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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

📢 📃 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 · 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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Reposted by Stefano Mangiola

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

#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

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 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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Reposted by Stefano Mangiola

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

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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Reposted by Stefano Mangiola

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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Reposted by Stefano Mangiola

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

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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Stefano Mangiola @stemang.bsky.social · 08/01/2025

Would you open your paper to a modular open-collaboration model? It was game-changing for #tidyomics If you love #crowdResearch and #CommunityBuilding have your say on the #crowdToPaper model guidelines Comment on the shared doc: docs.google.com/document/d/1... Please share 🙏

docs.google.com

CTP-1.0

CTP guidelines 1.0 Definition and Operational Details of the Crowd-to-Paper Model This document, called “CTP-1.0”, is a template that includes the guiding principles of projects based on the crowd-to-...

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Stefano Mangiola @stemang.bsky.social · 23/12/2024

📢🙏 Dear Research Community! A call 👇 to contribute to defining the #guidelines of the #CrowdToPaper research model, as tested for tidyomics doi.org/10.1038/s415... We welcome feedback from all research fields through comments on docs.google.com/document/d/1... 🙏 Plz Share! ❤️Thank you!

docs.google.com

CTP-1.0

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Reposted by Stefano Mangiola

Physalia-courses@ONLINE @physaliacourses.bsky.social · 21/11/2024

🚀 Ready to learn about Spatial Omics? Learn from @stemang.bsky.social & @lgmartelotto.bsky.social in this hands-on R/Bioconductor course! Master imaging vs. sequencing methods, experimental design & tidy data principles for cutting-edge spatial omics analysis www.physalia-courses.org/courses-work...

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Stefano Mangiola @stemang.bsky.social · 15/11/2024

📢💻🧪 2 #PhD #Scholarships available @SAiGENCI: 1) Hybrid wet-dry: #multiomics to predict neoadjuvant response in #cancer 2) #Bioinformatics, comp-bio: large-scale #singlecell modelling and infrastructure 🔗https://researchers.adelaide.edu.au/profile/stefano.mangiola#my-research Please share! 🙏

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Stefano Mangiola @stemang.bsky.social · 11/11/2024

Amazing #BiocAsia2024 event! Thanks to all who participated! Looking forward to next year! @bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · 28/10/2024

Love it! Great way to use #tidyHeatmap, with good taste for style! :)

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Stefano Mangiola @stemang.bsky.social · 21/08/2024

Hello Community! Don't miss the #tidyomics meeting in one week! All welcome! plz share 🙏 We'll present #HPCell, a pipe-to-HPC 📦 for popular single-cell and spatial tools. + we'll discuss ecosystem and community! 8.30AM (New York) 1.30PM (London) 10.30PM (Sydney)

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Stefano Mangiola @stemang.bsky.social · 05/08/2024

Great 2nd #tidyomics meeting! Next week @carroll_jono presents #DFplyr, and we'll chat community and ecosystem! This will be US, AU friendly (we will rotate) - 9AM Sydney (wed) - 4PM San Franc. US (tue) - 7PM NY (tue) unimelb.zoom.us/j/8833403951... Pswrd:542990 @mikelove.bsky.social

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Stefano Mangiola @stemang.bsky.social · 29/07/2024

Don't miss the #tidyomics meeting tomorrow! (Tuesday, details below) @JacquesSerizay will present #tidyCoverage + we'll discuss how to improve the ecosystem and community! 8.30AM US (New York) 1.30PM EU (London) 10.30PM AU (Sydney) www.bioconductor.org/packages/rel...

bioconductor.org

tidyCoverage

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization ...

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Stefano Mangiola @stemang.bsky.social · 17/07/2024

🧹🧬💻Exciting first #tidyomics @bioconductor meeting! We talked about community, development plans, and things to improve. Join us for the next one in two weeks. Details soon!

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Stefano Mangiola @stemang.bsky.social · 02/07/2024

Join us Tuesday 16th of JULY for a #tidyomics Zoom celebration and open discussion about #future plans! 8.30AM US time (New York, EDT) 1.30PM Europe time (London, BST) 10.30PM Australia time (Sydney, AEST) Zoom: unimelb.zoom.us/j/8833403951... Password: 542990 #everyone welcome!

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Stefano Mangiola @stemang.bsky.social · 19/06/2024

📢🎉 Our lab is recruiting x3! #Postdoc & #PhD Join from 🌏 inc AU, EU, US! Great scientific environment and a very attractive salary. 1. #AI for #singlecell biology 2. #Multiomics, immuno diagnosis (sc+spatial+metab.) 3. #tidyomics + #HPC Plz share! 🙏 mangiolalaboratory.github.io/Mangiola-Lab...

mangiolalaboratory.github.io

Mangiola-Lab-Open-Positions

This repository lists the current open positions in the Mangiola Laboratory

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