Artür Manukyan

A scenic mountain landscape with steep rocky peaks and green forested slopes under a partly cloudy sky. Overlaid text reads: “CSAMA 2026 – Biological Data Science, 22nd Edition, Bressanone-Brixen, Italy, 24–29 May 2026.”

📢 CSAMA 2026: Biological Data Science Summer School registrations are open for its 22nd edition, taking place in:

📍 Bressanone–Brixen, Italy
🗓 24–29 May 2026

🔗 Learn more and register: csama2026.bioconductor.eu

#CSAMA2026 #Bioconductor

🚀 We're looking for people to join Malva! 🧬 @danilexn.bsky.social

Malva is the first search engine for single-cell genomics: we process massive amounts of sequencing data to enable ultrafast analysis of millions of cells.

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Research Software Engineer - Spatial-omics The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework.

We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community.

🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

Registration now open for CSAMA!
📜 csama2026.bioconductor.eu

Highly recommend for learning data science with a scenery, plus a fantastic crowd of students and faculty alike!

📸 from the traditional mid-week hike during last year’s edition.

View from the hotel room

Poster session 2024, with Valentina Boeva, Constantin Ahlmann-Eltze and others

Wednesday afternoon hike incl. swim in the mountain river

Another view from the hotel room

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps.

ascona2026.sciencesconf.org

Thanks to the authors for sharing all components of this beautiful mouse embryo spatial transcriptomics data from cell gene counts to per-molecule coordinates: www.ahajournals.org/doi/full/10....

So I vibe coded an app to explore the 3D subcellular transcript organization: jef.works/CellCarto-Mo...

A hex sticker with a text that reads Hello Data Science with green, yellow and pink scatterplot points in the background. There is a web address www.hellodata.science

📖 Big news! We just released the first five chapters of our new book, Hello Data Science. It is a fully open-access resource written for beginners. Please help us spread the word! A few points about the book are below 👇

🔗 www.hellodata.science

#rstats #datascience #tidyverse

Figure illustrating some content of the Python course for biology students at UniBonn

“Analysis of Biological Data with Python” started today for biology bachelor students 🧬🐍

Want to learn Python for data analysis?
Slides are freely available:
github.com/bpucker/teac...

#Python #DataAnalysis #Biology #OpenScience #BigData #Bioinformatics #DataScience @puckerlab.bsky.social

Screenshot of the course website

CSAMA 2026 - Biological Data Science Summer School
Bressanone-Brixen, South Tyrol / Italy
24-29 May 2026
csama2026.bioconductor.eu

Statistical & computational methods for single cell and spatial omics, with lectures and hands-on exercises in R/Bioconductor.

Software Developer - Interoperability for Single-Cell and Spatial Omics Methods

We are looking for a Software Developer to work on R/Python interoperability for single-cell and spatial omics methods.

🔗 Apply here: jobs.dkfz.de/en/jobs/1683...

Come Take A Portrait With Me | a short film YouTube video by Prof. Jean Fan

Every year, I give my lab (+myself) a "mini-sabbatical" to pursue independent learning.

This year, I'm learning to use AI tools. So I made a short film to reflect on life/death + create art in an era where it can feel like AI has usurped the value of self-expression: youtu.be/YJjmKRlmI1Q

Amazing opportunity, we thank #Helmholtz ScienceServe Initiative for helping us recruit talented people to develop FAIR Software for spatial omics.

You will also have the chance to join hackathons and workshop we organize with developers across @scverse.bsky.social and @bioconductor.bsky.social.

Join us to the last #GESTALT seminar the year!

Free for all GESTALT member. If you are interested in anything #spatialbiology come be part of our growing community

GESTALT Seminar Series globalspatial.org/seminar-seri...

December 19 10am EST @ioavlachos.bsky.social @lgmartelotto.bsky.social

All scverse attendees

scverse conference organizers

First session

scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.

Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).

It’s been a joy working with you @estellayixingdong.bsky.social!

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

Switzerland is joining Horizon Europe!

We are uniting two research powerhouses.

For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more.

Today is a good day for science, and for our EU-Switzerland partnership.

Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem - Nature Methods Giotto Suite provides a comprehensive, flexible and scalable platform for technology-agnostic spatial omics analysis using R.

After years of hard work we're thrilled to announce our new Nature Methods paper:
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.

Another milestone for everyone working with Giotto!

www.nature.com/articles/s41...

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

#EuroBioC2025 just started at @prbb.org in beautiful Barcelona. Looking forward to meeting friends and collaborators to discuss new generation of data structures and file formats for spatial/single-cell biology.

Very honored to receive the 2025 ISCB Innovator Award at #ISMBECCB2025 and present our lab’s journey—from mapping cells to modeling their future.

Thanks to my amazing team and collaborators—this is our award! 🙌

📽️ Keynote: Atlases, AI & virtual cells
📝 doi.org/10.1093/bioi...

Exploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025 – Bioconductor community blog A blog for the Bioconductor community!

🚀 Reminder: Bioconductor Developer Forum is this Monday!

🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats #RustLang #OpenSource

Spatiotemporal dynamics of tumor microenvironment remodeling During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...

We’re happy to share our new preprint form
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...

🧬🖥️🧪 Interested in single-cell-informed cell-type #deconvolution? Have a look at our enhanced benchmarking study and #omnideconv ecosystem!

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

🔬Hands-on workshops kick off the Berlin Summer Meeting 2025 #BSM2025! Attendees dove into real-time sequence search, nucleic acid analysis of environmental samples, spatial transcriptomics for infectious diseases, AI-assisted genomics, and a behind-the-scenes tour of single-cell omics 🧬🧑‍🔬
#mdcBerlin

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?
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What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM:
- OMERO-vitessce
- IO-FAST initiative
- @nfdi4bioimage.bsky.social Data Stewardship
Talks, Workshops & Poster Session 2 up ahead today!🔬

False positives in study of memory-related gene expression - Nature Nature - False positives in study of memory-related gene expression

As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...