Robert Castelo

Pre-print alert 🚨: We have developed 2D and 3D stable iPSC endothelial-differentiation models through dox inducible ETS expression. We demonstrate endothelial identity and used these models for studying malaria pathogenesis research. www.biorxiv.org/content/10.1...

Tracing colorectal malignancy transformation from cell to tissue scale The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last—

www.biorxiv.org/content/10.1...

@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social

This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Bioconductor Training partners with Physalia Courses – Bioconductor community blog A new collaboration to expand access to bioinformatics training through co-branded courses, instructor support, and inclusive access.

🧬 New from the Bioconductor Training Committee:

We’re teaming up with @physaliacourses.bsky.social‬ for co-branded training in bioinformatics and computational biology.

Details here 👉 blog.bioconductor.org/posts/2025-0...

EuroBioC2025 late-breaking poster abstract submission Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

📣 Late-breaking poster call for #EuroBioC2025 is now open!

Submit by July 11 to present your work in Barcelona this September.
🔗 forms.gle/ewTGdKzB2xyE...
📅 Notifications by July 15

#Bioconductor #Bioinformatics

Two workshops on the analysis of bulk and single-cell RNA-seq with @bioconductor.bsky.social at @upf.edu Campus Mar. Do not miss the opportunity to learn with Carpentry-certified instructors👇

Flyer for EuroBioC2025 Carpentry Workshops in Barcelona, Sept 15–16, 2025. Includes two in-person workshops on bulk and single-cell RNA-seq analysis. Hosted at Universitat Pompeu Fabra. Features logos, QR code, and registration link: eurobioc2025.bioconductor.org.

🎓 Sharpen your RNA-seq skills at EuroBioC2025 Workshops!

📍 Barcelona | Bulk & Single-cell RNA-seq
📅 Sept 15–16 | Hands-on training
🎟️ Limited spots. Register now: eurobioc2025.bioconductor.org

#Bioinformatics #EuroBioC2025

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Delighted that our work on positional memory is now published. We asked how axolotl cells 'know' which part of the limb to regenerate after injury.
www.nature.com/articles/s41...
A joy to work with super team Sarah Plattner, Yuka Sugiura, Francisco Falcon and Elly Tanaka.
🧵1/14

Bioconductor in Africa: Highlights from Our First In-Person Course – Bioconductor community blog A blog for the Bioconductor community!

📝 New Bioconductor blog post!

We’ve just published a recap of our first in-person course in Africa, held in Nairobi this March 🇰🇪
Read about the highlights, feedback, and what’s next:
👉 blog.bioconductor.org/posts/2025-0...

#Bioinformatics #BioconductorAfrica #OpenScience #RStats #CapacityBuilding

registration – EuroBioC2025 The budget EuroBioC2025 is conceived to break even after the conference. As a result, the organization of the EuroBioC2025 is unable to offer individual refunds.

📣 EuroBioC2025 Registration is Open! 🎉

📍 Barcelona, 17–19 Sept 2025

Join us for keynotes, talks, workshops & more on open-source bioinformatics & Bioconductor.
🔗 eurobioc2025.bioconductor.org/pages/regist...

#EuroBioC2025 #Bioinformatics

Participate in the Bioconductor community by sharing your work in a meeting designed to maximize interactivity and productivity at the seafront of Barcelona! 👩‍💻🏖️🧬 #EuroBiocC2025

Bioconductor - Bioconductor 3.21 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…

Bioconductor 3.21 is released!

A huge thank you to all developers and community members for your contributions.
Explore what’s new in the full release announcement:
bioconductor.org/news/bioc_3_...

#Bioconductor #RStats

Submission Guidelines Essential details for submitting your abstract to GBCC 2025.

🚀 GBCC2025 Update! 🚀

Abstract deadline extended to April 8, 2025! 🎉

For ~10 min TALKS: Register first (no deposit needed now). Submission guidelines: gbcc2025.netlify.app/abstracts/su...

For ~1.5 hr TRAINING DEMOS: Fill out this form: forms.gle/i34Ag8SHMtBA...

Join us! 🌟

#GBCC2025

Learning and teaching biological data science in the Bioconductor community Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and b...

From @csoneson.bsky.social and colleagues in #arXiv | Learning and teaching biological data science in the #Bioconductor community | #Bioinformatics #Education #Rstats #OpenScience #OpenEducationalResources #OpenAccess #OpenData #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
arxiv.org/abs/2410.01351

The 'future' package hexlogo

Liberating the future!

Major progress to #Futureverse - new, exciting, frequently-requested features. RC 1 of 'future' package is now available as:

install.packages("future", repos = c("https://futureverse.r-universe.dev", "https://cloud.r-project.org'))

Please give it a try🙏

#rstats #parallel

EuroBioC2025 hex sticker design featuring the Sagrada Família in the centre, vibrant mosaic patterns inspired by Park Güell at the bottom, and other Barcelona landmarks like the crane and towers. The Bioconductor logo replaces the "i" in "BioC", and "bioconductor.org" is written across the top left. The overall shape is a yellow-bordered hexagon.

🎉 Announcing the EuroBioC2025 Sticker Winner!

🏆 Chaima Hkimi’s design features the Sagrada Família, Park Güell colours, and a nod to Bioconductor in the text. Pick up the sticker at #EuroBioC2025!

#Bioconductor #Bioinformatics #RStats #StickerContest

Big data to predict response to immunotherapy - El·lipse The study from Hospital del Mar Research Institute and MELIS-UPF within the programme GRIB has focused on bladder cancer.

🔬@maralbalab.bsky.social @jupererabel.bsky.social @oncobellmunt.bsky.social @robertclab.bsky.social team have developed a machine learning algorithm to see how bladder cancer patients respond to immunotherapy.
@grib-barcelona.bsky.social @researchmar.bsky.social @upf.edu
More👇

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

🎨 Reminder that EuroBioC2025 Sticker Contest is still open! Deadline Mar 10. Don't miss out on the chance to have your design featured at the conference and win free registration ✨
Submit buff.ly/42JiCLN

Abstracts are open for submission too!

#EuroBioC2025 #RStats #Bioinformatics #StickerContest

Given the recent and ongoing service interruptions in PubMed, National Library of Medicine, NIH Reporter, etc., I put together a status page that covers a few key resources and some NIH institute pages.
stats.uptimerobot.com/Zrqh8AhvKn
Let me know what other sites you'd like to see added.

HT to Sean Davis for creating a status page for NIH websites: stats.uptimerobot.com/Zrqh8AhvKn - simultaneous worth sharing and sad.

Our CITE-seq paper analysing 45 BAL samples from (un)treated kids with CF and contrls. BAL is tricky, 44 celltypes dominated by macrophages. Trailblazing analysis led by @jovmaksimovic.bsky.social @melanieneeland.bsky.social @shivanthans.bsky.social and collaborators www.medrxiv.org/content/10.1...

Bioconductor Carpentry: Celebrating Two Years of Global Training – Bioconductor community blog A blog for the Bioconductor community!

📝 New Bioconductor blog post on Bioconductor Carpentry!

We're celebrating two years of global training with Bioconductor Carpentry. Read about our progress and achievements so far. Check it out here: buff.ly/spm32wW

#Bioconductor #Carpentries #Bioinformatics #RStats #OpenScience

L’anàlisi massiva de dades permet avançar en la comprensió de com funciona la immunoteràpia Identifiquen marcadors predictors de la resposta al tractament amb immunoteràpia gràcies a un estudi amb dades de més de 700 pacients procedents de sis cohorts diferents, que publica 'Nature Communica...

#Recerca

L’anàlisi massiva de dades permet avançar en la comprensió de com funciona la immunoteràpia i buscar respostes per esbrinar per què els actuals tractaments amb aquesta tècnica només funcionen el 20% en els pacients amb càncer de bufeta avançat.

European Bioconductor Conference 2025 EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…

📣 EuroBioC2025: Abstract Submissions Open!

Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.

➡️ Submit https://buff.ly/3EN9w6P

#EuroBioC2025 #Bioinformatics #RStats #DataScience

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

🎨 EuroBioC2025 Sticker Contest!
Unleash your creativity for the European Bioconductor Conference in Barcelona! The winning sticker will be featured on our website and handed out at the event.
🗓 Deadline: Mar 10, 2025
🏆 Prize: Free reg to EuroBioC2025 for winning design!
Abstract call coming soon!

Come work at the European Molecular Biology Laboratory in the beautiful science & university city Heidelberg as a Research Software Engineer on R/Bioconductor tools for biological data science and AI !

embl.wd103.myworkdayjobs.com/EMBL/job/Hei...

A giraffe standing in the Nairobi National Park with the city skyline in the background. Above the image, the Bioconductor logo is displayed, followed by bold black text that reads: 'Apply Now for the Bioconductor Kenya 2025 Course!

🌍 Bioconductor Course, Kenya 2025 🎓

Join us for our first in-person Bioconductor course in Kenya, happening March 24–28, 2025, in Nairobi! This free course is for bioinformatics beginners and builds on our global Carpentry program.

🔗 Apply: https://buff.ly/40CJL02

#Bioinformatics #RStats #RNAseq