@VastDB

VastDB is a repository of quantitative profiles of alternative splicing events and GE data across different tissues and species. Developed at @CRGenomica

 Barcelona, Spain
vastdb.crg.eu
Joined July 2017
  • Tweets173
  • Following424
  • Followers307
17Media
We have released a new batch of functional annotations (v11): 600 entries from previous publications investigating the function of AS events. This makes a total of 3637 entries directly from publications, 397 from CRISPR screens and 1511 from experimentally validated ELMs.
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Cotyledon opening during seedling deetiolation is determined by ABA-mediated splicing regulation embopress.org/doi/full/10.10…
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This sounds like a dream!! Barcelona and Berlin with amazing scientists and great people. Having worked with both groups I would highly highly (yes twice :) recommend it.
Manuel Irimia@mirimiam21 Jan 2025
The job call is officially open. If you're interested, please apply through this link ASAP! 😃 mdc-berlin.de/career/jobs/po… Please RT! 🙏
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🐟Our new paper "Phenotypic impact of individual conserved neuronal microexons and their master regulators in zebrafish" is out in @eLife🐟 A nearly 10-year tour-de-force by Laura Lopez-Blanch and many others in the lab @CRGenomica & @UPFbiomed elifesciences.org/reviewed-p… Thread👇
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🚨🚨🚨 If you're a bioinformatician who loves: 🧬 #SingleCell #LongReadSequencing & #AlternativeSplicing 🚀 Collaborating and travelling Apply to work with us at the spectacular @BIMSB_MDC in Berlin + @UPFbiomed-@CRGenomica in Barcelona. Qs:transdevolab.com Please RT!🙏
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📢 We're hiring! We are looking for two excellent early career candidates to join #MELISupf as Junior Group Leaders in Computational Biology, and in Quantitative Biology More information and application links: upf.edu/web/biomed/job-offer… Deadline: 28 Jan 2025 #JobOffer
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Finally out nature.com/articles/s41586-0… the study (led by @xsalvatella1 & @RMendezLab) with the biophysical explanation for the profound effect of the microexon of CPEB4 as cause of autism, that we previously reported back in 2018 @ParrasAlbert @GeschwindLab @mirimiam @hervas_millan
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Who would have thought that an actual sequence of a #microexon (GCAAGGACATATGGGCGAAGGAGA from CPEB4) would be in the headline of an article in @elpais_espana! Congrats to the Mendez, @xsalvatella1 and @JJLucasLab labs for this amazing work! english.elpais.com/science-t…

The 24 DNA letters linked to autism: GCAAGGACATATGGGCGAAGGAGA

A team of Spanish scientists has discovered the mechanism that could explain a high percentage of autism spectrum disorders

english.elpais.com
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We’re recruiting a PhD student to use comparative omics to investigate why some viruses can efficiently infect both human and mosquito cells, but lead to different infection outcomes. Fully funded position by @EvoMG_Bcn at UPF-CRG with the @ViroUPF lab. crg.eu/en/content/training-p…
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Circular RNAs trigger nonsense-mediated mRNA decay: cell.com/molecular-cell/full…

Circular RNAs trigger nonsense-mediated mRNA decay

Boo and Shin et al. uncover that the EJC deposited onto circRNAs after back-splicing is spatially located near the 3′ UTR of mRNA through circRNA-mRNA interaction. The EJC on circRNA triggers NMD of...

cell.com
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Come to the dark side! Join the #darkproteome team to work on plant functional annotation within our OSCARS @HorizonEU project FAIRFUN4Biodiversity. Great project, great advisor, great city and great team! 👇👇 @CsicLifehub
Aureliano Bombarely@aubombarely9 Dec 2024
Are you interested in genome annotations? Do you want to work in Valencia, Spain. We have an open position at @IBMCP. Please contact me if you are interested or forward to who may you think that could be interested.
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Thrilled to share this new work resulting from a great collaboration of my lab with the labs of @imaesomar and @veronica_hinman, started with the dear José Luis Gómez-Skarmeta many years ago. Take a look! biorxiv.org/content/10.1101/…

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover...

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two groups...

biorxiv.org
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Big🧬news this week: we have launched the first Joint Program on Evolutionary Medical Genomics. Spearheaded by @mirimiam, Barcelona researchers will study and exploit the vast genomic diversity of life on Earth to enhance precision medicine. english.elpais.com/science-t…

The dawn of a new medicine: Researchers use the theory of evolution to fight cancer

The world’s first joint research program in evolutionary medical genomics has been launched in Barcelona, under the direction of biologist Manuel Irimia

english.elpais.com
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Great collaboration with @lrdesviat and @AndresenBrage to find ways to modulate inclusion of a microexon (CPEB4 exon 4) involved in autism! @sarapico7 @mirimiam @GeschwindLab @ParrasAlbert @RMendezLab @SENC_ @CBM_CSIC_UAM @CIBER_ISCIII
Lourdes Ruiz Desviat@lrdesviat30 Oct 2024
Interested in neuronal #microexons? #splicing? #antisense? #autism? Check out our new preprint👇👇 @CBM_CSIC_UAM @JJLucasLab @AndresenBrage @UAM_Madrid biorxiv.org/content/10.1101/…

OLIGONUCLEOTIDES TARGETING THE 3’ SPLICE SITE DOWNSTREAM OF A MICROEXON AS AN INNOVATIVE THERAPY...

Background Microexons are highly conserved and mostly neuronal-specific 3-27 nucleotide exons, enriched in genes linked to autism spectrum disorders (ASD). We have previously shown decreased inclus...

biorxiv.org
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🎉Excited to announce that our paper on the blueprint of the human spliceosome is now out in @ScienceMagazine ! A decade of work with Juan Valcárcel and the incredible team at @CRGenomica to uncover the intricate roles of this essential RNA machinery.science.org/doi/10.1126/scie…

Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome

The spliceosome is the complex molecular machinery that sequentially assembles on eukaryotic messenger RNA precursors to remove introns (pre-mRNA splicing), a physiologically regulated process...

science.org
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Out now: Using highly sensitive luminescence splicing reporters, we screened ~95,000 small-molecule compounds for modulators of neuronal microexons, a class of highly conserved alternative splicing misregulated in #autism & #NeuroendocrineCancer. 1/4 go.nature.com/3Wh6kp2

High-throughput sensitive screening of small molecule modulators of microexon alternative splicing...

Nature Communications - Here the authors perform a high-throughput screen to identify compounds that stimulate or repress the splicing of neuronal microexons. One of these compounds rescues the...

nature.com
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Published today! We found that cancer cells adapting to drug treatments don't simply switch from a sensitive to resistant state; instead there's a ‘resistance continuum’ of resistant phenotypes with epigenetically reprogrammed states. 🧵⬇️ nature.com/articles/s41586-0… @Gustavo_SFranca
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🚨 We're excited to announce our Inaugural Symposium on Evolutionary Medical Genomics (EvoMG) at @the_prbb in Barcelona, November 20-22 2024. 👇Our great speakers and topics! Further info: evomedgenomics.com/events/in… @CRGenomica @UPFbiomed @IBE_Barcelona
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Very excited to announce the inaugural symposium of our @EvoMG_Bcn Joint Program on Evolutionary Medical Genomics! Join us in Barcelona on the 20th-22nd of November (no registration free). Great speakers and cool and diverse topics! @CRGenomica @UPFbiomed @IBE_Barcelona
EvoMG Program@EvoMG_Bcn17 Jun 2024
🚨 We're excited to announce our Inaugural Symposium on Evolutionary Medical Genomics (EvoMG) at @the_prbb in Barcelona, November 20-22 2024. 👇Our great speakers and topics! Further info: evomedgenomics.com/events/in… @CRGenomica @UPFbiomed @IBE_Barcelona
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The peer-reviewed version of our study on the evolution of tissue-specific expression across vertebrates and insects is finally published in @NatureEcoEvo ! @FedeMantica @CRGenomica @UPFbiomed nature.com/articles/s41559-0…
Manuel Irimia@mirimiam16 Nov 2022
🚨Exciting pre-print from the lab!👉"Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects". Deep comparative #transcriptomics across #bilateria by @FedeMantica et al @CRGenomica. 👀biorxiv.org/content/10.1101/…. Summary👇

Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and...

Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled a vast RNA-seq dataset covering twenty bilate...

biorxiv.org
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Job alert! We offer two positions (Team leader & Bioinformatics developer) to work on the Biodiversity Cell Atlas database: unified pipelines, data curation, and cross-species integration. With @irenepapatheodo @RodericGuigo @ExpressionAtlas @emblebi 🗓️Apr-10 🔗Details below
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