Stefano Mangiola
@stemang.bsky.social
Computational cancer-immunology and tumour microenvironment
@SAiGENCI and @WEHI_research, VCA fellow @VicGovDH
@SAiGENCI and @WEHI_research, VCA fellow @VicGovDH
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
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
October 14, 2025 at 12:46 AM
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
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
Reposted by Stefano Mangiola
🚀 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...
🔥 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
www.physalia-courses.org
October 7, 2025 at 3:05 PM
🚀 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...
🔥 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...
Join us for another tidyomics meeting tomorrow!
We will chat about several news
- tidyprint
- tidybulk V2
- omicslog
- and more!
We will chat about several news
- tidyprint
- tidybulk V2
- omicslog
- and more!
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
Organized with Stefano @stemang.bsky.social
September 8, 2025 at 11:41 PM
Join us for another tidyomics meeting tomorrow!
We will chat about several news
- tidyprint
- tidybulk V2
- omicslog
- and more!
We will chat about several news
- tidyprint
- tidybulk V2
- omicslog
- and more!
Join us for an interesting discussion on using AI with foundational models in biology!
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...
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...
August 26, 2025 at 12:24 AM
Join us for an interesting discussion on using AI with foundational models in biology!
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
📢 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
August 6, 2025 at 2:56 AM
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
📢 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
- 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
July 30, 2025 at 12:46 AM
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
- 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.
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.
📣 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
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
July 14, 2025 at 6:23 AM
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.
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.
Reposted by Stefano Mangiola
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
Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬
@galaxyproject.bsky.social @bioconductor.bsky.social
July 1, 2025 at 1:14 PM
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
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!
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
Details & zoom info: doppeldata.au/events/event...
#Bioinformatics #SingleCell #HumanCellAtlas #Adelaide #Genomics
July 2, 2025 at 6:15 AM
What a cover! Looking forward to sharing our work with you!
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...
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...
May 23, 2025 at 6:18 AM
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...
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!
🚀 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
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
May 23, 2025 at 6:14 AM
Thanks @physaliacourses.bsky.social, it was a blast! And the great active audience made it so enjoyable!
Amazing crew! Tomorrow, we will show the Physalia crew how to use #tidyomics to manipulate and analyse spatial data!
🚀 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 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
May 19, 2025 at 11:10 AM
Amazing crew! Tomorrow, we will show the Physalia crew how to use #tidyomics to manipulate and analyse spatial data!
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
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
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
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
March 27, 2025 at 6:48 AM
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
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
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
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
March 17, 2025 at 6:32 AM
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
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
Reposted by Stefano Mangiola
🚀 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
🧨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
www.physalia-courses.org
March 14, 2025 at 7:52 AM
🚀 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
🧨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
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!
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
March 11, 2025 at 2:23 AM
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!
Wednesday 12th of March
- 4PM NY
- 9PM London
- 8AM (Thursday) Melbourne
details -> community-bioc.slack.com/archives/CEQ...
Pls share!
Reposted by Stefano Mangiola
📅 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
#Tidyomics #RStats
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…
buff.ly
March 4, 2025 at 3:58 PM
📅 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
#Tidyomics #RStats
📢 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
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
February 11, 2025 at 11:40 PM
📢 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
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
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...
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...
January 22, 2025 at 2:58 AM
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...
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...
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 🙏
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 🙏
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-...
docs.google.com
January 8, 2025 at 5:34 AM
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 🙏
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 🙏
📢🙏 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!
We welcome feedback from all research fields through comments on docs.google.com/document/d/1...
🙏 Plz Share! ❤️Thank you!
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-...
docs.google.com
December 23, 2024 at 10:41 PM
📢🙏 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!
We welcome feedback from all research fields through comments on docs.google.com/document/d/1...
🙏 Plz Share! ❤️Thank you!
Reposted by Stefano Mangiola
🚀 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...
Master imaging vs. sequencing methods, experimental design & tidy data principles for cutting-edge spatial omics analysis
www.physalia-courses.org/courses-work...
November 21, 2024 at 6:04 PM
🚀 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...
Master imaging vs. sequencing methods, experimental design & tidy data principles for cutting-edge spatial omics analysis
www.physalia-courses.org/courses-work...
📢💻🧪 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! 🙏
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! 🙏
November 15, 2024 at 1:02 AM
📢💻🧪 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! 🙏
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! 🙏
Amazing #BiocAsia2024 event! Thanks to all who participated!
Looking forward to next year!
@bioconductor.bsky.social
Looking forward to next year!
@bioconductor.bsky.social
November 11, 2024 at 8:19 AM
Amazing #BiocAsia2024 event! Thanks to all who participated!
Looking forward to next year!
@bioconductor.bsky.social
Looking forward to next year!
@bioconductor.bsky.social