Can Firtina

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!

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...

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.

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 ...

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...

GitHub - STORMgroup/RawHash2: RawHash2 can accurately map raw nanopore signals to small and large reference genomes without basecalling in real-time. Described by Firtina et al. (published at https://... RawHash2 can accurately map raw nanopore signals to small and large reference genomes without basecalling in real-time. Described by Firtina et al. (published at https://academic.oup.com/bioinforma...

We are also working on MinKNOW integration, as well as some additional features that will hopefully enable RawHash2's and Rawsamble's integration in in-the-field analysis scenarios. A new repository is being built here: github.com/STORMgroup/R...

Thanks, Jean. The discussion section of our paper also includes some interesting applications. We believe Rawsamble can enable many new applications that were not possible before, including its integration for error correction and more. Happy to chat if you are interested!

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

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

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.

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...

🧬 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! 🔄

Thanks, Ben. I really appreciate your comments while preparing my thesis and our discussions during and after the defense. They were very helpful!

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...

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’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.

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

@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

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 ☺️!

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 ...

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...

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

This is indeed weird. We have some of our review papers on arXiv. Is this a recent policy change?

Although not very common, I would also second the Zenodo option. Having a permanent DOI is potentially a plus for Zenodo.

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.

🌎👩‍🔬 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...

The Genome Informatics conference (@ Cold Spring Harbor Lab, Nov 5 - 8) abstract deadline is **today**. We welcome your submissions! Topics include:
- PanGenomes
- Genome Assembly & Seq. Algos.
- Algorithmic Evo. Bio
- Single Cell & Spatial Omics
- Microbial Genomics
- AI/ML & Integrative Omics
🙏🙏🙏

🧬🖥️ We are thrilled to be hosting the 25th International Conference on Algorithms for Bioinformatics (WABI 2025) next week at UMD! Look at this amazing lineup of proceedings papers: drops.dagstuhl.de/entities/vol...

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

Very excited this is finally published in the ISMB proceedings. This was @noorpratap.bsky.social's last conference-related paper in my lab (but look out for a new Genome Research paper soon), & a monumental effort. It's already integrated into simpleaf. Noor will be presenting it at ISMB next week!

Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals https://www.biorxiv.org/content/10.1101/2025.07.08.663658v1

Health Applications: 1st SAFARI Live Workshop (SaLWo) 2025 (Day 2) YouTube video by Onur Mutlu Lectures

🚀 Join us on Monday for Day 2 of our SAFARI Live Workshop (SaLWo) on Health Applications—don't miss it!

📽️ Livestream Mon, July 14 9-17:00 CEST: www.youtube.com/watch?v=nySa...

Website: events.safari.ethz.ch/SaLWo25/doku...

@firtinac.bsky.social @omutlu.bsky.social @agyaglikci.bsky.social

Memory Robustness: 1st SAFARI Live Workshop (SaLWo) 2025 (Day 1) YouTube video by Onur Mutlu Lectures

🚀 Join us this week for our 1st SAFARI Live Workshop (SaLWo), Day 1 on Memory Robustness, in CAB G11 or online.

📽️ Livestream Thurs July 10 8-17:00 CEST: www.youtube.com/live/KZmBmvJ...

SaLWo website: events.safari.ethz.ch/SaLWo25/
@agyaglikci.bsky.social @firtinac.bsky.social @omutlu.bsky.social

🖥️🧬 WABI '25 will not only have excellent keynotes, but an exciting program of papers. The titles and abstracts of all accepted WABI '25 papers are now available on the conference website (wabiconf.github.io/2025/talks/). I'm looking forward to seeing these talks!

Thanks, Igor! I should make a proper announcement about this soon too :)

I will give a talk today titled "Accelerating AI-Driven Genome Analysis via Algorithm-Architecture Co-Design" at PASC 25. The recording of my talk will be released soon.

You can find the links to my slides and recordings on canfirtina.com/talks

@safari-eth.bsky.social @omutlu.bsky.social

SAFARI-EFCL Seminar - Algorithms, Software & Hardware Accelerators for the Next Wave of Genomic Data Title: Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data Speaker: Prof. Yatish Turakhia, University of California San Diego (UCSD) https://turakhia.ucsd.edu Talk Detai...

Join us this week for our next SAFARI-EFCL Seminar! Yatish Turakhia will present "Algorithms, Software, and Hardware Accelerators for the Next Wave of Genomic Data" in ETZ E6 & online.

Livestream Wed June 18 10AM CEST: www.youtube.com/live/RNLXXz2...

@firtinac.bsky.social @omutlu.bsky.social

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.