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David Martínez Millán

@dmartmillan.bsky.social
38 followers 75 following 11 posts

I am an engineer in a biological world.

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Reposted by David Martínez Millán
IRB Barcelona @irbbarcelona.org · 24/09/2026
Today, on #WorldCancerResearchDay, we launch #Cancer Detective! Explore precision oncology and computational biology with this free online simulation for secondary students and the public, developed by the  @bbgalabb.bsky.social at #IRBBarcelona. More here: shorturl.at/MHn4A 🐡🧪
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Reposted by David Martínez Millán
Kurianlab @kurianlab.bsky.social · 01/09/2026
Drop your pipettes; we have an exciting meeting for you **The Spatial Logic of RNA in Health and Disease** When: 20.11.2026 Venue : Goethe University Frankfurt, Niederrad Campus, Haus 22, H22-1 Participation is free, but registration is required. Registration bit.ly/4gaXOBL 🫶Spread the word
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Reposted by David Martínez Millán
Mònica Sánchez-Guixé @guixe-m.bsky.social · 06/07/2026
1/17 We are very happy to announce our latest work about the genetic origin and evolution of one of the most aggressive pediatric tumors: “Variable latency between the founder genetic event and rhabdoid tumor expansion” www.biorxiv.org/content/10.6.... Follow the thread to know more 👇
biorxiv.org
Variable latency between the founder genetic event and rhabdoid tumor expansion
Rhabdoid tumors are very aggressive rare pediatric cancers with poor survival affecting very young children. They are characterized by the bi-allelic loss of SMARCB1 or SMARCA4, which is suspected to ...
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Reposted by David Martínez Millán
Kurianlab @kurianlab.bsky.social · 02/07/2026
Ribo-Tweezer by @mbarnalab.bsky.social, a modular platform to deplete proteins from mature ribosomes . www.cell.com/molecular-ce... @jakub-zeman.bsky.social and I wrote a Preview on why this helps to turn ribosome heterogeneity into an experimentally testable paradigm www.cell.com/molecular-ce...
cell.com
Tweezing apart ribosome heterogeneity
In this issue of Molecular Cell, Chen et al. introduce Ribo-Tweezer: a modular platform for conditionally and selectively depleting proteins from mature ribosomes, enabling direct tests of their ribos...
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Reposted by David Martínez Millán
IRB Barcelona @irbbarcelona.org · 23/04/2026
🌹 When science blooms for #SantJordi. Our April Image of the Month, “The Rose of Sant Jordi: Desmosomal Bonds of Life” by Berta Pi Benavent (#IRBBarcelona), reveals a microscopic rose formed by desmosomal junctions anchoring epithelial cells. Happy Sant Jordi! 🐉 📖
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Reposted by David Martínez Millán
Barcelona Biomedical Genomics Lab @bbglab.bsky.social · 21/04/2026
We are excited to announce the release of the new Cancer Genome Interpreter Platform developed within the EU-funded project @cgiclinics.bsky.social. It is adapted to the clinical context and reflect the latest advancements in precision oncology. bbglab.irbbarcelona.org/2026/04/new-...
bbglab.irbbarcelona.org
New Cancer Genome Interpreter Platform – BBGLab
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Reposted by David Martínez Millán
BSC-CNS @bsc-cns.bsky.social · 13/01/2026
✨𝗘𝘀𝗽𝗲𝗰𝘁𝗮𝗰𝘂𝗹𝗮𝗿 la nueva imagen de la capilla de Torre Girona! 🔨Tras meses de obras para retirar el falso techo, muy pronto reabriremos el acceso a las visitas. ⌛En breve os mostraremos➕. 💫 #WorkinProgress #StayTuned #ComingSoon #Próximamente
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Reposted by David Martínez Millán
Raquel Blanco @raquelbmi.bsky.social · 08/10/2025
Very happy to share that our paper on the influence of biological sex and smoking in the clonal landscape of the normal human bladder is out today in Nature. Kudos to all the authors and especially to @ferriol.bsky.social for coming along with me during this project's journey! 🧵Summary following ⬇️
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Reposted by David Martínez Millán
IRB Barcelona @irbbarcelona.org · 08/10/2025
🧪 Out in @nature.com: Smoking and biological sex shape healthy bladder tissue evolution, offering clues to #cancer risk. ✍️ #IRBBarcelona & University of Washington ➡️ bit.ly/42wcIN5 📌 DOI: 10.1038/s41586-025-09521-x #IRBScience #CancerResearch #BladderCancer @bbglab.bsky.social 🧵👇
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Reposted by David Martínez Millán
Barcelona Biomedical Genomics Lab @bbglab.bsky.social · 21/01/2025
As we are quite new in that network, we take the chance to share our research achievements of the last year. Here you can follow a short 🧵of our latest publications: 1️⃣ www.nature.com/articles/s41...
nature.com
Five latent factors underlie response to immunotherapy - Nature Genetics
Analysis of human tumor datasets shows that all features that appear significantly associated with immunotherapy response and survival may be collapsed into five latent factors: tumor mutation burden, T cell effective infiltration, TGF-β activity in the microenvironment, prior treatment and tumor proliferative potential.
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Reposted by David Martínez Millán
Alfonso Valencia @alfonsovalencia.bsky.social · 02/01/2025
En memoria de Joan Guinovart, por Francesc Posas, Raúl Mendez y Margarida Corominas en nombre del @irbbarcelona.org del Que fue fundador. DEP elpais.com/espana/catal...
elpais.com
Muere a los 77 años Joan Guinovart, fundador y exdirector del Institut de Recerca Biomèdica (IRB)
El científico y catedrático, Creu de Sant Jordi en 2014, fue una figura clave en el ámbito de la bioquímica
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
Thanks, Brendan! More than welcome to try it out!
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Reposted by David Martínez Millán
Stephen Turner @stephenturner.us · 03/12/2024
OpenVariant: a toolkit to parse and operate multiple input file formats academic.oup.com/bioinformatics/adv… 🧬🖥️🧪 github.com/bbglab/openvariant
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Reposted by David Martínez Millán
Javier Santoyo @jsantoyo.bsky.social · 04/12/2024
OpenVariant: a toolkit to parse and operate multiple input file formats. #Genomics #VariantFormats #InputFileFormats #Bioinformatics 🧬 🖥️ Github; github.com/bbglab/openv... academic.oup.com/bioinformati...
academic.oup.com
OpenVariant: a toolkit to parse and operate multiple input file formats
AbstractSummary. Advances in high-throughput DNA sequencing technologies and decreasing costs have fueled the identification of small genetic variants (suc
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
Thank you so much!!! ☺️
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
I would like to thank everyone involved in the development of the tool, Federica Brando, Miguel L. Grau, @guixe-m.bsky.social , Carlos López-Elorduy, Iker Reyes-Salazar, Jordi Deu-Pons, @nlbigas.bsky.social and Abel González-Pérez.
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
Overall, OpenVariant addresses a significant problem in the field by aggregating cohort-level data from multiple sources into a single harmonized result set. It replaces many of the tedious steps involved in curating data with a more robust and easier-to-document process.
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
OpenVariant is open-source software under BSD-3 Clause license, freely available for public use. It is designed in an easily extendable way to encourage collaboration in its development, available on GitHub: github.com/bbglab/openv...
github.com
GitHub - bbglab/openvariant: Read, parse and operate different multiple input file formats with OpenVariant
Read, parse and operate different multiple input file formats with OpenVariant - bbglab/openvariant
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
We integrated OpenVariant as the first step in the IntOGen pipeline (www.intogen.org), processing 257,898,749 somatic mutations across 33,218 tumor samples represented through 271 cohorts sequenced by different sources, and stored in different data formats.
IntOGen pipeline on Nextflow.
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
No existing tool matches OpenVariant's functionalities, setting it apart from other tools in the field. Its execution time was evaluated against similar Python-based tools using @brent-p.bsky.social benchmark (github.com/brentp/vcf-b...), ranking OpenVariant among the best peers.
github.com
GitHub - brentp/vcf-bench: evaluating vcf parsing libraries
evaluating vcf parsing libraries. Contribute to brentp/vcf-bench development by creating an account on GitHub.
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
OpenVariant is designed based on an annotation structure that serves as a core component in which describes how input files are parsed and how the output is represented. As well, a plugin system is incorporated to hone data transformation from the user.
Annotation structure of OpenVariant
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
We present OpenVariant, a Python package to encompass a wide range of functionalities to operate multiple variant file formats at once and manage the annotation of metadata relative to mutational datasets. You can consult the documentation at: openvariant.readthedocs.io
openvariant.readthedocs.io
OpenVariant documentation — OpenVariant
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
Despite efforts to homogenize data produced by variant callers and available processing tools, differences in the variants persist across projects. This variability hiders the integration of somatic mutations from different sources, key for large cancer genomics analyses.
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David Martínez Millán @dmartmillan.bsky.social · 12/12/2024
🎉 I'm thrilled to announce that OpenVariant is finally published! A comprehensive toolkit to facilitate reading, parsing and refinement of diverse input file formats in a customizable structure, all within a single process. @bbglab.bsky.social at @irbbarcelona.bsky.social doi.org/10.1093/bioi...
academic.oup.com
OpenVariant: a toolkit to parse and operate multiple input file formats
AbstractSummary. Advances in high-throughput DNA sequencing technologies and decreasing costs have fueled the identification of small genetic variants (suc
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