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PathoGenOmics Lab

@pathogenomics.bsky.social
340 followers 342 following 27 posts

PathoGenOmics research group at I2SysBio. Having fun learning how pathogens evolve.

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Ana Elena Pérez-Cobas @anaelenaperezcobas.bsky.social · 25/09/2026
New preprint on how drinking water treatment processes affect water-associated microbial communities, with a focus on opportunistic bacterial pathogens. Always great to work with the lab of @cbuch.bsky.social 😍. www.biorxiv.org/content/10.6...
biorxiv.org
Drinking water treatment drastically modifies multi-kingdom water communities, but clinically relevant opportunistic bacterial pathogens persist
Controlling pathogenic microorganisms during water treatment processes is a major public health concern. However, the impact of different water sources and treatment processes on the drinking water mi...
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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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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 · 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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European Society of Mycobacteriology @esmyco.bsky.social · 22/06/2026
🏅 Congratulations to Margo Diricks, winner of the Gertrud Meissner Award at #ESM2026! We're delighted to celebrate Margot's outstanding contribution to mycobacteriology, recognising the excellence and dedication she brings to our field. So well deserved 👏 #ESM2026 #ESMyco
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PathoGenOmics Lab @pathogenomics.bsky.social · 23/06/2026
Bouke's innovative thinking, rigorous pursuit of knowledge and colaborative way of conducting research make this recognition incredibly well-deserved. Thank you for your outstanding contributions to the field and your unique ability to inspire the mycobacterial community.
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Centro de Investigación Biomédica en Red (CIBER) @ciberisciii.bsky.social · 20/04/2026
Personal #CIBERBBN en la @upv.es desarrolla un biosensor rápido y de bajo coste para detectar #tuberculosis activa 🔎🔬 Más info en ➡️ www.upv.es/noticias-upv... @cipfvalencia.bsky.social
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CSIC @csic.es · 09/04/2026
🔬 El #CSIC e #ISGLOBAL firman un acuerdo de colaboración para reforzar la investigación en salud ➡️ Ambas entidades promoverán proyectos de investigación y asesoramiento, así como seminarios y jornadas especializadas 👉 tiny.cc/2ll1101
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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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PathoGenOmics Lab @pathogenomics.bsky.social · 02/04/2026
Un momento dulce compartiendo la mona de Pascua con los compañeros. Tradiciones que unen y alegran el día. @i2sysbio.es @paururo.bsky.social @ahmig.es
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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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Ana Conesa @anaconesa.bsky.social · 26/03/2026
The “curse of interdisciplinarity”: Fields like bioinformatics fall between the cracks in grant evaluation. 🧬 For bios: Too little mechanistic validation 🧮 For math: Not enough new theory 💻 For computing: “Just” applied computing Interdisciplinarity is essential, but evaluation hasn’t caught up.
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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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Ⓙⓐⓥⓘⓔⓡ🇵🇸🍉 Ⓑⓤⓒⓔⓣⓐ🇺🇦🇪🇺 @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
@i2sysbio.es 10th Aniversary Celebration, science and fun!
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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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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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Ⓙⓐⓥⓘⓔⓡ🇵🇸🍉 Ⓑⓤⓒⓔⓣⓐ🇺🇦🇪🇺 @javierbuceta.bsky.social · 13/10/2025
🚨JOB ALERT Dr. Buceta at @i2sysbio.es welcome applications for 36-month postdocs on: 👉 Mechanical markers of tissue dysfunction due to ageing – digital twins & machine learning Details here: fgcsic.es/convocatoria... 📩 Contact javier.buceta@csic.es to shape your proposal! @epimechfc.bsky.social
fgcsic.es
ComFuturo Fourth Edition: ComFuturo iAGE Call - FGCSIC
The Fundación General CSIC (FGCSIC) launches the fourth edition of its ComFuturo programme: ComFuturo iAGE, a postdoctoral initiative co-financed by the Marie Skłodowska-Curie Actions COFUND scheme of...
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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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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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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 · 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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I2SysBio @i2sysbio.es · 18/07/2025
El #I2SysBio (@csic.es - @uv.es) ha lanzado una serie de vídeos sobre los diferentes grupos de investigación en este centro. El nuevo video es sobre el grupo Orquestación transcripcional del metabolismo vegetal de Tomas Matús @jtmatus.bsky.social 🎥🌐 youtu.be/43V4MOtAf4k?... 🧪🧬🖥️ 🌾🌱🍇 #plantscience
youtu.be
Interview of Tomás Matus, PI of the Transcriptional Orchestration of plant metabolism group
YouTube video by Institute for Integrative Systems Biology I2SysBio
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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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Miguel 💻🧬 @ahmig.es · 30/06/2025
VIPERA v1.2.1 is here!! 🐍🐍🐍 Our workflow for SARS-CoV-2 intra-patient evolution analysis now fully supports Snakemake 8/9 (with dedicated CI tests), BIONJ trees, richer reports, added config parameters, modular Snakefiles and more! 🧪👉 github.com/PathoGenOmics-Lab/VIPERA
github.com
GitHub - PathoGenOmics-Lab/VIPERA: A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis - PathoGenOmics-Lab/VIPERA
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PathoGenOmics Lab @pathogenomics.bsky.social · 27/05/2025
‪@ahmig.es‬ presented the poster "Expanding the scope of evolution reporting and analysis: from intra patient dynamics to outbreaks" at MCEB 2025 in Granada thanks to the funding @bcbhubcsic.bsky.social and ‪@ageinves.bsky.social‬.
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Miguel 💻🧬 @ahmig.es · 20/05/2025
Just back from MCEB 2025 in Granada! I presented our year-long work expanding VIPERA🐍 to help us better track pathogen evolution, here at @pathogenomics.bsky.social - @i2sysbio.bsky.social. I learned so much and returned full of ideas! Thanks to @bcbhubcsic.bsky.social for funding my attendance! 🧪
A photo of a group of people with the Alhambra in the back
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I2SysBio @i2sysbio.es · 10/05/2025
Today, I2SysBio researchers were busy with #scienceoutreach activities at #Expociencia. Here are photos of the Pathogenomics lab @pathogenomics.bsky.social explaning in a playful way how our immune system works 🧬🖥🦠🧫🧪
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Paula @paururo.bsky.social · 10/05/2025
Nuestro 4to año superado con creces, #expociencia2025 @pathogenomics.bsky.social @i2sysbio.bsky.social
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PathoGenOmics Lab @pathogenomics.bsky.social · 04/04/2025
🔬 Beca JAE Intro en Bioinformática Desarrolla HaploScope, una pipeline híbrida (Illumina + Nanopore/PacBio) para reconstrucción de haplotipos bacterianos y virales en @i2sysbio.bsky.social Código: JAEINT25_EX_1603 🗓️ Solicita hasta 2 mayo 🔗 rb.gy/c6c8p2 #Bioinformática #Nextflow #JAEIntro #CSIC #TFM
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UCL-TB @ucltb.bsky.social · 24/03/2025
Today: Online link for World TB Day symposium 9-5 GMT: lshtm.zoom.us/j/92519123639. Programme information at ucl.ac.uk/tb/events/wo...
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PathoGenOmics Lab @pathogenomics.bsky.social · 24/03/2025
🧬 Estudiamos la genética tras la compatibilidad patógeno-hospedador en tuberculosis (laboratorios BSL2/BSL3). Dale play al vídeo: ¡que lo contagioso sea la ciencia! #EndTB #DíaMundialTuberculosis, Desde @csic.es, @ptisg.bsky.social, @i2sysbio.bsky.social y @paururo.bsky.social
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PathoGenOmics Lab @pathogenomics.bsky.social · 24/03/2025
🦠 ¿Amigos o enemigos? La infección por tuberculosis depende de la compatibilidad patógeno-hospedador. Si encajan bien, la bacteria prospera; si no, fracasa. ¡Cuestión de genética! #EndTB #DíaMundialTuberculosis
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PathoGenOmics Lab @pathogenomics.bsky.social · 24/03/2025
🦠 Friends or foes? Tuberculosis infection depends on host-pathogen compatibility. If they're genetically compatible, bacteria thrive; if not, they fail. It’s all about matching genes! #EndTB #WorldTBDay
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PathoGenOmics Lab @pathogenomics.bsky.social · 24/03/2025
🔬 On World TB Day, we show you how we study tuberculosis genomes safely in BSL2/BSL3 labs to understand and stop its spread. Hit play—spread science, not TB! #EndTB #WorldTBDay @i2sysbio.bsky.social & @paururo.bsky.social,
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PathoGenOmics Lab @pathogenomics.bsky.social · 03/03/2025
Visit to I2SysBio by ESTALMAT, the programme of mathematical talent promotion www.i2sysbio.es/communicatio...
i2sysbio.es
i2sysbio -
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I2SysBio @i2sysbio.es · 23/02/2025
#ESTALMAT is a project of the Spanish Royal Academy of Sciences @raciencias.bsky.social for detection and encouragement of mathematical talent in 12-13 years old students. They visited our research institite to learn about #DNA 🧪💻🧬 #outreach @javierbuceta.bsky.social @pathogenomics.bsky.social
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PathoGenOmics Lab @pathogenomics.bsky.social · 22/11/2024
Check out our tools for genomic analisis at github.com/PathoGenOmic... • get_MNV: Reclassifies SNVs as MNVs and predicts amino acid changes. • snpick: SNP extraction for large alignments. • VIPERA: Workflow for SARS-CoV-2 evolution. • mycolorsTB: R color palette for M. tuberculosis.
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PathoGenOmics Lab @pathogenomics.bsky.social · 21/11/2024
I2SysBio joins World Antimicrobial Resistance Awareness Week www.uv.es/institute-in...
uv.es
I2SysBio joins World Antimicrobial Resistance Awareness Week
Antimicrobial resistance (AMR) occurs when microorganisms become unresponsive to antimicrobial agents, making it difficult to treat infections and increasing health risks. Several lines of research at...
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Maria Dzunkova @dzunkovam.bsky.social · 20/11/2024
New bioinformatic tool SNPick for detection of SNPs developed at @i2sysbio.bsky.social @pathogenomics.bsky.social 🦠🔬🧫🧬🖥
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