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David Martínez Millán

@dmartmillan.bsky.social

29 followers 51 following 11 posts

I am an engineer in a biological world.

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David Martínez Millán @dmartmillan.bsky.social · Dec 12

🎉 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...

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

3 11 22

Reposted by David Martínez Millán

Raquel Blanco @raquelbmi.bsky.social · 1h

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 ⬇️

Nuria Lopez-Bigas @nlbigas.bsky.social · 2h

🚨 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 - 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

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Reposted by David Martínez Millán

IRB Barcelona @irbbarcelona.org · 3h

🧪 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 · Jan 21

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...

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

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Reposted by David Martínez Millán

Alfonso Valencia @alfonsovalencia.bsky.social · Jan 2

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...

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

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David Martínez Millán @dmartmillan.bsky.social · Dec 12

Thanks, Brendan! More than welcome to try it out!

Reposted by David Martínez Millán

Stephen Turner @stephenturner.us · Dec 3

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

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Reposted by David Martínez Millán

Javier Santoyo @jsantoyo.bsky.social · Dec 4

OpenVariant: a toolkit to parse and operate multiple input file formats. #Genomics #VariantFormats #InputFileFormats #Bioinformatics 🧬 🖥️
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

3 4

David Martínez Millán @dmartmillan.bsky.social · Dec 12

Thank you so much!!! ☺️

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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.

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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.

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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

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David Martínez Millán @dmartmillan.bsky.social · Dec 12

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.

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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

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David Martínez Millán @dmartmillan.bsky.social · Dec 12

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.

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David Martínez Millán @dmartmillan.bsky.social · Dec 12

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

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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.

David Martínez Millán @dmartmillan.bsky.social · Dec 12

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

3 11 22