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]

I got frustrated that using piscem-rs to map 10x Flex reads was entirely dominated by decompressing the single pair of input files. So, GPT5.6-Sol & I built a thing! Rapidgzip-rust (rapid-gzip algo in rust) github.com/COMBINE-lab/... 2.3 billion flex reads in <2 min? Parsing w paraseq. Yes plz!

📢 Genome Informatics 2026 (Hinxton UK + virtual, 2–4 Dec) is coming! Some confirmed speakers now listed: coursesandconferences.wellcomeconnectingscience.org/event/genome... Early-bird registration & bursary deadlines: 7 Sept. Abstract deadline: 5 Oct. Please submit your work & join us!

Very happy to be presenting "Taxonomic classification using Kraken 2" in today's #ISMB2026 tutorial "Metagenomic sequence analysis using k-mer based methods": www.iscb.org/ismb2026/wha... In about 15 minutes!

Some professional news: After adding use MoreResearch as _; use MoreMentoring as _; use MoreTeaching as _; use MoreService as _; the UMD trait solver has accepted the where-clause where Rob: Professor On this occasion, some thanks and some thoughts are in order! 1/5

salmon 1.12.0 is out (and on bioconda)! There are some important bug fixes and improvements. Also, this is the last planned C++ release of Salmon! github.com/COMBINE-lab/... "The last? What's happening, Rob?" 1/2

Release salmon 1.12.0 — final C++ release · COMBINE-lab/salmon

salmon 1.12.0 — release notes This is the final release of the C++ implementation of salmon. Future development continues in salmon 2.0, a from-scratch Rust rewrite that is faster, easier to build ...

github.com

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

Revamped the teaching materials site. Light/dark mode switch at the top. More consistent, compact presentation of all the materials. + Icons and such! www.langmead-lab.org/teaching.html

📢 𝑪𝒂𝒍𝒍 𝒇𝒐𝒓 𝑷𝒂𝒓𝒕𝒊𝒄𝒊𝒑𝒂𝒕𝒊𝒐𝒏: 𝑵𝒆𝒙𝒕-𝑮𝒆𝒏𝒆𝒓𝒂𝒕𝒊𝒐𝒏 𝑨𝒅𝒂𝒑𝒕𝒂𝒃𝒍𝒆 𝑪𝒐𝒎𝒑𝒖𝒕𝒊𝒏𝒈 𝒇𝒐𝒓 𝑶𝒎𝒊𝒄𝒔 @ 𝑭𝑪𝑪𝑴 𝟐𝟎𝟐𝟔 👉 Workshop Website: events.safari.ethz.ch/fccm2026-omi... 🗓️ 𝐖𝐡𝐞𝐧 𝐚𝐧𝐝 𝐖𝐡𝐞𝐫𝐞: 16th May 2026 (Saturday), Atlanta, Georgia, USA 🎥 Livestream: www.youtube.com/live/jUJqOY7... @omutlu.bsky.social @firtinac.bsky.social

Next-Generation Adaptable Computing for Omics @ FCCM 2026

FCCM 2026: 2nd Workshop on Next-Generation Adaptable Computing for Omics https://events.safari.ethz.ch/fccm2026-omics/ Date and Time: May 16, from 9:00 AM (EDT) to 01:00 PM (EDT) Organizers: Prof. Ma...

youtube.com

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.

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.

The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

QCatch is now published in Bioinformatics (academic.oup.com/bioinformati...)! Great work from Yuan and Dongze for quality control and analysis downstream of simpleaf/alevin-fry (taking advantage of its structured AnnData output). Give it a try: github.com/COMBINE-lab/...

QCatch: A framework for quality control assessment and analysis of single-cell sequencing data

AbstractMotivation. Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstrea

academic.oup.com

🎉 Congratulations to Onur Mutlu on being named 2025 AAAS Fellow "for foundational and innovative contributions to computer engineering research, education, and practice, especially in computer architecture and memory and storage systems” safari.ethz.ch/onur-mutlu-n... @omutlu.bsky.social @aaas.org

Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Can Firtina: CERN: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models https://arxiv.org/abs/2603.20420 https://arxiv.org/pdf/2603.20420 https://arxiv.org/html/2603.20420

𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗮𝗻𝗱 𝗣𝗵𝗗 𝗽𝗼𝘀𝗶𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝗖𝗼𝗺𝗽𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 / 𝗔𝗹𝗴𝗼𝗿𝗶𝘁𝗵𝗺𝗶𝗰 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 I am currently recruiting for both: 🔹 Postdoc position su.varbi.com/what:job/job... 🔹 PhD position su.varbi.com/en/what:job/... Please share with anyone who might be interested!

Postdoktor i Beräkningsbiologi

Matematiska institutionen består av cirka 120 forskare, lärare och administrativ personal och är organiserad i tre huvudsakliga avdelningar: Matematik, Matematisk statistik och Beräkningsmatematik

su.varbi.com

This is an important step in the right direction. The methods are improving to start collectively thinking about how we should analyze raw nanopore signals for various new applications that are not possible without signal analysis. Congratulations to the authors!

Mile Sikic@msikic.bsky.social · 6mo ago

Transformer-based AI has boosted @nanoporetech.com sequencing accuracy, but at a cost to portability due to GPU demands. Our new work, spearheaded by Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

Transformer-based AI has boosted @nanoporetech.com sequencing accuracy, but at a cost to portability due to GPU demands. Our new work, spearheaded by Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

Campolina: a deep neural framework for accurate segmentation of nanopore signals - Genome Biology

Nanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggl...

link.springer.com

1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed. link.springer.com/article/10.1...

Multi-context seeds enable fast and high-accuracy read mapping - Genome Biology

A key step in sequence similarity search is to identify shared seeds between a query and a reference sequence. A well-known tradeoff is that longer seeds offer fast searches but reduce sensitivity in ...

link.springer.com

This looks really interesting and perhaps might enable faster overlapping for HERRO @msikic.bsky.social , not sure academic.oup.com/bioinformati... , also not sure Rawsamble can overlap repetitive sequences, for which minimap2 can, but seems to slow down a lot compared to default settings

Rawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding Mechanism

AbstractMotivation. Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the s

academic.oup.com

I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...

COMBINE-lab - The skeptic’s guide to generative AI assisted coding

An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

combine-lab.github.io

🧬 Hiring Postdocs at @astar_gis ! We need Computer Scientists and Computational Biologists to develop novel algorithms for de novo assembly of cancer genomes or to help us reconstruct them. Experience in sequence alignment/assembly algorithms or assembly of complex genomes required Please RT! 🔄

Happy to share I recently received the ETH Doctoral Medal. More information on LinkedIn: www.linkedin.com/posts/canfir... @safari-eth.bsky.social @omutlu.bsky.social

I am humbled to receive the ETH Doctoral Medal in 2025. This award is given in recognition of the best doctoral theses at ETH Zurich. I am deeply grateful to my PhD advisor, Prof. Onur Mutlu, for… | ...

I am humbled to receive the ETH Doctoral Medal in 2025. This award is given in recognition of the best doctoral theses at ETH Zurich. I am deeply grateful to my PhD advisor, Prof. Onur Mutlu, for his...

linkedin.com

I’m recruiting a postdoc to work on algorithms for cancer genome reconstruction. We have access to a rich set of tumour samples sequenced across multiple technologies. If interested, feel free to DM. Please share.

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing

A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

github.com

Our department (Comp Sci) at UMD is hiring this cycle. We have an open-rank search (umd.wd1.myworkdayjobs.com/en-US/UMCP/j...). Consider applying to join our department; we’re a pretty cool group if I say so myself ☺️!

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon: docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques https://www.biorxiv.org/content/10.1101/2025.10.04.680405v1

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

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.

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...