Benjamin J. Buchfink

Benjamin J. Buchfink

@bbuchfink.bsky.social

Independent scientist, Tübingen, Germany. Developer of the DIAMOND protein aligner. https://github.com/bbuchfink/diamond https://www.linkedin.com/in/benjamin-j-buchfink-875692105

137 followers240 following11 posts

Benjamin J. Buchfink reposted

Emily M. Bender
@emilymbender.bsky.social

Software engineering could and should be done with the same care as any other type of engineering. This is a post in honor of Margaret Hamilton (and also a subtweet of all vibe-coders everywhere).

Benjamin J. Buchfink reposted

Nils Homer
@nilshomer.com

Bioinformatics rewrites miss the relational impact tofolks that are still actively maintaining and developing the software. I've been guilty of this myself, and I'll be sharing my story soon so others can learn from it.

Benjamin J. Buchfink reposted

César de la Fuente
@delafuentelab.bsky.social

A few additional thoughts following my post: 1. There's likely far more biological data than we often assume. The challenge's that it remains highly fragmented. Large international efforts to integrate them could greatly advance understanding of complex, dynamic biological systems.

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...

Benjamin J. Buchfink reposted

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...

Benjamin J. Buchfink reposted

Nature Methods
@natmethods.nature.com

OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @lauriebelch.bsky.social @stevenkelly.bsky.social @jonathancholmes.bsky.social @yiliu88.bsky.social www.nature.com/articles/s41...

nature.comOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature MethodsThe updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

Benjamin J. Buchfink reposted

Laurie Belcher
@lauriebelch.bsky.social

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

nature.comOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature MethodsThe updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

Benjamin J. Buchfink reposted

Zamin Iqbal
@zaminiqbal.bsky.social

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

npr.orgResearchers say the Trump administration is finding new ways to punish scienceEven with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

Benjamin J. Buchfink reposted

Paul Medvedev
@pashadag.bsky.social

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

Benjamin J. Buchfink reposted

Kai Blin
@kblin.bsky.social

I'm not looking forward to a future where all the tools are being vibe-rewritten into languages people don't want to learn. Who will maintain all this? The original maintainers won't. It's not the language they were comfortable with. Does the prompter understand the tool well enough?

Phil Ewels@ewels.bsky.social

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/

seqeralabs.github.ioWelcome to RustQCFast quality control tools for sequencing data, written in Rust.

Benjamin J. Buchfink reposted

Workshops
@evomics.bsky.social

The 2026 Workshop on Genomics comes to an end! It has been two intense and inspiring weeks of Genomics in Český Krumlov. We hope everyone is going back home with a renewed excitement for science and new friends and collaborations around the world! 🙆🏻‍♀️🧬 #evomics2026

Benjamin J. Buchfink reposted

Martin Steinegger 🇺🇦
@martinsteinegger.bsky.social

I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI

Recurse Center@recurse.com

What’s the lore behind choosing your career path ?

Benjamin J. Buchfink reposted

Emma Chory, Ph.D.
@chorye.bsky.social

NIH just early-expired its 1st & only software NOFO: “Building Sustainable Software Tools for Open Science.” Our proposal supported lab automation software infrastructure, with backing from major robotics companies. I guess “sustainable” is too risky now. So much for funding the STEM workforce.

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