Lightnews — Scholar-powered news

Reposted by Robert Castelo

Wolfgang Huber @wkhuber.bsky.social · 9d

Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?

Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

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Robert Castelo @robertclab.bsky.social · 19d

#EuroBioC2025 is over and it has been a blast! Thanks to all participants that came to @prbb.org for contributing to make such an enjoyable event and special thanks to the support from our sponsors, the organizing institutions @upf.edu @isglobal.org and the European @bioconductor.bsky.social Society

Group picture with all participants at EuroBioC2025

Vince Carey, Bioconductor project lead, giving the opening keynote lecture.

Audience carefully listening to Vince Carey in the Auditorium.

Christophe Vanderaa giving a workshop on msqrob2, a robust modelling workflow for mass spectrometry-based proteomics

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · 20d

EuroBioC2025 is in full swing here in Barcelona!

Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!

#EuroBioC2025 #Bioconductor #OpenScience #Community

EuroBioC2025 group photo on PRBB terrace with sea in background.

EuroBioC2025 welcome in PRBB auditorium by host Robert Castelo, showing slides with conference sticker and sponsor logos.

EuroBioC2025 hexwall banner with the hexwall creator Kevin Rue-Albrecht standing beside it.

EuroBioC2025 carved wooden keyring, a gift for all participants, created by Annekathrin Nedwed.

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Robert Castelo @robertclab.bsky.social · Aug 23

Last chance to attend EuroBioC2025 and/or learn about bulk or single-cell RNA-seq in the preceding Bioconductor Carpentry Workshops. Register by August 28th! Do not miss this opportunity at the seafront of Barcelona!!

Bioconductor @bioconductor.bsky.social · Aug 21

⏳ One week left to register!
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.

🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org

#EuroBioC2025 #RStats

European Bioconductor Conference 2025 – EuroBioC2025

The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…

eurobioc2025.bioconductor.org

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Reposted by Robert Castelo

Maria Bernabeu @mariabernabeu.bsky.social · Jul 11

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...

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Reposted by Robert Castelo

Helena Lucia Crowell @helucro.bsky.social · Jun 27

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

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...

www.biorxiv.org

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Reposted by Robert Castelo

Eric Topol @erictopol.bsky.social · Jun 23

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

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Jun 20

🧬 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...

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.

blog.bioconductor.org

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Jun 20

📣 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

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…

forms.gle

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Robert Castelo @robertclab.bsky.social · Jun 17

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👇

Bioconductor @bioconductor.bsky.social · Jun 12

🎓 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

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.

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Jun 12

🎓 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

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Reposted by Robert Castelo

Sean Eddy @cryptogenomicon.bsky.social · May 22

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.

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Reposted by Robert Castelo

Leo Otsuki @leootsuki.bsky.social · May 21

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

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · May 21

📝 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

Bioconductor in Africa: Highlights from Our First In-Person Course – Bioconductor community blog

A blog for the Bioconductor community!

blog.bioconductor.org

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · May 19

📣 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

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.bioconductor.org

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Robert Castelo @robertclab.bsky.social · Apr 22

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.bsky.social · Apr 22

⏳ Time’s running out! Submit your abstract for #EuroBioC2025 by 24 April.
Join us this Sept in Barcelona to share your research, meet the #Bioconductor community & explore all things #Bioinformatics + #RStats.

👉 eurobioc2025.bioconductor.org/pages/submis...

Screenshot showing the EuroBioC2025 abstract submission deadline as April 24, 2025, and key conference dates for the Bioconductor community event in Barcelona, Spain.

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Apr 16

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

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.org

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Apr 1

🚀 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

Submission Guidelines

Essential details for submitting your abstract to GBCC 2025.

gbcc2025.netlify.app

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Reposted by Robert Castelo

BF Francis Ouellette @bffo.bsky.social · Apr 1

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

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...

arxiv.org

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Reposted by Robert Castelo

Henrik Bengtsson @henrikbengtsson.bsky.social · Apr 1

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

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Mar 31

🎉 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

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Reposted by Robert Castelo

Parc de Recerca Biomèdica de Barcelona @prbb.org · Mar 21

🔬@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 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.

tuit.cat

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Reposted by Robert Castelo

Richard Sever @richardsever.bsky.social · Mar 11

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

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

openrxiv.org

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Reposted by Robert Castelo

Bioconductor @bioconductor.bsky.social · Feb 28

🎨 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

buff.ly

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Reposted by Robert Castelo

Sean Davis @seandavi.bsky.social · Mar 2

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.

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