Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
Graph of receptor binding curves showing an ancestral and recent H5N1. The ancestral virus does not bind NeuGc receptor well, whereas the recent virus birds NeuGc and NeuAc containing receptors equally.
Really excited to be able to share our latest preprint, describing how during its evolution in cattle, H5N1 has got better at using a type of alternative receptor that's abundant in cows, but not found in humans and birds.
www.biorxiv.org/content/10.6...
🧬 pathotypr is now on Bioconda! @pathogenomics.bsky.social
conda install -c bioconda pathotypr
Alignment-free lineage classification & drug resistance genotyping from WGS. Works with any pathogen bring your own SNP markers.
⚡ Rust, ~1s/sample
🖥️ CLI + GUI
🔗 github.com/PathoGenOmics-Lab/pathotypr
New paper from Hugh Cottingham, @katholt.bsky.social , @yekwah.bsky.social @nenadmacesic.bsky.social and co.
Great to see the speed/accuracy tradeoff info here, I don't think I've seen it laid out like this before.
www.microbiologyresearch.org/content/jour...
💥Our latest @embojournal.org on membrane damage and repair. Di @dichen02.bsky.social @crick.ac.uk found that calcium is a conserved signal for ATG8/LC3 lipidation on membranes using novel probes to record calcium leakage. Congratulations Di et al!
link.springer.com/article/10.1...
metode.cat/revistes-met...
Una magnífica exposició de @martidominguez.bsky.social per al @museuciencies.cat
Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance www.biorxiv.org/content/10.64898/2026.03...
Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance www.biorxiv.org/content/10.64898/2026.03...
In benchmarking, Pathotypr showed very high concordance with phylogenetic lineage assignment and achieved very fast analysis speeds, making near real-time TB genomic surveillance feasible even on standard desktop hardware. It is available as both a command-line tool and an easy desktop GUI.
The toolkit integrates multiple modules in one workflow:
Train / Predict for lineage classification, Split FASTQ / Classify for genotyping from reads or assemblies, and Match Ref to identify the closest reference genome for each sample.
Pathotypr supports all 14 currently recognised MTBC lineages, including human-adapted lineages L1-L10 and animal-adapted clades A1-A4. It also incorporates recently described diversity such as L10, helping standardise TB genomic surveillance across settings.
Excited to share Pathotypr with @paururo.bsky.social, our open-source toolkit for rapid, harmonised MTBC lineage assignment and drug-resistance genotyping from both genome assemblies and raw reads. @i2sysbio.es. tool github.com/PathoGenOmic.... preprint: doi.org/10.64898/202...
El trabajo diario a veces parece pequeño. Una muestra más, un genoma más, un dato más.
Pero sumado al de muchas otras personas, forma parte de algo mucho más grande: que esta enfermedad deje de estar tan presente.
La TB mata a 1,25 millones de personas al año. Es la enfermedad infecciosa más letal del mundo y las resistencias no dejan de crecer.
Investigación, diagnóstico, vigilancia genómica. Todo cuenta.
Interior del laboratorio BSL-3 durante trabajo rutinario con muestras de tuberculosis
🔬 Hoy es el Día Mundial de la Tuberculosis.
Esta imagen refleja algo que rara vez se ve: las horas dentro de un BSL-3, la bioseguridad, el trabajo silencioso detrás de cada avance.
@i2sysbio.es @pathogenomics.bsky.social
World TB Day 2026. TB is still a major public health challenge in Europe: 19,000 deaths, 204,000 cases, and up to 55,000 drug-resistant TB cases in 2024. ESM calls for stronger research, surveillance, and equitable access to diagnosis, treatment, and prevention. #WorldTBDay #TB
Researchers from the PathoGenOmics Lab @pathogenomics.bsky.social in #I2SysBio work daily to combat transmission of M. tuberculosis through genomics
#microsky #WorldTBDay #Tuberculosis
🔬 World TB Day 2026 — Behind the mask, inside BSL-3.
Our team works daily to understand M. tuberculosis evolution, resistance & transmission through genomics.
TB still kills 1.25M people/year. Research matters.
@i2sysbio.es
#WorldTBDay #EndTB #Tuberculosis
You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium):
taxonium.org/atb
That's a big tree!
(unless you're used to SC2 trees)
El Instituto de Biología Integrativa de Sistemas celebra su décimo aniversario con un acto conmemorativo en el Parc Científic de la Universitat de València
www.i2sysbio.es/communicatio...
@i2sysbio.es
Happy Bioinformatics Day!🧬💻Celebrate the power of data for understanding life at every level. In @pathogenomics.bsky.social we combine experiments with bioinformatics to understand bacterial evolution, virulence, and infection dynamics. #SoyBioinformatica @paururo.bsky.social @ahmig.es @i2sysbio.es
Proud to celebrate 10th anniversary of @i2sysbio.es 🎉 Being part of a community dedicated to discovery, collaboration, and advancing science is truly inspiring. Grateful to contribute, learn, and grow alongside such passionate colleagues. Here’s to many more years of knwledge and impact! 🔬✨
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
¿Quieres un impulso a tu formacion investigadora🔬? En
@i2sysbio.es ofertamos beca JAE Intro @amrhubcsic.bsky.social al. Plan formativo "Frenar la adquisición de resistencia en bacterias patógenas💊". 6 meses remuneración de 600 €/mes. Aplica antes del 10 marzo en www.convocatorias.csic.es/convoca/
🚀 #ESM2026 registration is open! 46th Annual Congress of the European Society of Mycobacteriology.
📍 Verona, Italy | 🗓️ 22–25 June 2026
🔗 www.esmycobacteriology.eu/event-home
get_mnv v1.0.1 🧬 It turns multiple SNVs in the same codon into true MNVs, so your protein impact annotation is correct. v1.0.1 adds GFF3 + multi-sample VCF support, bgzip/Tabix + BCF output, and reproducible JSON summaries/manifests.
github.com/PathoGenOmic... @i2sysbio.es @pathogenomics.bsky.social
Bien.
Ahora, imaginad: si nosotros con un orden de magnitud menos de pasta somos capaces de sacar trabajos equivalentes, ¿que pasaría si se invirtiera en los que ya estamos aquí?
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
