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Anna Esteve Codina

@annaesteveco.bsky.social

Functional Genomics Team Leader @CNAG 🧬💻🔎 omics, rare diseases, single-cell, long-reads, transposons.

13 Posts319 Follower745 Folgt
Tomàs Montserrat Ayuso@tmontsay.bsky.social · last yr.

🧵 1/ 🚨 New preprint alert! Excited to share my first PhD paper, supervised by @annaesteveco.bsky.social at @cnag-eu.bsky.social: 📄 A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses 📄 Preprint: www.biorxiv.org/content/10.1... 🧬 Read on for the dataset & code!

A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses

Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...

biorxiv.org

CNAG@cnag-eu.bsky.social · last yr.

📢New paper out in Frontiers in Immunology! 🔎A study by IRTA, IRTA-CReSA, @uab.cat and CNAG explores how heat-inactivated bacterium Rothia nasimurium boosts pig macrophage immunity — helping fight major pig viruses, such as PRRSV & ASFV www.frontiersin.org/journals/imm... #Sustainability #CNAG

Frontiers | Inactivated Rothia nasimurium promotes a persistent antiviral immune status in porcine alveolar macrophages

Globalization has increased the incidence of infectious diseases in livestock, further aggravated by the reduction of antibiotic usage. To minimize the resul...

frontiersin.org

Ming Tommy Tang@tommytang.bsky.social · last yr.

7/ In Tabula Muris and Tabula Sapiens, MALAT1 expression was tightly correlated with nuclear RNA content and intronic fractions. bmcgenomics.biomedcentral.com/articles/10...

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics

The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we will show that prominent initiatives such as the Human Cell Atlas [1], the Tabula Sapiens [2] and the Tabula Muris [3] contain a significant amount of contamination products (frequently affecting the whole organ) in their data portals due to suboptimal quality filtering. Our work addresses a critical gap by advocating for more stringent quality filtering, highlighting the imperative for a shift from existing standards, which currently lean towards greater permissiveness. We will show the importance of incorporating cell intronic fraction in quality control -or MALAT1 expression otherwise- showcasing its informative nature and potential to elevate cell atlas data reliability. In summary, here, we unveil the hidden intronic landscape of every tissue and highlight the importance of more rigo

bmcgenomics.biomedcentral.com

CNAG@cnag-eu.bsky.social · last yr.

🙌 Really excited about this recognition! Congratulations to our partners from @tum.de — Rebeka Luknárová, Vicente Yépez, and Julien Gagneur — together with our Functional Genomics Team Leader at CNAG, @annaesteveco.bsky.social, and Solve RD #research #eshg2025 #bestposter

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European Society of Human Genetics@eshg.bsky.social · last yr.

Best Poster in Clinical Research Rebeka Luknárová, Munich, Germany P16.006.A - "Harmonized framework for RNA-seq-based rare disease diagnostics in a pan-continental consortium - Solve-RD"

Hani Goodarzi@genophoria.bsky.social · last yr.

And this is happening today. @vevotherapeutics.bsky.social and @arcinstitute.org Institute are joining forces to release Tahoe100M and scBaseCamp (>200M AI-curated cells from Arc). Arc’s Virtual Cell Atlas launches as the largest single cell data repository! arcinstitute.org/news/news/ar...

Arc Virtual Cell Atlas launches, combining data from over 300 million cells | Arc Institute

Arc Institute today launched the Arc Virtual Cell Atlas, a growing resource for computation-ready single-cell measurements, starting with data from over 300 million cells. The initial release of the A...

arcinstitute.org

Anna Esteve Codina@annaesteveco.bsky.social · 2y ago

🧬Check our asms tool 🛠, fast alternative to detect allele-specific methylation & imprinting using long-reads without the need of phasing www.biorxiv.org/content/10.1...

ASMS: finding allele specific methylation in human genomes without phasing

Motivation: Allele-specific methylation (ASM) refers to differential DNA methylation patterns between two alleles at a given locus. This phenomenon is often driven by genetic variants, such as single ...

biorxiv.org

Lee Zamparo@lzamparo.bsky.social · 2y ago

Also filter on markers like MALAT1, cell intronic mapping reads cf. bmcgenomics.biomedcentral.com/articles/10....

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics

The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

bmcgenomics.biomedcentral.com

Ming Tommy Tang@tommytang.bsky.social · 2y ago

2/ Mistake 1: Ignoring QC metrics Low-quality cells can ruin your results. Always assess metrics like: • Mitochondrial gene percentage • Total UMI counts • Gene counts Filter cells systematically to avoid noise and bias.

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

Tomàs Montserrat Ayuso@tmontsay.bsky.social · 2y ago

scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified! 2/8

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Collectively as a community, we need to stop overhyping, dramatically reduce the fire-hose mentality of publishing & bean counting & be really honest about the strengths & limitations of our work. It is in our hands to elevate the integrity of the science we all do. 4/4