Independent computer scientist. Developer of the DIAMOND protein aligner. https://xitter.cf/t.co/3XQrtFHwM7

Tübingen, Deutschland
Joined August 2014
We’ve lost an icon. Margaret Hamilton, a computer science pioneer best known for her work at MIT leading development of the flight software for the Apollo missions to the moon, has died at 90. Read about her legacy via MIT News: news.mit.edu/2026/margaret-h…
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“We had to find a way and we did. Looking back, we were the luckiest people in the world; there was no choice but to be pioneers.” —Margaret Hamilton Rest in peace, Margaret. Your trailblazing work leading the development of the on-board flight software for the Apollo spacecraft will forever be remembered. 🫡
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Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR. We don’t yet understand what this system does, but only a handful of known systems share its features, and all of them are able to cut, copy, and paste DNA. Historically, the discovery of such programmable systems has helped revolutionize medicine. CRISPR, for instance, is now the foundation of genetic medicines. But it will take much more work to learn what this system does, and whether it can be put to similar use. Read more: anthropic.com/news/claude-di…
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Biology manifests through sequences, and we can learn a lot from examining sequence databases. That is traditionally hard because the databases are huge. So we put troops of Claude on a mission: find new partner genes of reverse transcriptases (RTs) in 1.9B protein clusters. We were surprised by what came back. Claude turned up a strange CRISPR-like RT system we didn't ask for. It is an RT from jumbo phages with an array of repeats upstream and a dedicated partner gene. We call these array-associated RTs (ART).
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Biology has no shortage of data. The challenge is to organize it well enough that scientists—and machines—can learn from it. Our latest preprint presents AllTheBacteria: an open, community-built platform that transforms 2.44 million public bacterial and archaeal genomes into a uniformly processed, searchable, and AI-ready resource. To demonstrate what becomes possible at this scale, we used the platform to discover new peptide antibiotics. One candidate, ATB20, reduced Acinetobacter baumannii burden in a murine skin-abscess model, with efficacy comparable to polymyxin B. More broadly, this work illustrates how open, standardized biological data can help us use machines to understand and engineer biology—and accelerate the discovery of new potential solutions for human health. Deeply grateful to the remarkable international team behind this work: Martin Hunt, Daniel Anderson, Maria Luiza Andreani, Josefin Blom, Michael B. Hall, Samuel T. Horsfield, Hyun-Su Lee, Leandro Lima, Neil MacAlasdair, William Matlock, Vignesh Ramnath, Vishnu Raghuram, Matthew J. Russell, Liam P. Shaw, Gerry Tonkin-Hill, Jackie Toussaint, Fangping Wan, Laura M. Carroll, Matthew A. Croxen, @mdt_torres, @happy_khan, @GB13Faithless, @fionabrinkman, @AndresFloto, @yekwah, @bfjia, @Jake_A_Lacey, @sudaraka_m, @Ahmed_Microbes, @rpetit3, @theosanderson, @TimoSaratto, @oschwengers1, @torstenseemann, @shenwei356, @nrt_thomson, @thanhleviet, @vWachsmann, @aaron_weimann, @WheatleyRM, @wiatrak_maciej, @ouli_xie, @johnlees6, and @ZaminIqbal. With colleagues across @sangerinstitute, @emblebi, @NDMOxford, @Penn, @TheQuadram, @TheCGPS, Universidade Estadual de Campinas, @Ucmr_sweden, @BHIresearch, @mbbsfu, @WCHRIUofA, @LKSIoV, @CC4AIM, @HLRI_Cambridge, @AlfredMonash_ID, @CentreImpactAMR, @UniNeuchatel, @TheDohertyInst, @PeterMacCC, @UniOslo, @MilnerCentre, @LSHTM, @jlugiessen, @BristolBiochem, @Cambridge_SBS, and Theiagen Genomics. biorxiv.org/content/10.1101/…
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🧬Possibly one of the most important genetics preprints of 2026 has just been published: the flagship paper of the Vertebrate Genomes Project. An ambitious effort to generate near-complete and near-error-free reference genomes for all living vertebrate species. The authors present 816 high-quality reference genomes covering around 95% of major vertebrate evolutionary lineages. Most assemblies are at chromosome-level quality and some are fully diploid telomere-to-telomere genomes. Using this resource the authors reconstructed the genome of the last common ancestor of vertebrates, studied the evolution of sex chromosomes, explored 3D genome organization and compared epigenetic landscapes across hundreds of species. This dataset will likely become a foundational platform for evolutionary biology and comparative genomics. biorxiv.org/content/10.64898… #VGP #evolution #ComparativeGenomics #vertebrates #genomes
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Sandpiper 2 is up. 913,000 metagenomic community profiles w GTDB R232 via SingleM, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroney_samuel @IAmTotesBrett Josh Mitchell and especially the new kid @StefanHerh
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Benjamin J. Buchfink retweeted
The SPEC CPU 2026 benchmark suites are here! As the industry standard for vendor-neutral performance, this suite uses 52 real-world apps to help server buyers evaluate how the latest CPUs, memory & compilers handle intense workloads. 🔗 spec.org/pressreleases/2026/… #SPEC #Server #CPU
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Me coding using Claude and Codex @AnthropicAI @OpenAI
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nr database @NCBI hits one billion sequences 🤩
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🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... Thank you to all bug reporters and contributors! github.com/oschwengers/bakta…
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DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/diamond
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