Giulio Ermanno Pibiri
@jermp.bsky.social
Associate Prof. of CS at Ca' Foscari University of Venice. Indexing, Data Compression, Algorithms.
If you are a US citizen or permanent resident looking for a postdoc, the President's Postdoctoral Fellowship Program is a great opportunity faculty.umd.edu/presidentspo...! If you are eligible, working in computational genomics, and interested in my lab, let me know!
President's Postdoctoral Fellowship Program | Office of Faculty Affairs
faculty.umd.edu
I have known about this result for about 3 years, but since Thomas and Jakob are working in industry it took some time to get the paper written. A nice contrast to the rush to publish that we see too often, and as a bonus the paper is (partly) Lean formalized. Congratulations on this achievement!
PSA: @jermp.bsky.social has a new release of sshash! It eliminates the ‘canonical’ choice when indexing, b/c the new index gives the best of both worlds by adopting a forward canonical minimizer scheme. Size of the unidirectional index/speed of canonical (faster in fact) github.com/jermp/sshash...
Release Version 6.0.0 · jermp/sshash
What's Changed Refactor SSHash indexing to unify parsing modalities and optimize performance by @jermp in #93 Full Changelog: v5.1.1...v6.0.0
github.com
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
César de la Fuente@delafuentelab.bsky.social · 3mo agoBiology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...
Of course, I agree 😄 Thank you again @robp.bsky.social for taking care of the presentation of our paper. doi.org/10.1093/bioi...
naturepoker@binomicalabs.org · 3mo agoFellas, that HIT-SEQ talk on faster k-mer dictionaries should be a textbook example on how to communicate a technical topic simply and efficiently at a conference. #ismb2026
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!
Optimizing sparse and skew hashing: faster k-mer dictionaries
AbstractMotivation. Representing a set of k-mers—strings of length k—in small space under fast lookup queries is a fundamental requirement for several appl
academic.oup.com
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!!
Genetics Society UK@gensocuk.bsky.social · 4mo agoCongratulations to Prof @zaminiqbal.bsky.social, recipient of the 2026 Mary Lyon Medal, on delivering an inspiring lecture at Genetics Society Anniversary Day 2026 in Edinburgh.
Rob and his work are unique gifts for our field. I'm glad our paths crossed!
Rob Patro@robp.bsky.social · 5mo agoOur comms folks in the CS dept reached out and we had a nice Q&A chat for a faculty spotlight! Thanks, especially, to Samuel Malede Zewdu for starting the faculty spotlight series. cc @umdscience.bsky.social @univofmaryland.bsky.social : www.cs.umd.edu/article/2026...
📢 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?
Robert Aboukhalil@robert.bio · 5mo agoI've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI
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.
Hash functions in nucleotide sequence analysis
Randomness is a powerful tool in the design and analysis of algorithms and data structures for nucleotide sequence data. Nucleotide sequences are not themselves random but are often randomized using hash functions. Despite their widespread use in genomics, there is no comprehensive review of the types of hash functions used and their various applications. In this survey intended for bioinformatic methods developers, we divide hash functions into four categories: scattering hash functions, permutations, minimum perfect hash functions, and locality-sensitive hash functions. For each category, we provide examples of both general-use hash functions that have been applied in nucleotide sequence analysis and hash functions that have been designed specifically for nucleotide sequence analysis. We highlight their salient properties, commonalities, differences, and application areas.
doi.org
PPaul Medvedev @pashadag.bsky.social · last yr.
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.
🔍 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
Alessio Campanelli@ale-campa.bsky.social · 6mo agoWith @jermp.bsky.social & @robp.bsky.social, we have just released Fulgor v4.1.0 (also on bioconda! bioconda.github.io/recipes/fulg...). Here's what's new, and what's to come. 🧵 (1/6)
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!
jermp.github.io
Giulio Ermanno Pibiri@jermp.bsky.social · 9mo agoThis 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 ☺️
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.
Rob Patro@robp.bsky.social · 7mo agoI've been wanting to do a big refactor and build system update for salmon for a looong time. I finally got around to it, and updated the backend index to use the newest SSHash while I was at it : github.com/COMBINE-lab/... (also with native ARM support & on bioconda!)
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...
Karel Břinda on research at Harvard and working with bacteria as if they were books
Karel Břinda sheds light on how curiosity, mobility, and interdisciplinarity can shape a modern researcher’s path in a world where science increasingly transcends borders.
english.radio.cz
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...
piscem - bioconda | Anaconda.org
Install piscem with Anaconda.org. piscem is a next-generation compacted colored de Bruijn Graph-based indexer and mapper
anaconda.org
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...
sshash
Python bindings for the sshash compressed k-mer dictionary
pypi.org
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!
Rob Patro@robp.bsky.social · 8mo agoI’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...
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
Nice work @npmalfoy.bsky.social! Can't wait for this at DSB :)
Antoine Limasset@npmalfoy.bsky.social · 8mo agoPreprint 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:
Deadline for registration is Jan 31. Don’t miss it! See you all in beautiful Venice 😉
Giulio Ermanno Pibiri@jermp.bsky.social · 10mo agoThe 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/
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 ☺️
Rob Patro@robp.bsky.social · 9mo agoVery 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...
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...
biorxiv.org
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
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.
Rob Patro@robp.bsky.social · 11mo agoThis 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 !