Raphael Gottardo

New preprint 🧫🧬

Spatial transcriptomics (~550,000 cells, 2,432 patient-derived organoids): we map gene expression, shape, and function in space to understand cancer biology and drug response. w/ @marianna-raps.bsky.social @khomicsko.bsky.social and Maxim Norkin

www.biorxiv.org/content/10.6...

Loosing connection breaks the heart

Huge congrats to Teofila, Jeremy & Antoine on the 2026 Pfizer Research Prize 👏 #PrecisionDermatolology driven by translational #DataScience at #CHUV & @unil.bsky.social. More to come with #AI & #SpatialBiology. Hats off to Michel Gilliet for this vision.

🔗 www.pfizerresearchprize.ch/awardees-202...

Shout out and thanks to everyone who was a part of this; one couldn’t have done it alone.

@rgottardo.bsky.social
@markrobinsonca.bsky.social
@stephaniehicks.bsky.social
@lmweber.bsky.social
and many more.

@rgottardo.bsky.social @dilibertomd.bsky.social @inserm.fr @hcl-recherche.bsky.social

📄 Study published in @natcomms.nature.com and led by Laurence de Leval, @rgottardo.bsky.social @khomicsko.bsky.social & Elo Madissoon.

@unil.bsky.social #chuv @owkin.bsky.social

ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets - Nature Communications Here the authors present a computational method that expands the potential of multimodal single-cell analyses by delivering an accurate, fast, and user-friendly approach for normalizing and comparing ...

🧬 New paper out!
🔗 www.nature.com/articles/s41...

Frustrated by noisy CITE-seq data?
ADTNorm helps normalize it and introduces a staining index to assess antibody quality.

Great work by former postdoc Ye Zheng. Supported by @hipcproject.bsky.social

#CITEseq #SingleCell #ADTNorm

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...

Big shoutout to our own Jieran Sun onesinglecell.bsky.social for leading this team effort!
🧠📍 Benchmarking clustering in spatial transcriptomics isn’t easy — but here is SACCELERATOR
Preprint: www.biorxiv.org/content/10.1...
With markrobinsonca.bsky.social, Naveed Ishaque, Ahmed Mahfouz, Brian Long

Are you interested in #Xenium panel comparisons: 5K vs targeted? Want to increase cell-type resolution with Xenium? Read our paper and check out our SPLIT method.

www.biorxiv.org/content/10.1...
Collaboration with @khomicsko.bsky.social
cc: @10xgenomics.bsky.social
#SpatialTranscriptomics

🚀 First MOSAIC consortium paper and MOSAIC Window: a rich 60-patient public (multimodal) dataset accessible via EGA.

📄 www.biorxiv.org/content/10.1...
#CancerResearch #SpatialTranscriptomics #SingleCell #PrecisionOncology #AI
cc: @owkin.bsky.social @10xgenomics.bsky.social

All data are available including manually annotated single-cells (snRNAseq) and Visium spots! Great for benchmarking algorithms and computational tools!

Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity - Nature Communications Currently, there is an urgent need to evaluate the strengths and limitations of various probe-based full transcriptome methods for formalin-fixed paraffin-embedded tumor tissues. Here, the authors ana...

🎉 New paper alert. We benchmarked Visium, GeoMx, and Chromium for FFPE tumor analysis. Thanks @estellayixingdong.bsky.social for pushing this forward, & MOSAIC collaborators!
📄 www.nature.com/articles/s41...
#SpatialTranscriptomics #CancerResearch cc: @owkin.bsky.social @10xgenomics.bsky.social

New expanded @hipcproject.bsky.social starter pack: go.bsky.app/AozZWPx

Congratulations @rrmsky.bsky.social !

tagtango: an application to compare single-cell annotations AbstractSummary. In this article, we present tagtango, an innovative R package and web application designed for robust and intuitive comparison of single-c

Our collaborators @rgottardo.bsky.social and Ken Stuart (+ others) describe tagtango, an application to compare #single-cell annotations.
#bioinformatics
academic.oup.com/bioinformati...

#NIH HIPC consortium starter pack with added members @slimfourati.bsky.social @bjoernpeters.bsky.social @joanndarce.bsky.social @immunespace.bsky.social
go.bsky.app/AozZWPx

Precision Dermatology 2.0: #DataScience + #Immunology + #Genomics + #Clinical Science. Interdisciplinary collaboration at its best at the @CHUV.
www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...

L'IA générative dans le secteur de la santé: une révolution imminente Les avancées de l'intelligence artificielle générative dans le domaine de la santé ouvrent de nouvelles perspectives. Alors que Google lance Med-PaLM 2, un outil d'IA médicale, des professionnels suis...

An older article on why I remain cautiously optimistic about generative #AI in #healthcare: www.rts.ch/info/science...

Done. I have also added @evnewell.bsky.social Please flag other people and I will add them.

1 Genomic Test Can Diagnose Nearly Any Infection A decade-long effort has resulted in a new, rapid genomic test to diagnose rare infectious diseases in the brain and lungs.

Very cool! One genomic test can diagnose nearly any infection! Comes out of the lab of Charles Chiu @ucsfhealth.bsky.social
www.ucsf.edu/news/2024/11...

Thanks #Spotify for letting me know that #Vulfpeck was my #1 artist for 2024. Top 0.05% of listeners worldwide. Almost significant! Of course, not surprised.

Thank you Stephanie.

By popular demand, I have updated our starter pack in Stats, ML & Omics. Let me know if you'd like to be added. #ML #AI #singlecell #spatial #omics #statistics
go.bsky.app/73rcuJn

Two appointments at the School of Life Sciences The Board of the Swiss Federal Institutes of Technology has announced the appointment of professors at EPFL. Among them, are Professors Markus Jeschek and Raphael Gottardo at the School of Life Scienc...

Great news! Thrilled about this new appointment at EPFL to strengthen collaborations in biomedical data science across CHUV, @unil.bsky.social, and the EPFL. Excited to work closely with EPFL colleagues and students ! #datascience #AI #medicine #biology
actu.epfl.ch/news/two-app...

I am afraid there is a real tendency by this community to overlook previous work (especially from statisticians). Am I missing something?

Probabilistic weather forecasting with machine learning - Nature GenCast, a probabilistic weather model using artificial intelligence for weather forecasting, has greater skill and speed than the top operational medium-range weather forecast in the world and provid...

Interesting work from @deep-mind.bsky.social on probabilistic weather forecasting (aka GenCast) www.nature.com/articles/s41...

BUT why didn't they cite previous work in this space by Raftery and colleagues: www.science.org/doi/full/10....
journals.ametsoc.org/view/journal...
and many other papers!

Here is a starter pack for the #NIH Human #Immunology Project Consortium (@hipcproject.bsky.social). #HIPC members, please reach out if you'd like to be added.
go.bsky.app/AozZWPx

Please add me. Thanks!

Done.

Ok, as requested, here’s an updated list with additional people:
go.bsky.app/73rcuJn

Reach out if you want to be added!
#AI #ML #DataScience #Omics #SingleCell #SpatialBiology

@lpachter.bsky.social Interesting! Also, Louvain/Leiden determine the number of clusters automatically (through the resolution), often leading users to assume the default is optimal! However, identifying the correct number of clusters is a complex statistical problem, which shouldn't be ignored.