Join us! With a fully funded PhD scholarship. www.linkedin.com/feed/update/... @saigenci.bsky.social

📢 Fully funded PhD position in AI foundation models for cancer immunology Our lab https://lnkd.in/gmgsXEZt This project will develop and apply artificial intelligence models, including foundation… |...

📢 Fully funded PhD position in AI foundation models for cancer immunology Our lab https://lnkd.in/gmgsXEZt This project will develop and apply artificial intelligence models, including foundation mo...

linkedin.com

📢 📃 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!

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...

biorxiv.org

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

EuroBioC2026 Tidyomics Hackathon – tidyomicsBlog

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

tidyomics.github.io

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

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

Performance optimisation of tidySummarizedExperiment and related benchmark.

tidyomics.github.io

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...

#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...

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...

Omicslog – tidyomicsBlog

Providing logging capabilities for SummarizedExperiment objects.

tidyomics.github.io

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

Stefano Mangiola@stemang.bsky.social · 8mo ago

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

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

Stefano Mangiola@stemang.bsky.social · last yr.

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

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

The Tidyomics Ecosystem – tidyomicsBlog

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

tidyomics.github.io

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

Feargal Ryan@feargalr.bsky.social · 8mo ago

That’s a wrap! Huge thank you to everyone who joined us for #ABACBS2025 & a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval. @wessidepraxis.bsky.social @linsalrob.bsky.social

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

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. 🚀

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!

Stefano Mangiola@stemang.bsky.social · 10mo ago

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

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

🚀 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...

spatial Omics in R/Bioconductor

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

physalia-courses.org

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

Michael Love@mikelove.bsky.social · 11mo ago

Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis. Organized with Stefano @stemang.bsky.social

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

Australian BioCommons@ausbiocommons.bsky.social · 12mo ago

Next in our #AI webinars: Stefano Mangiola @saigenci.bsky.social talks AI models in #SingleCell and if they can uncover biological patterns Anh TN Nguyen @monashuniversity.bsky.social shares how deep learning is accelerating #DrugDiscovery for GPCRs More info www.biocommons.org.au/events/ai-se...

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

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

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.

Bioconductor@bioconductor.bsky.social · last yr.

📣 BioCAsia 2025: Call for Workshops Join the Bioconductor stream at ABACBS 2025 in Adelaide! Submit your hands-on workshop EOI by August 1. Flexible 90-min blocks. ➡️ www.abacbs.org/abacbs-2025-... #Bioconductor #BioCAsia2025 #RStats

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

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

Doppeldata - Adelaide Bioinformatics@doppeldata.au · last yr.

Seminar this Friday July 4th 1.00pm: “Modelling and Democratising the Human Cell Atlas” with @stemang.bsky.social, Haroon Shakeel & Chen Zhan (@saigenci.bsky.social) Details & zoom info: doppeldata.au/events/event... #Bioinformatics #SingleCell #HumanCellAtlas #Adelaide #Genomics

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...

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

Physalia-courses@ONLINE@physaliacourses.bsky.social · last yr.

🚀 We’re wrapping up our 3-day Spatial Omics in R/ @bioconductor.bsky.social workshop! A huge THANK YOU to @stemang.bsky.social Malvika and all our attendees who made this event a success 🎉 Until next time — www.physalia-courses.org/courses-work... 🧬🗺️ #SpatialOmics #Bioconductor #RStat

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

Physalia-courses@ONLINE@physaliacourses.bsky.social · last yr.

🚀 Just kicked off our Spatial Omics in R/Bioconductor course with @stemang.bsky.social In this 3-day course, we're gonna explore spatial technologies & hands-on data analysis in R and Bioconductor using tidy principles🧬🧠📊 www.physalia-courses.org/courses-work... #SpatialOmics #RStats #Bioconductor

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

Stefano Mangiola@stemang.bsky.social · last yr.

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

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

Stefano Mangiola@stemang.bsky.social · last yr.

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!

🚀 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

spatial Omics in R/Bioconductor

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

physalia-courses.org

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 - tidyomics/tidyprint

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

github.com