 2 days ago • 0 comments

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 3 days ago • 5 comments

📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8

submitted 4 days ago • 1 comment

Hear hear, simd-minimizers uses wide for the simple vectorized stuff, and wide supports WASM's 128-bit simd primitives. Again, all this stuff just comes for free by using a modern language 😍

submitted 4 days ago • 0 comments

New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo. We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries. www.biorxiv.org/content/10.1...

submitted 5 days ago • 2 comments

De Bruijn Graph Partitioning for Scalable and Accurate DNA Storage Processing https://www.biorxiv.org/content/10.1101/2025.05.19.654814v1

submitted 7 days ago • 0 comments

Sequence alignment with k-bounded matching statistics https://www.biorxiv.org/content/10.1101/2025.05.19.654936v1

submitted 6 days ago • 0 comments

Kaminari: a resource-frugal index for approximate colored k-mer queries https://www.biorxiv.org/content/10.1101/2025.05.16.654317v1

submitted 10 days ago • 0 comments

Really impressive and moving interview by @baym.lol about the Harvard cuts.

submitted 14 days ago • 0 comments

I am thinking a lot today about how heavy things feel in my world of faculty doing scientific research. There's the immediate chaos and panic about our ability to pay people and continue our research. But there's also a deeper grief at watching everything get bulldozed for no reason

submitted 16 days ago • 25 comments

Here are all the posters I designed for RustWeek 2025! 1. "Box<impl Future>" (Back tot the Future) #rustweek #rustweek2025

submitted 18 days ago • 5 comments

The list of proceedings papers for #ISMB2025 is up on the website www.iscb.org/ismbeccb2025... ! It's an exciting collection of papers, as always :).

submitted 32 days ago • 0 comments

Together with @rickbitloo.bsky.social we're working on a tool for approximate string searching for short patterns. Currently we can search patterns up to 32bp at around 2GB/s per thread, with full IUPAC (ACTG+N+Y+R+...) support! Do you have uses for this? Maybe for longer patterns? Let us know!

submitted 33 days ago • 2 comments

Next up is Nathaniel Brown from @benlangmead.bsky.social's group presenting col-bwt, a new algorithm for computing chain statistics using multi-maximal unique matches. www.biorxiv.org/content/10.1...

submitted 34 days ago • 2 comments

The sequence analysis session of #RECOMB2025 is off to a great start with @jimshaw.bsky.social presenting devider, a new algorithm for haplotyping small sequences from long-read sequencing. www.biorxiv.org/content/10.1...

submitted 34 days ago • 1 comment

I'll be presenting our work on hyper-k-mers at #RECOMB today at 10:40 KST! You can get a sneak peek at the slides here: igor.martayan.org/slides-recom... Come say hi if you'd like to chat, or just get one of these cute stickers!

submitted 35 days ago • 1 comment

We finally concluded the meeting. Thanks to all attendees for their scientific contributions and for traveling (near or far) to the meeting! Thanks to the local organizers for the infrastructure and catering, and thanks to the co-organizers @yaronorenstein.bsky.social @camillemrcht.bsky.social!

submitted 36 days ago • 1 comment

1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata. It uses a colored de Bruijn graph under the hood.

submitted 38 days ago • 1 comment

Finding vegetarian and vegan food in Korea can be tricky. I added a mini-guide to the #RECOMB2025 things-to-do site with some resources. Let me know if you want more recommendations! recomb.org/recomb2025/t...

submitted 40 days ago • 2 comments

Just 9 days to go! #RECOMBseq hits Seoul on April 24 🧬🇰🇷 Join us for two days of cutting-edge high-throughput sequencing algorithms, global scientific minds, and vibrant city vibes. 📄 Check out the full program here: recomb-seq.github.io/program/ #RECOMB2025 #Genomics #Bioinformatics

submitted 46 days ago • 0 comments

I'm excited to release what I've been cooking up the past few months at @arcinstitute.org BINSEQ is a family of binary file formats for sequencing data built with paired records and parallel processing in mind with big performance gains (2x-40x) over gzip-fastq with similar storage

submitted 46 days ago • 2 comments

I first got into smoothed analysis and linear programming during my master's. Now, 9 years later, we finally have matching upper and lower bounds. I spent a huge part of my life on this, and it feels weird that it's now finished.

submitted 53 days ago • 1 comment

Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI

submitted 56 days ago • 0 comments

Introducing cornetto, an adaptive genome assembly paradigm using @nanoporetech.com adaptive sampling. - greatly reduces cost per genome assembly - reference agnostic, so works for non-humans - assembly just using saliva - & many more Relies on 2 excellent software #readfish & #hifiasm.

submitted 56 days ago • 1 comment

Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...

submitted 60 days ago • 0 comments

Can Firtina: Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques https://arxiv.org/abs/2503.02997 https://arxiv.org/pdf/2503.02997 https://arxiv.org/html/2503.02997

submitted 86 days ago • 1 comment

Fully funded positions + included travels between Simon Puglisi's and our group. Dm/email if you have questions.

submitted 64 days ago • 0 comments

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

submitted 65 days ago • 2 comments

Playing with #vizitig again to prepare for the 1.0 release. This is the SNAP25 human gene expressed in 3 SRA datasets linked to cancers. Exons have one color each, and exon junctions are in yellow. The rest is new/noise.

submitted 66 days ago • 2 comments

We are hiring PhD students in Computational Mathematics and Mathematics at Stockholm University in various subjects: su.varbi.com/en/what:job/... Application deadline: April 22. (1/3)

submitted 66 days ago • 1 comment

Open question for CS community: What to teach from modern parallel algorithms to 2nd CS undergrads? We teach sorting networks (bitonic sort) and boolean circuits (summation, multiplication), which is fine but does not feel very modern. What else to show about parallelism in, say, 2 lectures?

submitted 67 days ago • 2 comments

Just published simd-sketch, a crate for fast bucket sketches. It's 7x to 30x faster than BinDash, by using the simd-minimizers crate for fast hashing, and a nearly branch-free implementation. Here's a blogpost with a survey of minhash history & methods, and evals: curiouscoding.nl/posts/simd-s...

submitted 78 days ago • 1 comment

Last week I got to present my work on lexicographical minimizers at DSB, in Pisa. It was a wonderful moment, thanks again to everyone involved!

submitted 80 days ago • 1 comment

openRxiv has arrived! We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences. openrxiv.org/introducing-... #openRxiv #OpenScience #Preprints #bioRxiv #medRxiv

submitted 81 days ago • 3 comments