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Alejandro Reyes @areyesq.bsky.social · 18/08/2025

Our study about splicing modulating compounds is out! Molecules like Branaplam tweak exon inclusion. We describe how RNA structure and sequence dependencies shape exon selectivity. We're even able to reprogram the specificity by co-treatment with modified U1 snRNAs. www.biorxiv.org/content/10.1...

biorxiv.org

Specificity and exon target space of splicing modifying compounds

Modulation of splicing has become an established therapeutic strategy, with proven clinical applications and continued potential to target specific exons to influence gene expression. Recent advanceme...

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Reposted by Alejandro Reyes

Wolfgang Huber @wkhuber.bsky.social · 13/06/2025

I sometimes overhear conversations about tool choice in bioinformatics, where implementation language is stated as the primary criterion. Such thinking stands in the way of scientific quality and productivity. It is a form of self-harm. What should one really care about? (1/5)

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Alejandro Reyes @areyesq.bsky.social · 11/04/2025

This paper is a great example of the use of multiomic/multimodal data from patient cohorts for target identification. All evidence pointing towards ZNF469 as a regulator of collagen in liver fibrosis. Lots of potential here! insight.jci.org/articles/vie...

insight.jci.org

JCI Insight - The transcription factor ZNF469 regulates collagen production in liver fibrosis

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Reposted by Alejandro Reyes

Constantin Ahlmann-Eltze @const-ae.bsky.social · 12/02/2025

I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉 It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility. #rstats

$xp_compose_plots( xp_text("Welcome to \\texttt{exactplot} with \\LaTeX{} support", x = 1, y = 2, fontsize = xp$fontsize_large, fontface = "bold"), xp_text("A) Flipper length vs.\\ beak size", x = 1, y = 8), xp_plot(scatter_plot, x = 0, y = 12, width = 80, height = 40), xp_text("B) Beak sizes", x = 84, y = 8), xp_plot(beak_lengths, x = 82, y = 12, width = 58, height = 40), xp_text(density_formula, x = 99, y = 12, fontsize = xp$fontsize_small), width = 140, height = 52, keep_tex_file = FALSE, filename = "example.pdf" )$

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Reposted by Alejandro Reyes

Davide Risso @davi1893.bsky.social · 27/01/2025

Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!

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Reposted by Alejandro Reyes

Joselyn C. Chávez-Fuentes @josschavezf.bsky.social · 28/01/2025

All the videos from the #cdsb2024 workshop are available now on our @cdsbmexico.bsky.social YouTube channel. If you’re interested in learning about creating R packages go take a look! All the materials are available in Spanish youtube.com/@cdsb

youtube.com

Community of Bioinformatics Software Developers

YouTube channel for the Community of Bioinformatics Software Developers (CDSB in Spanish)

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Reposted by Alejandro Reyes

Rafael Irizarry @rafalab.bsky.social · 22/11/2024

New method for identifying spatially variable genes in spatial transcriptomics. We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity. with @PhillipNicol et al. www.biorxiv.org/content/10.1...

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