Raphael Gottardo
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rgottardo.bsky.social
Raphael Gottardo
@rgottardo.bsky.social
1.8K followers 910 following 36 posts
Biomedical Data Science Center Director @CHUV. Professor at @UNIL and @EPFL. AI, ML, and statistical learning for high-dimensional (single-cell/spatial) data in clinical and translational medicine. Interdisciplinary scientist passionate about data.
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Reposted by Raphael Gottardo
helucro.bsky.social
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.
November 21, 2025 at 5:31 PM
Reposted by Raphael Gottardo
fbm-unil.bsky.social
@rgottardo.bsky.social @dilibertomd.bsky.social @inserm.fr @hcl-recherche.bsky.social
September 30, 2025 at 9:39 AM
Reposted by Raphael Gottardo
fbm-unil.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
July 10, 2025 at 12:40 PM
rgottardo.bsky.social
🧬 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
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 ...
www.nature.com
July 1, 2025 at 1:49 PM
rgottardo.bsky.social
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
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...
www.biorxiv.org
June 30, 2025 at 2:55 PM
rgottardo.bsky.social
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
www.biorxiv.org
June 23, 2025 at 12:15 PM
rgottardo.bsky.social
🚀 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
www.biorxiv.org
June 22, 2025 at 7:13 AM
rgottardo.bsky.social
🎉 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
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...
www.nature.com
June 22, 2025 at 6:20 AM
rgottardo.bsky.social
New expanded @hipcproject.bsky.social starter pack: go.bsky.app/AozZWPx
June 22, 2025 at 6:12 AM
rgottardo.bsky.social
Congratulations @rrmsky.bsky.social !
March 28, 2025 at 3:53 PM
Reposted by Raphael Gottardo
hipcproject.bsky.social
Our collaborators @rgottardo.bsky.social and Ken Stuart (+ others) describe tagtango, an application to compare #single-cell annotations.
#bioinformatics
academic.oup.com/bioinformati...
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
academic.oup.com
February 17, 2025 at 9:34 PM
rgottardo.bsky.social
#NIH HIPC consortium starter pack with added members @slimfourati.bsky.social @bjoernpeters.bsky.social @joanndarce.bsky.social @immunespace.bsky.social
go.bsky.app/AozZWPx
January 15, 2025 at 8:46 AM
rgottardo.bsky.social
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...
Eczéma, psoriasis, lupus et autres maladies inflammatoires de la peau : des signatures génomiques pour améliorer le diagnostic et le traitement
www.chuv.ch
December 22, 2024 at 7:22 AM
rgottardo.bsky.social
An older article on why I remain cautiously optimistic about generative #AI in #healthcare: www.rts.ch/info/science...
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...
www.rts.ch
December 22, 2024 at 7:17 AM
Reposted by Raphael Gottardo
atulbutte.bsky.social
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...
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.
www.ucsf.edu
December 6, 2024 at 8:11 PM
rgottardo.bsky.social
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.
December 5, 2024 at 8:01 PM
rgottardo.bsky.social
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
December 5, 2024 at 4:36 PM
rgottardo.bsky.social
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...
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...
actu.epfl.ch
December 5, 2024 at 4:33 PM
rgottardo.bsky.social
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!
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...
www.nature.com
December 5, 2024 at 8:12 AM
rgottardo.bsky.social
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
November 28, 2024 at 6:36 AM
rgottardo.bsky.social
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
rgottardo.bsky.social Raphael Gottardo @rgottardo.bsky.social · Nov 24
Ok, I’ve added a few more people to the list:
go.bsky.app/73rcuJn

Please reach out if you want to be added! The more the better.
#AI #ML #DataScience #Omics #SingleCell #SpatialBiology
rgottardo.bsky.social Raphael Gottardo @rgottardo.bsky.social · Nov 24
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn
November 27, 2024 at 8:43 PM
rgottardo.bsky.social
@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.
lpachter.bsky.social Lior Pachter @lpachter.bsky.social · Nov 25
Another example of the different results one gets from a Scanpy vs. Seurat analysis, in this case a Visium HD dataset from academic.oup.com/bioinformati...
13 vs. 20 clusters. And qualitatively different results, corroborating what we saw in biorxiv.org/content/10.1...
November 26, 2024 at 10:15 AM
rgottardo.bsky.social
Thanks @tsanglab.bsky.social for putting this together! #immunology #datascience

go.bsky.app/PjH2Fuj
November 25, 2024 at 9:34 AM
rgottardo.bsky.social
Ok, I’ve added a few more people to the list:
go.bsky.app/73rcuJn

Please reach out if you want to be added! The more the better.
#AI #ML #DataScience #Omics #SingleCell #SpatialBiology
rgottardo.bsky.social Raphael Gottardo @rgottardo.bsky.social · Nov 24
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn
November 24, 2024 at 3:10 PM
rgottardo.bsky.social
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn
November 24, 2024 at 7:50 AM