Giulio Ermanno Pibiri

Wow, super cool visualization!

Matt Henderson@matthen.com

Visualising the distribution of substrings in the genomes of different organisms. Going up to depth eight by recursively splitting into quadrants, we get these fractal-like pictures.

Giulio Ermanno Pibiri reposted

faculty.umd.eduPresident's Postdoctoral Fellowship Program | Office of Faculty Affairs

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!

Giulio Ermanno Pibiri reposted

Rasmus Pagh

@rasmuspagh.net

14 Sept

Replying to @rasmuspagh.net

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!

Giulio Ermanno Pibiri reposted

github.comRelease Version 6.0.0 · jermp/sshashWhat's Changed Refactor SSHash indexing to unify parsing modalities and optimize performance by @jermp in #93 Full Changelog: v5.1.1...v6.0.0

30 Aug

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...

Giulio Ermanno Pibiri reposted

Zamin Iqbal

@zaminiqbal.bsky.social

20 July

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

Biology 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...

biorxiv.orgAllTheBacteria: a community resource empowers biology and discovers novel peptide antibioticsPublic microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

14 July

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

Fellas, 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

Giulio Ermanno Pibiri reposted

academic.oup.comOptimizing sparse and skew hashing: faster k-mer dictionariesAbstractMotivation. Representing a set of k-mers—strings of length k—in small space under fast lookup queries is a fundamental requirement for several appl

12 July

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!

Giulio Ermanno Pibiri reposted

Zamin Iqbal

@zaminiqbal.bsky.social

25 June

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

Congratulations 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.

cs.umd.eduRob Patro on Making Biological Data Easier to SearchUniversity of Maryland Associate Professor of Computer Science Rob Patro works in computational genomics, where his research addresses the growing need to process and interpret large amounts of biolog...

27 May

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

Rob Patro@robp.bsky.social

Our 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...

Giulio Ermanno Pibiri reposted

RECOMB Conference Series

@recombconf.bsky.social

18 May

📢 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.

youtu.beI interviewed 5 bioinformatics experts about AI rewritesYouTube video by OMGenomics

14 May

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

Robert Aboukhalil@robert.bio

I'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

Giulio Ermanno Pibiri reposted

Paul Medvedev

@pashadag.bsky.social

5 May

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.

doi.orgHash functions in nucleotide sequence analysisRandomness 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.

Paul Medvedev @pashadag.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.

tinyurl.comDropbox

Giulio Ermanno Pibiri reposted

Bioinformatics Advances

@bioinfoadv.bsky.social

7 May

🔍 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

bioconda.github.ioPackage Recipe 'fulgor' — Bioconda documentation

20 Apr

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

With @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)

jermp.github.iojermp.github.io

13 Apr

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!

Giulio Ermanno Pibiri@jermp.bsky.social

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 ☺️

github.comGitHub - jermp/sshash: 📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers. - jermp/sshash

13 Apr

C++ code is here github.com/jermp/sshash and also available via Bioconda bioconda.github.io/recipes/ssha.... Rust code is here instead github.com/COMBINE-lab/... (thank you again @robp.bsky.social!)

14 Mar

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.

github.comRelease v1.11.4 · COMBINE-lab/salmonReleased: 2026-03-11 Full Changelog: v1.10.3...v1.11.4 Overview Salmon v1.11.2 is a major release representing the most substantial architectural overhaul of the salmon codebase since the transiti...

11 Mar

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

I'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!)

Giulio Ermanno Pibiri reposted

Karel Břinda

@brinda.eu

9 Mar

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...

english.radio.czKarel Břinda on research at Harvard and working with bacteria as if they were booksKarel Břinda sheds light on how curiosity, mobility, and interdisciplinarity can shape a modern researcher’s path in a world where science increasingly transcends borders.

Giulio Ermanno Pibiri reposted

anaconda.orgpiscem - bioconda | Anaconda.orgInstall piscem with Anaconda.org. piscem is a next-generation compacted colored de Bruijn Graph-based indexer and mapper

28 Feb

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...

Giulio Ermanno Pibiri reposted

pypi.orgsshashPython bindings for the sshash compressed k-mer dictionary

21 Feb

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...

21 Feb

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

combine-lab.github.ioCOMBINE-lab - The skeptic’s guide to generative AI assisted codingAn easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.

15 Feb

A truly nice read!

Rob Patro@robp.bsky.social

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...

dl.acm.orgModern Minimal Perfect Hashing: A Survey | ACM Computing SurveysGiven 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...

12 Feb

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

arxiv.orgQuadRank: Engineering a High Throughput RankGiven 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...

13 Feb

I’d like to thank very much the (anonymous) reviewers for their valuable feedback!

Giulio Ermanno Pibiri reposted

Ragnar {Groot Koerkamp}

@curiouscoding.nl

5 Feb

Replying to @curiouscoding.nl

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

arxiv.orgZOR filters: fast and smaller than fuse filtersProbabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...

5 Feb

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

Antoine Limasset@npmalfoy.bsky.social

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:

dsb-meeting.github.ioDSB 2026 Venice - February 18-19Workshop Data Structures in Bioinformatics

26 Jan

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

Giulio Ermanno Pibiri@jermp.bsky.social

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/

23 Jan

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

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.orgbiorxiv.org

Giulio Ermanno Pibiri reposted

22 Jan

biorxiv.orgbiorxiv.org

dsb-meeting.github.ioDSB 2026 Venice - February 18-19Workshop Data Structures in Bioinformatics

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/

View full thread

forms.gleDSB 2026 - Registration

We are less than 1 month away from abstract submission! **REGISTRATION** HERE: forms.gle/V9yrUXYvAsTP... Registrations will be open until January 31st, 2026. **ABSTRACT SUBMISSION** HERE: forms.gle/baHkDCZW1Lvx... Submissions of abstracts for an oral presentation are open until January 2nd, 2026.

raven-laboratory.github.ioAboutResearch on Algorithms VENice

DSB 2026 is organized by the RAVEN (Research on Algorithms VENice) research group at Ca' Foscari University of Venice, raven-laboratory.github.io. Looking forward to seeing you in Venice!

dsb-meeting.github.ioDSB 2026 Venice - February 18-19Workshop Data Structures in Bioinformatics

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-meeting.github.ioDSBWorkshop Data Structures in Bioinformatics

The workshop "Data Structures in Bioinformatics" is an annual scientific meeting at the crossroads of CS and biology. It is a unique forum to discuss compact data structures and algorithms in the context of data processing for the life sciences. More details on DSB at dsb-meeting.github.io

26 Nov 2025

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

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 !

22 Oct 2025

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.

Mohsen Zakeri@mohsenzakeri.bsky.social

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.

Giulio Ermanno Pibiri reposted

umd.wd1.myworkdayjobs.comPostdoctoral AssociateJob Description Summary Organization's Summary Statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks,...

10 Oct 2025

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! 🖥️🧬

Rob Patro@robp.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!

docs.google.comPostdoc Description.docxTitle: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

9 Oct 2025

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

Rob Patro@robp.bsky.social

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...

17 Sept 2025

Very interesting opportunity!

This post is unavailable.

9 Sept 2025

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

Camille Marchet ⚡@camillemrcht.bsky.social

Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London

Giulio Ermanno Pibiri reposted

reiner.orgHashed sorting is typically faster than hash tablesBenchmarks and theoretical explanation of why and when hashed radix sort beats hash tables.

8 Sept 2025

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

Giulio Ermanno Pibiri reposted

Ragnar {Groot Koerkamp}

@curiouscoding.nl

4 Sept 2025

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

github.comRelease paraseq-0.4.0 · noamteyssier/paraseqWhat's Changed [WIP] inline reading into worker threads and split paired-end reading by @RagnarGrootKoerkamp in #39 Dev by @noamteyssier in #41 New Contributors @RagnarGrootKoerkamp made their f...

Ragnar {Groot Koerkamp}@curiouscoding.nl

Sorry I couldn't break the news.

bioconda.github.ioPackage Recipe 'sshash' — Bioconda documentation

4 Sept 2025

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.

dsb-meeting.github.ioDSB 2026 Venice - February 18-19Workshop Data Structures in Bioinformatics

1 Sept 2025

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

1 Sept 2025

DSB is an annual scientific meeting at the crossroads of computer science and biology. It is the unique forum to discuss compact data structures and their applications for processing data from life sciences.

1 Sept 2025

As in previous years, the workshop will be free to attend, but *registration will be required* in order to participate. The call for abstracts will be announced around mid-November, and registrations will open shortly thereafter. Can't wait to meet you all in Venice :)

Giulio Ermanno Pibiri reposted

github.comIndexing issue · Issue #46 · COMBINE-lab/oarfishHi Rob and team, This is Khi Pin from PacBio. I was testing oarfish recently and I tried creating an index with a FASTA file that had custom header: oarfish --only-index --annotated problematic.fas...

30 Aug 2025

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!

Rob Patro@robp.bsky.social

One of the best things you can do for your burgeoning software is to find a serious early user. That tests the software out "in the wild", leads to new ideas and feature requests, highlights subtle bugs, and if you user is a dev, often leads to code contributions! It's a win-win!

Giulio Ermanno Pibiri reposted

Ragnar {Groot Koerkamp}

@curiouscoding.nl

30 Aug 2025

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

github.comGitHub - RagnarGrootKoerkamp/sassy: Fast approximate string searchingFast approximate string searching. Contribute to RagnarGrootKoerkamp/sassy development by creating an account on GitHub.

github.comRelease Version 4.0.0 · jermp/sshashWhat'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...

28 Aug 2025

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 ☺️