Sign in

Melé Lab

@melelab.bsky.social
159 followers 248 following 26 posts

We are the Melé Lab, the Transcriptomics and Functional Genomics Lab (TFGL) at the Barcelona Supercomputing Center (BSC). Account by lab members

PostsRepliesMedia
Reposted by Melé Lab
Guigó Lab @guigolab.bsky.social · 05/12/2025
Thrilled to share! 🧬🌍 Our 800M+ long-read RNA-seq dataset from 8 diverse populations reveals big gaps in gene annotations for non-European transcripts. Let’s build global inclusive annotations. @bsc-cns.bsky.social @crg.eu @melelab.bsky.social www.nature.com/articles/s41...
nature.com
Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation - Nature Communications
Current human gene annotations are predominantly based on individuals of European ancestry. Here, the authors use long-read RNA sequencing across diverse human populations to reveal ancestry-specific ...
062
Reposted by Melé Lab
elDiario.es @eldiario.es · 03/12/2025
El mapa de los genes humanos tiene un ‘agujero negro’: “Hemos dejado fuera a gran parte de la humanidad”
eldiario.es
El mapa de los genes humanos tiene un ‘agujero negro’: “Hemos dejado fuera a gran parte de la humanidad”
Investigadores españoles han encontrado más de cuatrocientos posibles nuevos genes que todavía no figuran en los catálogos oficiales porque se construyeron principalmente con datos de individuos de as...
04420
Reposted by Melé Lab
Centre de Regulació Genòmica (CRG) @crg.eu · 03/12/2025
Human gene maps contain major blind spots that leaves out a vast majority of the world's biological diversity, according to a new study led by the CRG's @rodericguigo.bsky.social with @bsc-cns.bsky.social. The researchers uncovered tens of thousands of new transcripts and entirely new genes.
nature.com
Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation - Nature Communications
Current human gene annotations are predominantly based on individuals of European ancestry. Here, the authors use long-read RNA sequencing across diverse human populations to reveal ancestry-specific ...
0179
Melé Lab @melelab.bsky.social · 04/12/2025
📣 Yesterday our study uncovering the ancestry bias in gene annotations was finally published in @natcomms.nature.com! www.nature.com/articles/s41... If you work in human genetics or transcriptomics, do not miss our tweetorial!👇 @guigolab.bsky.social @bsc-cns.bsky.social @crg.eu
nature.com
Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation - Nature Communications
Current human gene annotations are predominantly based on individuals of European ancestry. Here, the authors use long-read RNA sequencing across diverse human populations to reveal ancestry-specific ...
1128
Reposted by Melé Lab
Marta Melé @martamele.bsky.social · 04/12/2025
the @melelab.bsky.social is hiring postdoctoral researchers !! come and work with us in sunny Barcelona!! auspire.eu/research-tea...
auspire.eu
BSC-PF2
Computational Transcriptomics Barcelona Supercomputing Center | RMIT University Research fields: Transcriptomics; Genomics; Human Genetics; Machine Learning; Single-cell Transcriptomics; Long-read T...
021
Melé Lab @melelab.bsky.social · 03/12/2025
📣 We are hiring postdoctoral researchers!! Come and work with our wonderful team in sunny Barcelona. 👇 auspire.eu/research-tea...
auspire.eu
BSC-PF2
Computational Transcriptomics Barcelona Supercomputing Center | RMIT University Research fields: Transcriptomics; Genomics; Human Genetics; Machine Learning; Single-cell Transcriptomics; Long-read T...
031
Melé Lab @melelab.bsky.social · 23/05/2025
Our study reveals that menopause is a biological inflection point that initiates divergent aging trajectories across reproductive tissues. Aging is asynchronous — and that’s a roadmap to smarter, more targeted interventions. 🔗 www.biorxiv.org/content/10.1... 8/8🧵
biorxiv.org
000
Melé Lab @melelab.bsky.social · 23/05/2025
Age-associated genes across uterus, myometrium & ovary overlap with genes from large GWAS or WES studies for: - Menopause timing - Age at Menarche - Pelvic organ prolapse The uterus isn’t just a passive player—it might hold the keys to predicting and preventing post-menopausal disorders. 7/8🧵
100
Melé Lab @melelab.bsky.social · 23/05/2025
💡 Bulk RNA-seq isn’t tissue-specific. But paired with histology, it can be. We uncovered tissue-specific aging pathways: 🔻 Myometrium: ↓ ECM & muscle genes 🔺 Vaginal epithelium: ↓ epithelial +↑ immune genes 🔻 Ovarian cortex: ↓ angiogenesis Organs don’t age as one. 6/8 🧵
100
Melé Lab @melelab.bsky.social · 23/05/2025
The vaginal epithelium showed a menopause-timed crash in thickness. This is more than known thinning: we saw extensive histological remodeling and sharp trajectory shifts at ~51 yrs. ❗Histology beats gene expression at capturing this transition. 5/8🧵
100
Melé Lab @melelab.bsky.social · 23/05/2025
We zoomed in further. Segmenting tissues with a vision transformer revealed that the myometrium (uterine muscle) is the most age-sensitive tissue. Its histology transforms —collagen builds up, structure changes— with aging. 4/8🧵
100
Melé Lab @melelab.bsky.social · 23/05/2025
Using CNNs, we trained aging classifiers per organ. Result? 📈 Ovaries & vagina show gradual aging ⚡️ Uterus shows abrupt transition around age 51—right at menopause! Transcriptomic data mirrored this: gene expression shifts sharply in the uterus but not in the ovary or vagina. 3/8🧵
110
Melé Lab @melelab.bsky.social · 23/05/2025
We combined: 🖼️ 1,112 histological images 🧬 659 RNA-seq samples 🧠 Deep learning + vision transformers 📊 Multi-omics integration All from 304 women aged 20-70 (GTEx dataset). Across 7 organs: uterus, ovary, vagina, breast, ectocervix, fallopian tubes, and endocervix. 2/8🧵
110
Melé Lab @melelab.bsky.social · 23/05/2025
📢Menopause affects half the population — yet it's been one of the most overlooked areas in aging research. We found that aging in the female reproductive system unfolds in unexpected, organ-specific ways. 🔗 www.biorxiv.org/content/10.1... 1/8🧵
193
Reposted by Melé Lab
Guigó Lab @guigolab.bsky.social · 14/05/2025
Our lab had dual presence at #BoG25 @cshlmeetings.bsky.social! 🧬 Silvia González-López spoke on chromatin dynamics & transcriptional regulation. 🌍 @fairlie.bsky.social presented ancestry-aware gene annotations — a @guigolab.bsky.social × @melelab.bsky.social collab: www.biorxiv.org/content/10.1...
073
Reposted by Melé Lab
Winona Oliveros @oliveroswinona.bsky.social · 05/05/2025
Excited to share our new preprint: The impact of sex, age, and genetic ancestry on DNA methylation across tissues. Briefly, we explored how sex, age, and genetic ancestry shape DNA methylation across tissues and individuals. Want to know a bit more? Follow this “bluetorial”! doi.org/10.1101/2025...
biorxiv.org
The impact of sex, age, and genetic ancestry on DNA methylation across tissues
Background: Understanding the consequences of individual DNA methylation variation is crucial for the study of human biology and disease. However, the collective impact of demographic traits on DNA me...
1115
Melé Lab @melelab.bsky.social · 20/03/2025
We want to thank everyone 👩‍🔬 involved in this work: @pclavell.bsky.social, @fairlie.bsky.social, @scarbonells.bsky.social, @fdegalez.bsky.social, Carme Arnan, @oliveroswinona.bsky.social‬, @rodericguigo.bsky.social, @martamele.bsky.social as well as the institutions: @bsc-cns.bsky.social, @crg.eu ✨
181
Melé Lab @melelab.bsky.social · 20/03/2025
🟢Overall, our work suggests that to overcome gene annotation ancestry biases we require: 🥇long-read sequencing of transcriptomes from diverse human populations 🥈the development of transcript discovery tools for the pangenome @humanpangenome.bsky.social to bypass reference biases Preprint ⬇️⬇️⬇️ 13
biorxiv.org
Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation
Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic...
151
Melé Lab @melelab.bsky.social · 20/03/2025
🔴We saw that 🧬👤 full personal genome assemblies: 1️⃣ enable the discovery of novel transcripts that can not be found with GRCh38 2️⃣ contain regions not found in GRCh38 that harbor potentially novel genes (albeit at very low densities compared to the rest of the genome) 12
120
Melé Lab @melelab.bsky.social · 20/03/2025
🔴This shows that the genome assembly of choice can potentially hide 🙈 transcripts due to genetic diversity. To further explore the impact of *ALL* genetic diversity on transcript discovery, we did similar analyses comparing GRCh38 with 🧬👤 full personal genome assemblies ⬇️ 11
120
Melé Lab @melelab.bsky.social · 20/03/2025
💥We find that personalized-GRCh38s enable the discovery of >3% more novel transcripts than using GRCh38. 🌍More importantly, this increase is uneven between populations, with African individuals benefiting most (LWK, YRI). 10
130
Melé Lab @melelab.bsky.social · 20/03/2025
💡Our hypothesis was that genetic variants differing from the reference genome sequence could interfere in the transcript discovery process. So we compared transcript discovery when using GRCh38 and modified (👤personalized) versions of GRCh38 containing each sample's SNPs ⬇️ 9
120
Melé Lab @melelab.bsky.social · 20/03/2025
So far, we’ve shown that reference gene annotations are European biased ✅ ❓However, would it be enough to sequence RNA from genetically diverse cohorts to build truly representative gene annotations? So we searched 🔎 for potential biases caused by using reference genome assemblies (GRCh38) ⬇️ 8
120
Melé Lab @melelab.bsky.social · 20/03/2025
This is precisely what happens when linking 🧬 genetic variation to 📈 transcript expression ⬇️ 🔴We show that a population-diverse gene annotation increases the discovery of associations between SNPs and transcript expression, especially in non-European populations 🌍 7
130
Melé Lab @melelab.bsky.social · 20/03/2025
❓Why is this important? Gene annotations enable the interpretation of the human genome sequence by providing context on how the molecular actors (RNA/proteins) play a role to produce different phenotypes. ➡️If gene annotations are biased, so too might be our interpretation of the genome 6
120
Melé Lab @melelab.bsky.social · 20/03/2025
➡️This is a direct consequence of the systematic underrepresentation of non-European samples 🌍 throughout the -omics fields. 🔴In other words, the data used to build current gene annotations is not representative of global human genetic diversity. 5
120
Melé Lab @melelab.bsky.social · 20/03/2025
In all samples, we found many transcripts that have never been seen before (~40k total) 👀 ❗Interestingly, we find more novel transcripts in non-European ancestry samples than in European ones. 🔴This means that gene annotations systematically miss more transcripts from non-European individuals. 4
120
Melé Lab @melelab.bsky.social · 20/03/2025
Together with @guigolab.bsky.social 🙌 we deeply sequenced RNA of 43 cell lines (LCL) 🧫 from 8 human populations 👥with distinct genetic ancestries 🌍 using ONT (@nanoporetech.com) to capture full-length mRNA and lncRNA molecules. 3
120
Melé Lab @melelab.bsky.social · 20/03/2025
⚠️Most transcriptomic data comes from European-descent individuals; implying that data used to build gene annotations does too. Furthermore, there are no long-read transcriptomic datasets that sample 🌍 diverse human populations ❓We wondered if this could bias reference gene annotations 2
120
Melé Lab @melelab.bsky.social · 20/03/2025
Do you work in 💫human genetics💫? Have you ever worried about what’s inside your gene annotation GTF⁉️ WELL, YOU SHOULD! 😱 Especially when studying a genetically diverse 🌍 cohort! 🔴We discover that gene annotations are European-biased 👉 impacting downstream analyses! Don't miss this thread🧵⬇️ 1/13
biorxiv.org
Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation
Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic...
33113
Melé Lab @melelab.bsky.social · 07/02/2025
Really interesting talk by our talented PhD student @mariasopenarios.bsky.social at #WomensHealth2025 conference!
030
Melé Lab @melelab.bsky.social · 04/02/2025
AMAZING JOB by our postdoc Oleksandra presenting her results at #WomensHealth2025
030