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Stefano Mangiola @stemang.bsky.social · 01/10/2026

Only one more week to apply for the #BiocAsia Travel Scholarship, to join us at #BiocAsia2026 and #ABACBS2026. Don't miss the opportunity! Please share with your peers who might be interested. 🙏 @bioconductor.bsky.social @abacbs.bsky.social

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Stefano Mangiola @stemang.bsky.social · 03/09/2026

Great news! @saigenci.bsky.social, through its Computational System Oncology Program, is a main supporter of #BiocAsia2026! With their support, we will be able to provide travel scholarships; news soon! @bioconductor.bsky.social @abacbs.bsky.social

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Stefano Mangiola @stemang.bsky.social · 17/08/2026

You still have time to submit your workshop!

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Stefano Mangiola @stemang.bsky.social · 09/06/2026

🤞 We hope these results motivate the community to rethink narrow-task benchmarking and narrow-task applications, and to pivot towards open-ended biological inference in zero-shot settings. @saigenci.bsky.social

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Stefano Mangiola @stemang.bsky.social · 09/06/2026

We call this pattern #finetuning_masking: supervised adaptation on narrow tasks can compensate for weaker pretraining and mask representational quality. This matters because many current benchmarks may not be measuring the properties that cell foundation models are intended to provide.

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Stefano Mangiola @stemang.bsky.social · 09/06/2026

📢 📃 Finetuning masking challenges narrow-task evaluation of cell foundation models shorturl.at/dcz3l We tested foundation model architectures across extreme reductions in pretraining scale. We found that standard narrow tasks were insensitive to pretraining scale, up tp 128-fold reduction!

biorxiv.org

Finetuning masking challenges narrow-task evaluation of cell foundation models

Single-cell foundation models are large, self-supervised deep learning networks pretrained on millions of cellular transcriptomes. These models promise to deliver cell representations that are transfe...

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Stefano Mangiola @stemang.bsky.social · 30/05/2026

First #tidyomics hackathon at #EuroBioC2026 in Turku! tidyomics.github.io/tidyomicsBlo... Join us at Euro Bioc (eurobioc2026.bioconductor.org) for a dive into our ecosystem, where you can learn about it and, hands-on, improve and extend it. Plz share! 🙏 @bioconductor.bsky.social

tidyomics.github.io

EuroBioC2026 Tidyomics Hackathon – tidyomicsBlog

An invitation to join the Tidyomics community hackathon at EuroBioC2026 in Turku, Finland.

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Stefano Mangiola @stemang.bsky.social · 13/05/2026

Well done! It was a great way to start. 🚀

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Stefano Mangiola @stemang.bsky.social · 08/05/2026

New #tidyomics blog post! 🎉 #tidySummarizedExperiment greatly simplifies your omics workflows, giving tidyverse capabilities. We have improved its performance 30x on large datasets with tens of thousands of samples! tidyomics.github.io/tidyomicsBlo... Plz share! @mpibiochem.bsky.social

tidyomics.github.io

Speeding up tidySummarizedExperiment through query optimisation and the plyxp backend – tidyomicsBlog

Performance optimisation of tidySummarizedExperiment and related benchmark.

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Michael Love @mikelove.bsky.social · 03/05/2026

Another Bioc 3.23 update: new dplyr function support for a number of tidyomics packages @stemang.bsky.social Adding slice_sample, *_head, *_tail, *_min, and *_max to: - tidySingleCellExperiment - tidySeurat - plyranges The dplyr descriptions for these: dplyr.tidyverse.org/reference/sl...

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Stefano Mangiola @stemang.bsky.social · 24/04/2026

This work started as an internal resource and has now become public with helpful APIs. It was 3+ years in the making, with a massive Thanks to Mengyuan Shen and the whole Team! We hope you find it useful 🙏 @saigenci.bsky.social @wehi-research.bsky.social @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 24/04/2026

#cellNexus is out! -> "Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data" - QC layers - Consensus cell annotation layers - Pseudobulk aggregation of the whole human atlas - R/Python APIs cellNexus.org Preprint: www.biorxiv.org/content/10.6...

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Stefano Mangiola @stemang.bsky.social · 06/01/2026

Juan Henao has published a post on the #tidyomics blog introducing *omicslog*, which tracks and stores data manipulation directly from tidy R (and base R) workflows, in the data object itself! Inspired by `tidylog`. Feedback welcome! @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 06/01/2026

Reproducibility is key to science. In computational biology, we routinely manipulate high-dimensional data (spatial, single-cell, bulk) through filtering, normalisation and transformation. Capturing those steps clearly improves reproducibility and transparency. tidyomics.github.io/tidyomicsBlo...

tidyomics.github.io

Omicslog – tidyomicsBlog

Providing logging capabilities for SummarizedExperiment objects.

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Stefano Mangiola @stemang.bsky.social · 18/12/2025

A great last #tidyomics meeting of the year, looking forward to more of these in 2026! @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 15/12/2025

The last #tidyomics meeting of the year is in 2 days. Everyone welcome! - 16 Dec, 3:30 pm (EST; New York) - 16 Dec, 9:30 pm (CET; Berlin) - 17 Dec, 7:30 am (AEDT; Melbourne) We will chat about plans for next year. Zoom link: shorturl.at/Epbbc @mikelove.bsky.social @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 07/12/2025

It's official! The #tidyomics blog is up! 🚀 Here, the introductory post tidyomics.github.io/tidyomicsBlo... This blog aims to publish not only news about our community but also anything related to tidy interfaces, opinions, events, and more. Plz share! 🙏 @bioconductor.bsky.social #rstats

tidyomics.github.io

The Tidyomics Ecosystem – tidyomicsBlog

An introduction to the tidyomics ecosystem, including principles, core packages, publications, and community resources for tidy omic analysis.

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Stefano Mangiola @stemang.bsky.social · 29/11/2025

Amazing event! It is good to see the Adelaide community coming together! #ABACBS2025

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Stefano Mangiola @stemang.bsky.social · 27/11/2025

Well done, William Hutchison! For an amazing talk about prostate cancer tumour microenvironment at #ABACBS2025 Also, well done on a great workshop on #tidyomics and his #tidySpatialExperiment @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 27/11/2025

The Euro Bioc 2026 in Turku is official!

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Stefano Mangiola @stemang.bsky.social · 27/11/2025

The first conference for our Lab! Amazing environment at #ABACBS2025! 🙏 Congrats, Mengyuan, Chen and Galen, for the great posters, and Haroon for being a finalist with his talk on the democratisation of foundational models. 🚀

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Stefano Mangiola @stemang.bsky.social · 20/11/2025

Registrations for the @abacbs.bsky.social and @bioconductor.bsky.social #BiocAsia workshops close TOMORROW at 5PM! Don't miss the opportunity to learn the new trends in computational biology!

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Stefano Mangiola @stemang.bsky.social · 14/10/2025

ABACBS/BioC Asia 2025 Workshops are coming! @ Adelaide 27-28 November. Join us in November for two days of deep-dive sessions on scalable bioinformatics, spatial omics, AI-driven genomics, and more blackochrelabs.au/abacbs2025_w... #Bioinformatics @abacbs.bsky.social @bioconductor.bsky.social

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Physalia-courses@ONLINE @physaliacourses.bsky.social · 07/10/2025

🚀 Curious about #SpatialOmics? Want to master spatial omics data analysis using #Rstats and @bioconductor.bsky.social ? 🔥 Registrations are now OPEN for the 3rd edition of our hands-on course with @stemang.bsky.social ! 📅 Save the dates: 18–20 May 2026 www.physalia-courses.org/courses-work...

physalia-courses.org

spatial Omics in R/Bioconductor

18-20 May 2026 To foster international participation, this course will be held online

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Stefano Mangiola @stemang.bsky.social · 09/09/2025

Join us for another tidyomics meeting tomorrow! We will chat about several news - tidyprint - tidybulk V2 - omicslog - and more!

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Stefano Mangiola @stemang.bsky.social · 26/08/2025

Join us for an interesting discussion on using AI with foundational models in biology!

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Stefano Mangiola @stemang.bsky.social · 06/08/2025

Join #AI and #Immunology! 📢 Fully funded #PhD @saigenci.bsky.social: develop AI to chart immune diversity across the population, in #cancer. CV, transcript, and a one-page statement by 30 August 2025 → www.linkedin.com/feed/update/... #PhDOpportunity #MachineLearning #SingleCell

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Stefano Mangiola @stemang.bsky.social · 30/07/2025

Two days to apply for a BiocAsia workshop! - Did you develop a package you want to showcase? - You want to share an analysis workflow for your favourite data type? This is your time to share this with the community! Submission -> biocasia2025.bioconductor.org @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 14/07/2025

BiocAsia will collaborate with ABACBS for the 2025 conference (Adelaide) to bring you a full day of workshops! Have you thought about teaching a workshop about your or someone else's package or a workflow? This is the time! Submit your proposal by the 1st of August.

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Reposted by Stefano Mangiola

Bioconductor @bioconductor.bsky.social · 01/07/2025

Big thanks to everyone who made #GBCC2025 a fantastic week of science, collaboration, and community! Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬 @galaxyproject.bsky.social @bioconductor.bsky.social

Vince Carey opening GBCC2025 with a slide highlighting Bioconductor’s technical and community advances.

Charlotte Soneson delivering her keynote titled “From classes to community: how Bioconductor has advanced my research.”

Slide showing GBCC2025 sponsors and supporters - CZI, Limagrain, GalaxyWorks, Bristol Myers Squibb, R Consortium, Gigascience, ELIXIR, NHGRI

Large group photo of GBCC2025 attendees outdoors at Cold Spring Harbor Laboratory, smiling and gathered on the steps.

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Stefano Mangiola @stemang.bsky.social · 02/07/2025

What a cover! Looking forward to sharing our work with you!

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Stefano Mangiola @stemang.bsky.social · 23/05/2025

Today, I had a blast at the @mig-unimelb.bsky.social MIG symposium, showcasing our use of mixed linear models at scale and #AI tools to study #singlecell cancer immunology. Thanks Heejung, Kim-Anh and all the MIG! events.unimelb.edu.au/MIG/event/45...

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Stefano Mangiola @stemang.bsky.social · 23/05/2025

Thanks @physaliacourses.bsky.social, it was a blast! And the great active audience made it so enjoyable!

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Stefano Mangiola @stemang.bsky.social · 19/05/2025

Amazing crew! Tomorrow, we will show the Physalia crew how to use #tidyomics to manipulate and analyse spatial data!

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Stefano Mangiola @stemang.bsky.social · 27/03/2025

In few hours we have the second #tidyomics meeting! where we will talk about workshops, communication and education and more. Thursday March 27 with a Europe friendly meeting time (12:00 CET) Join the @bioconductor.bsky.social slack channel to know more #tidiness_in_bioc channel Join us

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Stefano Mangiola @stemang.bsky.social · 17/03/2025

We encourage diverse participation regardless of background, gender, or beliefs. The meetings are friendly and open! You don't need to participate actively; you can join simply to stay updated on #tidyomics development. We welcome you!

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Stefano Mangiola @stemang.bsky.social · 17/03/2025

Great first #tidyomics meeting, covering 3 continents! 🌍 We discussed data representation with #tidyprint. Stay tuned for the next one to discuss workshop delivery, education and more! Join the slack channel #tidiness_in_bioc community-bioc.slack.com/archives/CEQ... @bioconductor.bsky.social

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Physalia-courses@ONLINE @physaliacourses.bsky.social · 14/03/2025

🚀 Interested Spatial Omics with R/Bioconductor? 🧨Do you want to learn how to analyse these data in R with the #tidyverse? Join us in May for this course with @stemang.bsky.social & @lgmartelotto.bsky.social 🔗 www.physalia-courses.org/courses-work... #SpatialOmics #Bioinformatics #RStats

physalia-courses.org

spatial Omics in R/Bioconductor

19-21 May 2025 To foster international participation, this course will be held online

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Stefano Mangiola @stemang.bsky.social · 11/03/2025

Tomorrow, we will have our first #tidyomics meeting for 2025! We will discuss how to centralise tidy display for biological data -> github.com/tidyomics/ti... Wednesday 12th of March - 4PM NY - 9PM London - 8AM (Thursday) Melbourne details -> community-bioc.slack.com/archives/CEQ... Pls share!

github.com

GitHub - tidyomics/tidyprint

Contribute to tidyomics/tidyprint development by creating an account on GitHub.

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Bioconductor @bioconductor.bsky.social · 04/03/2025

📅 Tidyomics next meeting is Wed, Mar 12 at 4PM NY / 9PM London / 8AM (Thurs) Melbourne. They'll discuss enhancing SummarizedExperiment display & seek feedback on tidyprint package. See Bioconductor Slack #tidiness-in-bioc channel or events calendar for more info: buff.ly/rdhL3jL #Tidyomics #RStats

buff.ly

Bioconductor - Events

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…

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Stefano Mangiola @stemang.bsky.social · 11/02/2025

📢 An exciting #Postdoc position opened in our laboratory for a junior #Bioinformatician! Developing #Bioinformatic and #AI tools to advance precision oncology using the available #singlecell / #spatial data universe. careers.adelaide.edu.au/cw/en/job/51... Pls share! 🙏 #postdocposition

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Stefano Mangiola @stemang.bsky.social · 22/01/2025

The Python implementation is in Beta, and we welcome feedback!

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Stefano Mangiola @stemang.bsky.social · 22/01/2025

We (Chen Zhan!) just launched #sccomp for #Python! Testing for differences in cell-type proportion in #singlecell #spatial data? #sccomp is a mixed-effect Bayesian model - Use sum-constrained BetaBinomial distribution - Outliers detect. - Remove unwanted effects github.com/MangiolaLabo...

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