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Reposted by Raphael Gottardo

fbm-unil.bsky.social @fbm-unil.bsky.social · 9d

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

Reposted by Raphael Gottardo

fbm-unil.bsky.social @fbm-unil.bsky.social · Jul 10

📄 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

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Raphael Gottardo @rgottardo.bsky.social · Jul 1

🧬 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

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Raphael Gottardo @rgottardo.bsky.social · Jun 30

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

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Raphael Gottardo @rgottardo.bsky.social · Jun 23

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

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Raphael Gottardo @rgottardo.bsky.social · Jun 22

🚀 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

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Raphael Gottardo @rgottardo.bsky.social · Jun 22

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

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Raphael Gottardo @rgottardo.bsky.social · Jun 22

🎉 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

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Raphael Gottardo @rgottardo.bsky.social · Jun 22

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

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Raphael Gottardo @rgottardo.bsky.social · Mar 28

Congratulations @rrmsky.bsky.social !

Ruth Montgomery @rrmsky.bsky.social · Mar 28

Very honored by recognition from AAAS reflecting a career studying how cells work & the underpinnings of health. Gratitude to stellar colleagues & lab members at Yale and beyond. ❤️ family/friends. @yalemed.bsky.social #TeamScience #WomenInSTEM @hipcproject.bsky.social
news.yale.edu/2025/03/27/e...

Eight Yale faculty members named AAAS fellows

The American Association for the Advancement of Science has elected eight Yale faculty members as part of its latest class of fellows.

news.yale.edu

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Reposted by Raphael Gottardo

HIPC @hipcproject.bsky.social · Feb 17

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

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Raphael Gottardo @rgottardo.bsky.social · Jan 15

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 22

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 22

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 14

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

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Reposted by Raphael Gottardo

Atul Butte @atulbutte.bsky.social · Dec 6

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 5

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.

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Raphael Gottardo @rgottardo.bsky.social · Dec 5

Thank you Stephanie.

Raphael Gottardo @rgottardo.bsky.social · Dec 5

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 5

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 5

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

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Raphael Gottardo @rgottardo.bsky.social · Dec 5

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

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Raphael Gottardo @rgottardo.bsky.social · Nov 28

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

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Raphael Gottardo @rgottardo.bsky.social · Nov 27

Please add me. Thanks!

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Raphael Gottardo @rgottardo.bsky.social · Nov 27

Done.

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