David Martínez Millán
@dmartmillan.bsky.social
I am an engineer in a biological world.
Pinned
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
academic.oup.com
🎉 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...
doi.org/10.1093/bioi...
Reposted by David Martínez Millán
✨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
🔨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
January 13, 2026 at 10:22 AM
✨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
🔨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
Reposted by David Martínez Millán
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 ⬇️
🧵Summary following ⬇️
🚨 New paper alert!
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Sex and smoking bias in the selection of somatic mutations in human bladder
www.nature.com/articles/s41...
by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)
Sex and smoking bias in the selection of somatic mutations in human bladder - Nature
Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.
www.nature.com
October 8, 2025 at 5:10 PM
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 ⬇️
🧵Summary following ⬇️
Reposted by David Martínez Millán
🧪 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
🧵👇
✍️ #IRBBarcelona & University of Washington
➡️ bit.ly/42wcIN5
📌 DOI: 10.1038/s41586-025-09521-x
#IRBScience #CancerResearch #BladderCancer @bbglab.bsky.social
🧵👇
October 8, 2025 at 3:01 PM
🧪 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
🧵👇
✍️ #IRBBarcelona & University of Washington
➡️ bit.ly/42wcIN5
📌 DOI: 10.1038/s41586-025-09521-x
#IRBScience #CancerResearch #BladderCancer @bbglab.bsky.social
🧵👇
Reposted by David Martínez Millán
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...
Here you can follow a short 🧵of our latest publications:
1️⃣
www.nature.com/articles/s41...
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.
www.nature.com
January 21, 2025 at 3:51 PM
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...
Here you can follow a short 🧵of our latest publications:
1️⃣
www.nature.com/articles/s41...
Reposted by David Martínez Millán
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...
DEP
elpais.com/espana/catal...
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
elpais.com
January 2, 2025 at 3:22 PM
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...
DEP
elpais.com/espana/catal...
Thanks, Brendan! More than welcome to try it out!
December 12, 2024 at 2:59 PM
Thanks, Brendan! More than welcome to try it out!
Reposted by David Martínez Millán
OpenVariant: a toolkit to parse and operate multiple input file formats https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae714/7914924 🧬🖥️🧪 https://github.com/bbglab/openvariant
December 3, 2024 at 9:00 PM
OpenVariant: a toolkit to parse and operate multiple input file formats https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae714/7914924 🧬🖥️🧪 https://github.com/bbglab/openvariant
Reposted by David Martínez Millán
OpenVariant: a toolkit to parse and operate multiple input file formats. #Genomics #VariantFormats #InputFileFormats #Bioinformatics 🧬 🖥️
Github; github.com/bbglab/openv...
academic.oup.com/bioinformati...
Github; github.com/bbglab/openv...
academic.oup.com/bioinformati...
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
academic.oup.com
December 4, 2024 at 10:49 PM
OpenVariant: a toolkit to parse and operate multiple input file formats. #Genomics #VariantFormats #InputFileFormats #Bioinformatics 🧬 🖥️
Github; github.com/bbglab/openv...
academic.oup.com/bioinformati...
Github; github.com/bbglab/openv...
academic.oup.com/bioinformati...
Thank you so much!!! ☺️
December 12, 2024 at 10:24 AM
Thank you so much!!! ☺️
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.
December 12, 2024 at 10:11 AM
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.
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.
December 12, 2024 at 10:11 AM
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.
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 - 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
github.com
December 12, 2024 at 10:11 AM
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...
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.
December 12, 2024 at 10:11 AM
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.
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 - brentp/vcf-bench: evaluating vcf parsing libraries
evaluating vcf parsing libraries. Contribute to brentp/vcf-bench development by creating an account on GitHub.
github.com
December 12, 2024 at 10:11 AM
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.
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.
December 12, 2024 at 10:11 AM
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.
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 documentation — OpenVariant
openvariant.readthedocs.io
December 12, 2024 at 10:11 AM
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
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.
December 12, 2024 at 10:11 AM
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.
🎉 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...
doi.org/10.1093/bioi...
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
academic.oup.com
December 12, 2024 at 10:11 AM
🎉 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...
doi.org/10.1093/bioi...