Alejandro Reyes

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...

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...

18.08.2025 07:46 — 👍 1    🔁 0    💬 0    📌 0

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)

13.06.2025 17:23 — 👍 18    🔁 6    💬 1    📌 0

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

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...

11.04.2025 11:39 — 👍 1    🔁 0    💬 0    📌 0

Plot produced with exactplot

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" )

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

12.02.2025 11:40 — 👍 103    🔁 23    💬 6    📌 0

CSAMA 2025 flyer

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!

27.01.2025 08:16 — 👍 28    🔁 15    💬 1    📌 3

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

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

28.01.2025 17:21 — 👍 3    🔁 4    💬 0    📌 0

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...

22.11.2024 20:04 — 👍 41    🔁 11    💬 0    📌 0

Bioconductor - Bioconductor 3.20 Released The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and dat...

Bioconductor 3.20 is released! 🎉🌟
Thanks to all developers and community members for contributing to the project! 🙌
👉 See the full release announcement: bioconductor.org/news/bioc_3_...

#Bioconductor #DataScience #Bioinformatics #OpenSource

30.10.2024 22:04 — 👍 22    🔁 13    💬 0    📌 1

Hello bluesky!

14.11.2024 06:44 — 👍 2    🔁 0    💬 0    📌 0