Photos and videos
Interested in how metabolism shapes the tissue environment?
We introduce Harreman, an algorithm and open-source software to infer metabolic exchanges directly from spatial transcriptomics.
To learn more, check out @EtxezarretaOier's tweetorial below! 👇🧵
13 Nov 2025
🚀 I'm excited to share our new method called Harreman - an open-source algorithm from the @YosefLab to infer metabolic exchanges directly from spatial transcriptomics data.
doi.org/10.1101/2025.11.11.6…
🧵👇
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Yosef Lab retweeted
25 Sep 2025
Check out our latest work with @khushipde and @elhamazizi on inferring cell-cell interactions from spatial transcriptomics data!
25 Sep 2025
1/ I’m excited to share recent work on inferring cell-cell interactions using attention by @justjhong and me, supervised by @elhamazizi. Open the thread 🧵for a brief tweetorial of our method. bioRxiv link: biorxiv.org/content/10.1101/…
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🚀scVI-tools 1.4 is here!
🔥New models including resolVI, cytoVI, sysVI, scVIVA
⚡️MultiGPU support
📊scIB-metrics optimization
🛠️Custom dataloaders
🔎Feature interpretability
📖Read the blogpost:
scvi-tools.org/blog/v13/#fnr…
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One week to go before kicking off the Computational Spatial Biology seminar!
Find the full schedule here csbseminar.github.io/
2 Apr 2025
To kick off the Computational Spatial Biology seminar series with @nathan_levyy, we will be discussing LUNA with @yistyu. LUNA is a generative AI model that reassembles complex tissue structures from gene expressions of cells.
Tune in next Wednesday, April 9 @ 11AM ET!
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Exciting opportunity to learn about cutting-edge approaches from the community and discover new techniques for your own spatial research!
26 Mar 2025
Announcing the Computational Spatial Biology seminar!
With @justjhong, we’re bringing together researchers at the intersection of AI & spatial biology to share their work.
Kicking off April 9th with Yist Yu presenting LUNA!
Explore the lineup here:
csbseminar.github.io/
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Yosef Lab retweeted
11 Nov 2024
Tomorrow at 2024-11-12 18:00 CET will be another community meeting!
@_canergen will talk about about Scvi-hub, a repository for model-based analysis of single-cell genomic data. For more information check the Biorxiv paper: doi.org/10.1101/2024.03.01.5…
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Yosef Lab retweeted
25 Aug 2024
Dear community, we hope you are safe these days🙏
Towards our meeting, don’t miss the chance to share your sc-ience, poster submission deadline is coming up, Aug. 29th⌛️.
👉 forms.gle/biKowkrPhFVPo85t8
Looking forward to seeing you Sept, 26th, 10AM @ELSCbrain, Givat Ram, JLM.
30 Jul 2024
Join us for the 1st Annual Single Cell Network Israel Meeting, Sep. 26 at @HebrewU focused on getting to know each other better! 💘
The core of the meeting will feature "Let’s talk sc-ience!" parallel sessions. 🗨️
Registration: forms.gle/sRgzQXRXRaxrovo56
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Yosef Lab retweeted
5 Aug 2024
Aging is a complex process, and one of its hallmarks is the accumulation of senescent cells. These cells, while once healthy, have become damaged and dysfunctional.
But why do they stick around? 🤔
Our new research sheds light on this! #aging #senescentcells #aging #immunotherapy
@JuliaMMagdalena @KrizhanovskyLab @UriAlonWeizmann @WeizmannScience nature.com/articles/s41556-0…
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Yosef Lab retweeted
31 Jul 2024
SCG2024 program is now online! 🔥 conferences.weizmann.ac.il/S…
Continuing our tradition with never heard before-unpublished work in the leading edge of single cell biology, analysis and technology.
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Yosef Lab retweeted
13 May 2024
How can we better reveal cellular 🦠and sample🧍variation from large-scale scRNA-seq studies? We have released a new and improved deep generative model, #MrVI, in scvi-tools and on bioRxiv, accompanied by real-world use cases. A thread... 🧵1/
biorxiv.org/content/10.1101/…
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We are hiring a software engineer! An amazing opportunity to join our team - be at the core of the development and maintenance of our open-source Python packages, engage with the single-cell omics community within the @scverse_team consortium and beyond!
linkedin.com/jobs/view/38692…
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Are you an international PhD graduate interested in doing a postdoc at @WeizmannScience ?
Don’t miss the opportunity to apply to the Azrieli fellowship. Conduct research at a leading Israeli university and become part of a network of top-tier scientists!
11 Mar 2024
Attention international postdocs:
Applications for the Azrieli International Postdoctoral Fellowship are now being accepted and are due by May 9!
The Azrieli International Postdoctoral Fellowship supports the best and brightest minds in their postdoctoral research in Israel, connecting them with world-class academics and leading researchers.
Please note that candidates are required to have an academic sponsor, who is a faculty member at an eligible Israeli academic institution.
@azrielifdn
ALT Photo by Shauli Lendner
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Yosef Lab retweeted
13 Feb 2024
Excited to announce the release of scvi-tools v1.1 today! We’re including various new features, models, and critical bug fixes in this release, some of which I will highlight in this thread:
docs.scvi-tools.org/en/1.1.0…
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Excited to share our study on how aging affects the human immune system at different tissues, with single cell genomics.
Fantastic teamwork with @psimslab, Jo Jones, @DonnaFarber3 and @teichlab; and with Cambridge CBTM and @liveonny.
Fresh on bioRxiv: doi.org/10.1101/2024.01.03.5…
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Yosef Lab retweeted
18 Dec 2023
🚨1/ New to CZ #CELLxGENE: models & embeddings that integrate up to 36M cells in the Census corpus.
Use embeddings to explore the corpus directly, or download the models to run your own data through them to enable direct comparisons to the reference. 🧵
bit.ly/census_models
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Yosef Lab retweeted
10 Nov 2023
Hi! We have just released VI-VS, a new framework for exploring molecular dependencies in multi-omics. It combines deep learning and rigorous statistical inference to provide interpretable discoveries with high predictive power.
biorxiv.org/content/10.1101/…
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Expanded Yosef Lab meeting at the SCG conference this week!
In his talk Nir presented mrVI, a deep generative model for analyzing sample-level heterogeneity in single-cell RNA-seq datasets. Find out more:
github.com/YosefLab/mrvi
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Yosef Lab retweeted
21 Sep 2023
veloVI enhances RNA velocity analysis with uncertainty quantification and extensibility by deep generative modeling of gene-specific transcriptional dynamics. @adamgayoso @PhilippWeiler7 @fabian_theis @YosefLab
OA paper: nature.com/articles/s41592-0…
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