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Paula

@paururo.bsky.social
1.1K followers 339 following 29 posts

Decoding #TB 🦠 mysteries at @pathogenomics.bsky.social | Bioinformagician wielding data to unlock genetic secrets 🧬💻 | Check out my code on GitHub github.com/paururo

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Reposted by Paula
PathoGenOmics Lab @pathogenomics.bsky.social · 25/09/2026
Participaremos en el espectáculo de arte y ciencia VirArt organizado por Álvaro Chiner en @teatremusical.bsky.social. @gvafisabio.bsky.social @dicv.csic.es @cipfvalencia.bsky.social
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Paula @paururo.bsky.social · 17/09/2026
Working with bacterial sequencing data and want to get more out of it? ONE-BAG 2026 is a hands-on course covering the full bacterial genomics workflow, from raw reads to phylogenetics. Valencia, 14–17 Dec 2026. Applications close 1 Oct. onebag.uv.es
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PathoGenOmics Lab @pathogenomics.bsky.social · 15/09/2026
Want to analyse bacterial genomes yourself? ONE-BAG 2026 at @i2sysbio.es takes you from raw reads to interpretable phylogenies, with hands-on training in QC, SNPs, assembly, annotation, pangenomes, outbreaks, AMR and typing. Learn more: onebag.uv.es
onebag.uv.es
ONE-BAG 2026 | Bacterial Genomics for One Health
From raw reads to a tree you can defend. Four days in Valencia, free for EOHA full members and 300 euro for everyone else. Applications close 1 October 2026.
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Paula @paururo.bsky.social · 16/08/2026
Your variant annotator may be reporting amino acids that never existed. Two SNVs in one codon can mean one real protein change, not two separate ones. That’s what get_MNV fixes. v1.1.5 is out 🚀 Try it, read the docs, and ⭐ the repo if useful: github.com/PathoGenOmics-Lab/get_MNV
github.com
GitHub - PathoGenOmics-Lab/get_MNV: Turns same-codon SNVs into MNVs and computes the true amino acid change
Turns same-codon SNVs into MNVs and computes the true amino acid change - PathoGenOmics-Lab/get_MNV
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Paula @paururo.bsky.social · 27/06/2026
Back from #ESM2026 in Verona, grateful and proud. Two of my research contributions, co-authored with Mireia @pathogenomics.bsky.social, were presented. Honoured to receive the Travel Award and Best Oral Presentation. Thank you, Mireia, for your guidance and support. @i2sysbio.es @esmyco.bsky.social
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Juli Peretó @julipereto.bsky.social · 02/06/2026
Sempre atent amb els usuaris, el primer dia de les PAU #metrovalencia ofereix el seu exclusiu tram-llauna de sardines per accedir al campus de Burjassot-Paterna de la @uv.es
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Dr Emma Hodcroft @firefoxx66.bsky.social · 14/05/2026
Nextstrain #ANDV trees updated with a few improvements: - 2 outbreaks marked - host scientific/common name added - province now visible on map - date colouring added Here's a quick tour of how to change colours, geography & names! Links to trees here (scroll down): nextstrain.org/groups/hodcr...
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European Society of Mycobacteriology @esmyco.bsky.social · 04/05/2026
📢 Abstract deadline extended! Submit your abstract for the ESM Annual Congress 2026 by 10 May 2026 final deadline. Share your research, case studies & innovations in mycobacteriology. Submit/register: www.esmycobacteriology.eu/event-regist... #Mycobacteriology #ESM2026
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Jaebeom Kim @jbeom.bsky.social · 09/04/2026
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
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Tom Peacock @peacockflu.bsky.social · 06/04/2026
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...
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.
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Paula @paururo.bsky.social · 02/04/2026
🧬 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
bioconda.github.io
Package Recipe 'pathotypr' — Bioconda documentation
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Zamin Iqbal @zaminiqbal.bsky.social · 02/04/2026
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...
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Max Gutierrez @maxgg.bsky.social · 31/03/2026
💥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...
link.springer.com
Ca²⁺ leakage is a conserved signal for non-canonical ATG8/LC3 lipidation and membrane repair - The EMBO Journal
Endomembrane damage of intracellular vesicles triggers signals that activate membrane repair in mammalian cells to restore homeostasis. However, the signals that drive diverse membrane repair recruitm...
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Juli Peretó @julipereto.bsky.social · 30/03/2026
metode.cat/revistes-met... Una magnífica exposició de @martidominguez.bsky.social per al @museuciencies.cat
metode.cat
El món vegetal de Darwin - Revista Mètode
«Darwin Botànic» és el títol de l’exposició que el Museu de Ciències Naturals de Barcelona ha instal·lat en l’Hivernacle del parc de la Ciutadella. El subtítol «Les plantes com a evidència de l’evoluc...
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bioRxivpreprint @biorxivpreprint.bsky.social · 27/03/2026
Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 27/03/2026
Pathotypr: harmonised MTBC lineage assignment and resistance-associated variant detection for genomic surveillance www.biorxiv.org/content/10.64898/20…
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PathoGenOmics Lab @pathogenomics.bsky.social · 30/03/2026
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.
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PathoGenOmics Lab @pathogenomics.bsky.social · 30/03/2026
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.
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PathoGenOmics Lab @pathogenomics.bsky.social · 30/03/2026
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.
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PathoGenOmics Lab @pathogenomics.bsky.social · 30/03/2026
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...
github.com
GitHub - PathoGenOmics-Lab/pathotypr: Genome classificator using machine learning and SNP markers.
Genome classificator using machine learning and SNP markers. - PathoGenOmics-Lab/pathotypr
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Paula @paururo.bsky.social · 24/03/2026
🔬 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
Interior del laboratorio BSL-3 durante trabajo rutinario con muestras de tuberculosis
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European Society of Mycobacteriology @esmyco.bsky.social · 24/03/2026
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
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I2SysBio @i2sysbio.es · 24/03/2026
Researchers from the PathoGenOmics Lab @pathogenomics.bsky.social in #I2SysBio work daily to combat transmission of M. tuberculosis through genomics #microsky #WorldTBDay #Tuberculosis
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PathoGenOmics Lab @pathogenomics.bsky.social · 24/03/2026
🔬 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
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John Lees @johnlees.bacpop.org · 17/03/2026
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)
taxonium.org
Taxonium
Interactive exploration of large phylogenetic trees
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Alvaro San Millan @sanmillan.bsky.social · 13/03/2026
Final version of our last paper is out! www.nature.com/articles/s41...
nature.com
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
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Ⓙⓐⓥⓘⓔⓡ🇵🇸🍉 Ⓑⓤⓒⓔⓣⓐ🇺🇦🇪🇺 @javierbuceta.bsky.social · 12/03/2026
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
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PathoGenOmics Lab @pathogenomics.bsky.social · 11/03/2026
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
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PathoGenOmics Lab @pathogenomics.bsky.social · 10/03/2026
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! 🔬✨
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Theo Sanderson @theo.io · 08/02/2026
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
bluesky-map.theo.io
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
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PathoGenOmics Lab @pathogenomics.bsky.social · 04/03/2026
¿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/
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European Society of Mycobacteriology @esmyco.bsky.social · 01/03/2026
🚀 #ESM2026 registration is open! 46th Annual Congress of the European Society of Mycobacteriology. 📍 Verona, Italy | 🗓️ 22–25 June 2026 🔗 www.esmycobacteriology.eu/event-home
esmycobacteriology.eu
Current meeting | ESM
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Paula @paururo.bsky.social · 26/02/2026
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
github.com
Release 1.0.1 · PathoGenOmics-Lab/get_MNV
Added --gff support for gene annotation (GFF/GFF3). --chrom support for selecting one or multiple contigs. --sample support for selecting a sample in multi-sample VCFs. --strict validation mode fo...
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Carmen @carmenagustin.bsky.social · 30/01/2026
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?
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
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...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Paula Ramiro-Martínez @paularamiro.bsky.social · 27/01/2026
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
pnas.org
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 27/01/2026
New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...
Cover of PNAS in which we show plasmids as colourful concentric circles, with dots scattered. The image kind of resembles an eye, although it’s visibly a plot.
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I2SysBio @i2sysbio.es · 19/12/2025
🎥El investigador @fgonzalef.bsky.social lidera el grupo de Epidemiología Molecular en el #I2SysBio (@csic.es- @uv.es) ➡️Mira esta breve presentación si quieres saber más sobre su trayectoria y sus principales líneas de investigación. @dicv.csic.es www.youtube.com/watch?v=W4Ja...
youtube.com
Interview of Fernando González, Principal Investigator of the Molecular Epidemiology group
YouTube video by Institute for Integrative Systems Biology I2SysBio
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PathoGenOmics Lab @pathogenomics.bsky.social · 16/10/2025
Come and join us in Valencia next January for the meeting of the Spanish Society of Evolutionary Biology. Deadline for abstracts October 22nd. sesbe2026.es/registration/
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EvoMG Program @evomg-bcn.bsky.social · 12/10/2025
Then, we Mireia Coscollà ( @pathogenomics.bsky.social ), from I2SysBio ( @i2sysbio.es ) talked about compatibility between hosts in bacterial infections.
Mireia Coscollà, CSIC, I2SysBio
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Paula @paururo.bsky.social · 10/10/2025
Back from #MycoVLC2025 after presenting our M. tuberculosis work. Huge thanks to Mireia for stellar mentorship. Proud of my @pathogenomics.bsky.social mycolegas for standout posters. Energized to turn ideas into results. #TB #TBResearch @i2sysbio.es
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Jim Shaw @jimshaw.bsky.social · 08/09/2025
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N
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Paula @paururo.bsky.social · 13/08/2025
From fàstic to fantastic population genetics with @pathogenomics.bsky.social :announcing Fstic a high-performance Rust CLI that computes N×N genetic distance matrices from VCFs or allele-frequency tables at scale. (fàstic=Valencian/Catalan for annoyance)Code: github.com/PathoGenOmic... @i2sysbio.es
github.com
GitHub - PathoGenOmics-Lab/fstic: Calculates pairwise distances between samples using alelle frequencies
Calculates pairwise distances between samples using alelle frequencies - PathoGenOmics-Lab/fstic
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European Virus Bioinformatics Center @evbc.bsky.social · 08/08/2025
🎉The EVBC Newsletter 95 - July/Aug 2025 - includes the newest EVBC publications, virus bioinformatics tools, members, upcoming events and more! 🔗 evbc.uni-jena.de/evbc-newslet...
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Paula @paururo.bsky.social · 01/08/2025
Our R package, mycolorsTB, has officially landed on CRAN! We created mycolorsTB to provide easy-to-use, standardized color palettes for visualizing Mycobacterium tuberculosis complex data. install.packages("mycolorsTB") @pathogenomics.bsky.social github.com/PathoGenOmic...
github.com
GitHub - PathoGenOmics-Lab/mycolorsTB: R Color package for Mycobacterium tuberculosis complex
R Color package for Mycobacterium tuberculosis complex - PathoGenOmics-Lab/mycolorsTB
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Maria Dzunkova @dzunkovam.bsky.social · 30/07/2025
🚨 Abstract submission is open for Pangenome2025 in Valencia! #microsky #bioinformatics 🧪🦠🧬🖥️ I’m one of the invited speakers. Looking forward to the talks by my @i2sysbio.es colleague Pilar Domingo-Calap @pilardomingoc.bsky.social, and many other great researchers. www.alocongress.com/pangenome2025 🧵
alocongress.com
PANGENOME2025
The biology of prokaryotic cells is directly dependent on the differential gene pools that characterize each cell or strain. This has been a fundamental aspect of epidemiology for delimiting outbreaks...
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Dr. Jessie Christiansen @aussiastronomer.bsky.social · 23/07/2025
'Who killed Hannibal'? meme from the Eric Andre show. In the top panel a man in a grey suit (labeled 'NATURE') kills a man sitting in a chair (labeled 'NULL RESULTS'). In the bottom panel the man in the grey suit turns to the camera and says "WHY DON'T SCIENTISTS PUBLISH NULL RESULTS?"
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 15/07/2025
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
pathoplexus.org
Pathoplexus | Pathoplexus July Update
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
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Pathoplexus @pathoplexus.org · 15/07/2025
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility! 📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update 1/9
Screenshot of the July Update News article on the Pathoplexus website
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PathoGenOmics Lab @pathogenomics.bsky.social · 14/07/2025
Spanish Society Evolutionary Biology meeting January 2026 in the botanical Garden ‪@uv.es‬ in Spain. Registration 200-350€. Preliminary program with confirmed keynote speakers: sesbe2026.es/programme/. Abstract submission until September 15th. sesbe2026.es/abstract/. Come to Valencia and join us!
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