Big Data Biology Lab

Quarterly updates from the Lab! This June, the focus is on @alex_areiasc , who is working on metabolic modeling of the microbiome with the aim of giving us a new view on microbial composition, focused of "functional roles" instead of taxonomy

Out in @NatureBiotech: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. doi.org/10.1038/s41587… A 🧵

Back in 1962 microscopy was used to pen a hypothesis about eukaryote-microbe relationships. ~65 years later we have coupled the latest advancements in long read MetaG, MetaP and EUK SAGs to help explain what this means for wider rumen microbiome function nature.com/articles/s4146…

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Check out our team's paper on SingleM, a metagenomic taxonomy profiler that doesn't ignore unknown species! doi.org/10.1038/s41587…

New version of argNorm! Will be available frombioconda & funcscan in the next few days NCBI genes are now handled in a fundamentally more principled way and this should fix a few corner cases (particularly if data has been run through hARMonization) pypi.org/project/argnor…

📥 You have only until 24 June to submit your abstract for 'The human microbiome'❗ 🔬💊 Explore cutting-edge breakthroughs in microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. #EESMicrobiome ➡️ s.embl.org/ees25-08-x…

Interested in joining our lab in Berlin as a postdoc? Please consider the Marie-Sklodowska-Curie Postdoctoral Fellowship. Deadline is 10 September, but if you're interested, please reach out soon, since our university offers training. …sklodowska-curie-actions.ec.europa.eu/actions/postdo…

Join us at #EESMicrobiome! Organisers @microbiomix (@uni_copenhagen), Ami Bhatt (@Stanford), Peer Bork (@BorkLab) and @nsegata (@CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl!

Heads up! The live coding workshop on Genome Quality Evaluation starts next Tuesday, June 10th at 9am with @luispedrocoelho Still time to register here if you're interested in bioinformatics, working with genomic data, or want to see Polars in action for scientific computing.

Anyone from Europe who wants to spend two years in sunny Queensland working on the global microbiome? Get in touch (even if all you have right now is a vague idea, just email early)! We also have a lot of friends in Europe for the return phase. …sklodowska-curie-actions.ec.europa.eu/calls/msca-pos…

Artificial intelligence may be one of the most important tools we have in the global fight against AMR, which now contributes to 4.5 million deaths each year. AI allow us to probe DNA and proteins from both extinct and living organisms for new and optimal antibiotics far more…

New #MicrobiomeDigest is OUT microbiomedigest.com/2025/04/30/apr… - Herrgårds cheese / Juan Antonio Rodríguez - Asian Skin Microbiome Program / Chengchen Li - long-read assemblers / @FlorianTrigodet - argNorm / Vedanth Ramji (@BigDataBiology) See you next week at @MicrobiomeVIF!

Happy birthday 🎂 to our amazing guide @luispedrocoelho ! He’s the heart of the team and we had the sweetest celebration🎉!! #TeamLuis @BigDataBiology @alex_areiasc @AnPokhrel

The argNorm tool to normalize the Output of Metagenomic #AMR analysis by @SEARCHER_JPIAMR’s @svetlana_up, @luispedrocoelho et al. is now published

argNorm is published now academic.oup.com/bioinformatics…

Strobealign v0.16.0 has been released. It comes with both runtime and accuracy improvements. Full changelog here github.com/ksahlin/strobe…

ArgNorm 0.8.0 released! More information including English language names for outputs and a bugfix for handling abricate+resfinder outputs argnorm.readthedocs.io/en/latest/what…