Giulio Ermanno Pibiri

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!

Of course! I’ll be on vacation soon, too :) enjoy your vacation!

Hi Zamin! Any update on this? No pressure, but feel free to drop me a line to discuss this matter.

Rust code is available here github.com/u-index/u-in.... Check it out! 6/6

This simple framework is thus *universal*, in that it allows you to use any index and any locally-consistent sketching algorithm. Results indicate that we reduce building time, building memory, index size while keeping competitive query times wrt an index directly built for T. 5/6

In particular, we sketch T using random minimizers, obtaining a new shorter text S which can be indexed with your favourite data structure (SA, CSA, FM-index, r-index, etc.). To match a pattern P, we compute its sketch Q and solve Locate(Q,S). Then we map back these occurrences in T and match. 4/6

The core idea of U-index is to compute a *sketch* of the text T, to solve pattern matching using less resources (less space/time). 3/6

First of all: a nice collaboration with many friends! I, @curiouscoding.nl, and @robp.bsky.social were discussing this project a long time ago, before discovering Solon and Gabriele were working on this independently. We decided to join efforts! 2/6

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!

Cool stuff boys! It would be interesting to compare against kmer matches under Hamming distance. Since your method is specialized for short patterns, maybe kmer under H. dist could give similar results, but hopefully in an even shorter time :)

Sassy solves approximate string matching: finding all matches of a pattern in a text.

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...

Also, lost count on how many papers are titled like “A compact and fast index…” and variations of it 😌

😂

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

GreedyMini: generating low-density DNA minimizers AbstractMotivation. Minimizers are the most popular k-mer selection scheme in algorithms and data structures analyzing high-throughput sequencing (HTS) dat

The GreedyMini paper is finally out as part of #ISMBECCB2025 proceedings: academic.oup.com/bioinformati.... Arseny will present it on the last day (July 24th) and last session (14:20) of the HiTSeq meeting.

Nice! Congratulations!

Volume 41 Issue Supplement_1 | Bioinformatics | Oxford Academic Publishes scientific papers and review articles on new developments in bioinformatics and computational biology. Shorter papers report biologically interesting discoveries using computational methods ...

🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...

Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜Graduate School of Frontier Scienc... Call for applications (professor or associate professor), Department of Computational Biology and Medical Sciences (Deadline Sep 30) ｜Job Opportunities｜Information｜GSFS offers both master‘s and doct...

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated):

www.k.u-tokyo.ac.jp/en/informati...

Zamin! I've seen this post only now; sorry. Yeah, we've got plan with @ale-campa.bsky.social and @robp.bsky.social to make Fulgor indexes available. We'll try to do it asap!

Last afternoon in Tokyo 🇯🇵 It's been so nice to be back here again after 2018...Next time won't take 7 years 😅 @kampersanda.bsky.social

This builds on top of several compression tools that I (quickly) summarized in this other invited lecture (again at RIKEN AIP): jermp.github.io/assets/pdf/s....

Alessio Campanelli on X: "With @giulio_pibiri and @nomad421, we are about to release Fulgor v4.0.0, which is much faster to build and query, without affecting its memory efficiency. You can find all the information in our #WABI2025 paper (https://t.co/foLYdhsC2Z). 🧵 (1/7)" / X With @giulio_pibiri and @nomad421, we are about to release Fulgor v4.0.0, which is much faster to build and query, without affecting its memory efficiency. You can find all the information in our #WABI2025 paper (https://t.co/foLYdhsC2Z). 🧵 (1/7)

A special thank to both @robp.bsky.social and @ale-campa.bsky.social for being great co-authors! Also, check this thread on X by Alessio on our upcoming WABI'25 paper where we boosted Fulgor perf by a lot! x.com/AlessioCampa...

I gave an invited talk today in beautiful Tokyo for a workshop organized by Yasuo Tabei, at RIKEN AIP 🇯🇵. My slides are here jermp.github.io/assets/pdf/s.... This surveys recent development in indexing colored de Bruijn graphs in little space while supporting fast pseudoalignment.

ahah I cannot imagine you away from your laptop for more than 40 min :) Let me know how this thing goes!

Done!

🧬🖥️ In addition to an update to oarfish, a new version (0.14.0) of piscem (zenodo.org/records/1509...) has just been released. This version pulls in some of the latest improvements to sshash by @jermp.bsky.social! 1/2