Giulio Ermanno Pibiri
@jermp.bsky.social
Associate Prof. of CS at Ca' Foscari University of Venice. Indexing, Data Compression, Algorithms.
A truly nice read!
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
February 15, 2026 at 4:33 PM
A truly nice read!
Just accepted! dl.acm.org/doi/10.1145/...
Modern Minimal Perfect Hashing: A Survey | ACM Computing Surveys
Given a set S of n keys, a perfect hash function for S maps the keys in S to the first m ≥ n integers without collisions. It may return an arbitrary result for any key not in
S and is called minimal i...
dl.acm.org
February 12, 2026 at 3:03 PM
Just accepted! dl.acm.org/doi/10.1145/...
Reposted by Giulio Ermanno Pibiri
Now also on arxiv:
arxiv.org/abs/2602.04103
arxiv.org/abs/2602.04103
QuadRank: Engineering a High Throughput Rank
Given a text, a query $\mathsf{rank}(q, c)$ counts the number of occurrences of character $c$ among the first $q$ characters of the text. Space-efficient methods to answer these rank queries form an i...
arxiv.org
February 5, 2026 at 10:53 AM
Now also on arxiv:
arxiv.org/abs/2602.04103
arxiv.org/abs/2602.04103
Nice work @npmalfoy.bsky.social! Can't wait for this at DSB :)
Preprint alert!
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
arxiv.org/abs/2602.03525
TLDR:
ZOR filters are STATIC filters with false positives.
-Almost memory optimal: <1% overhead over the theoretical lower bound (!!!)
-Fast queries: ~100 ns
-Construction cannot fail
A thread:
ZOR filters: fast and smaller than fuse filters
Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...
arxiv.org
February 5, 2026 at 12:28 AM
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 😉
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/
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
January 26, 2026 at 3:47 PM
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...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 8:55 AM
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 ☺️
Reposted by Giulio Ermanno Pibiri
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...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 22, 2026 at 9:15 PM
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...
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/
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
December 10, 2025 at 2:29 PM
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.
This is AMAZING! And it's so fantastic to see Fulgor helping out in these large-scale search tasks cc @jermp.bsky.social @ale-campa.bsky.social !
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
November 26, 2025 at 8:07 PM
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.
5/6 On the 466 haplotypes from the 2nd release of HPRC, the fastest Movi 2 index is under 50 GB. It can be reduced to 24 GB while remaining over 3x faster than SPUMONI. Movi 2 is smaller and faster than ropebwt3, although it computes PMLs, which are easier to get than the SMEMs found by ropebwt3.
October 22, 2025 at 7:41 AM
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.
Reposted by Giulio Ermanno Pibiri
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! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
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.
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...
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
October 9, 2025 at 6:45 AM
Wow! You should definitely consider applying. Rob is an amazing scientist and professor, and a leader in the field.
Very interesting opportunity!
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 6:23 PM
Very interesting opportunity!
Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)
Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London
September 9, 2025 at 11:40 AM
Oh right, this is the SPIRE week! Enjoy SPIRE everyone and congrats to all contributors :)
Reposted by Giulio Ermanno Pibiri
Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️
Hashed sorting is typically faster than hash tables
Benchmarks and theoretical explanation of why and when hashed radix sort beats hash tables.
reiner.org
September 8, 2025 at 12:37 PM
Hashing vs. sorting; interesting! reiner.org/hashed-sorting. Also I wonder if, depending on your use case, semi-sorting provides an even greater benefit? 🧬🖥️
Reposted by Giulio Ermanno Pibiri
Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)
github.com/noamteyssier...
github.com/noamteyssier...
September 4, 2025 at 10:41 PM
Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)
github.com/noamteyssier...
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.
Package Recipe 'sshash' — Bioconda documentation
bioconda.github.io
September 4, 2025 at 7:12 AM
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
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
September 1, 2025 at 6:10 PM
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
Reposted by Giulio Ermanno Pibiri
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!
August 30, 2025 at 1:53 PM
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!
Reposted by Giulio Ermanno Pibiri
Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :)
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/sassy: Fast approximate string searching
Fast approximate string searching. Contribute to RagnarGrootKoerkamp/sassy development by creating an account on GitHub.
github.com
August 30, 2025 at 1:26 PM
Just released Sassy 0.1.4, which now supports macos/arm NEON instructions :)
Also some smaller fixes by @tfenne.bsky.social.
github.com/RagnarGrootK...
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 ☺️
Release Version 4.0.0 · jermp/sshash
What's Changed
General renaming of functions/methods and project structure (e.g., now main tools are in a folder named tools).
Added CI workflows.
Refactored CMakeLists.txt: added option to suppor...
github.com
August 28, 2025 at 5:09 PM
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...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...
www.biorxiv.org
August 28, 2025 at 12:16 PM
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...
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
August 23, 2025 at 10:51 AM
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
My collaborator (whom I just met in person today) and @jermp.bsky.social's student, @ale-campa.bsky.social presenting "Fast pseudoalignment queries on compressed colored de Bruijn graphs"! #WABI25
August 21, 2025 at 6:58 AM
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
Reposted by Giulio Ermanno Pibiri
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 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
August 20, 2025 at 2:45 AM
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!