Of course, I agree 😄 Thank you again @robp.bsky.social for taking care of the presentation of our paper. doi.org/10.1093/bioi...

Excited to be at #ISMB2026 this year and to be presenting the work @jermp.bsky.social and I have done on improving the SSHash data structure academic.oup.com/bioinformati.... Presentation is tomorrow, July 13 at 2:20 in the International Ballroom Center. Stop by if you're attending!

Honoured to be awarded the Mary Lyon medal by the Genetics Society today, here in Edinburgh. V grateful to mentors and all my previous group members and colleagues. Medal is an X chromosome!!

Rob and his work are unique gifts for our field. I'm glad our paths crossed!

📢 We are thrilled to announce the keynote speakers for #RECOMB2026: 🧬 Sara Mostafavi 🧬 Manolis Kellis 🧬 Paul Medvedev 🧬 Alexandros Stamatakis Join us in Thessaloniki for inspiring talks from leaders in computational biology.

Well... we read&debug the code, for example?

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.

🔍 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

Really proud of @ale-campa.bsky.social for his amazing contributions to the Fulgor ⚡ index! I'm very excited for what's next 🙂 CC @robp.bsky.social @zaminiqbal.bsky.social

Accepted to ISMB'26. Revised paper is here: jermp.github.io/assets/pdf/p.... I'd like to thank @robp.bsky.social once again and all the received feedback from the reviewers. To me, ISMB has had the highest quality review process over the past few years!

I made this sculpture (clay and acrylic paints) for my mother’s birthday present 🎂 Artistic expression has always been part of my life, besides science.

Wow! What a tool: half million downloads from Bioconda - Congrats @robp.bsky.social and Combine-Lab! 👏 Happy to see SSHash plugged here.

I was pleased to give an interview to @radiopraguefr.bsky.social about my academic journey across Czechia, France, and the United States, and about my research. english.radio.cz/karel-brinda...

The first fully Rust version of piscem! scRNA, scATAC, and bulk-RNA -> RAD files, accurately, in low memory, and FAST. And all in Rust :) anaconda.org/channels/bio...

Another Claude Code win. Did you ever want to be able to use SSHash from Python? To have access to the tiny space and query power of that index from directly within your high-level scripts? Now, with you can (for sshash-rs, at least)! Hope to do the same for piscem-rs soon pypi.org/project/ssha...

Haven't checked BlueSky for a few days. Very nice to see people commenting on DSB and its beautiful location! Thanks again to all contributors! It's been our pleasure to welcome you all in Venice 🙂 #DSB2026

A truly nice read!

Just accepted! dl.acm.org/doi/10.1145/...

Now also on arxiv: arxiv.org/abs/2602.04103

Nice work @npmalfoy.bsky.social! Can't wait for this at DSB :)

Deadline for registration is Jan 31. Don’t miss it! See you all in beautiful Venice 😉

This preprint significantly improves the original design of SSHash to accelerate query and construction time. Looking back at one’s own work is very important and sometimes surprising ☺️

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster! www.biorxiv.org/content/10.6...

The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/

Congratulations to @brinda.eu and Francesca for this impressive work!! We will surely give you a hand in integrating the latest Fulgor version, which is considerably faster thanks to @ale-campa.bsky.social.

Great work and congrats to all authors! 🥳 Can't wait to read the preprint. Just for reference: a Fulgor index ⚡ on the same HPRC collection takes 8.26 GB (not in its most succinct representation). Fulgor, however, can be regarded as a "lossy" method here since it is based on kmers.

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Wow! You should definitely consider applying. Rob is an amazing scientist and professor, and a leader in the field.

Very interesting opportunity!

Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)

Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :) github.com/noamteyssier...

After requests from the community, SSHash lands on Bioconda package index: bioconda.github.io/recipes/ssha.... Cool! Thanks @robp.bsky.social for all the help and support.

We are glad to announce that the next workshop “Data Structures in Bioinformatics” (DSB 2026) will take place in Venice, Italy, on *February 18-19*, 2026. dsb-meeting.github.io/DSB2026/ Book the dates! #DSB26

Without our own users, I have no idea when I would have learned about this extremely subtle limitation of the minimap2 serialized index github.com/COMBINE-lab/... (reference names > 255 bytes don't roundtrip). Users push your software in ways you might not even think to!

Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :) Also some smaller fixes by @tfenne.bsky.social. github.com/RagnarGrootK...

There we go: github.com/jermp/sshash.... What a big release! Many thanks to all contributors and people from the community for their suggestions. Happy to keep maintaining (and improving on) these tools ☺️

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...

I'm about to release SSHash v4.0.0. More details in a future post. Among other things, now indexes store the pos. of minimizers instead of super-kmers. Compared to the latest post (last jun), this somehow had a very positive effect of streaming queries for larger k (e.g., 63)! ☺️ CC @robp.bsky.social

Wow, fantastic room: haven't seen so many screen for a single presentation at a CS conference! ☺️ @ale-campa.bsky.social has been doing some amazing development on the Fulgor index. Soon enough, more exciting news. Stay tuned! ⚡ 🧬 #WABI25

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

WABI is definitely my favourite annual meeting; the community is amazing. I won’t attend this year but @ale-campa.bsky.social will illustrate our latest development around the Fulgor ⚡️index: faster query algorithms this time! Don’t miss his talk!

Wow, congrats Rayan! 🎉

It was a great honour for me to introduce prof. Sebastiano Vigna today at SEA’25. His contributions to large-scale indexing are broad and far-reaching. Inspirational for future generations of computer scientists and professors.

Well deserved indeed! Looking forward to chairing the session :)

Congratulations Ben! Fantastic news!

Today was the first day at SEA'25 in Venice. I've presented the "U-index" framework :) Here are the slides from my talk + a short recap of the main highlights. 1/6 jermp.github.io/assets/pdf/s...

Better features for Piscem🐟 Check this out! Continuous tool maintenance and improvements is what makes a tool rock in the long term. Congrats @robp.bsky.social!

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

Last-minute opportunity to disseminate your new algorithm in Comput. Bio! Submit guys :)