Today we released scvi-tools v0.20.0. This is one of our most feature-packed releases yet. In this thread I highlight a few of these features... docs.scvi-tools.org/en/stable/rele…

We’re excited to share that our work describing theoretically-motivated algorithms and design insights for CRISPR-Cas9 single-cell lineage tracing is now out: pnas.org/doi/10.1073/pn…

The scverse project provides a computational ecosystem for single-cell omics data analysis go.nature.com/3Gz8JUV

scverse is out Nature Biotechnology: it provides an ecosystem for single-cell analysis in python, centered around shared data structures & core packages. Excited about the great community scverse, colleagues & contributors! See nature.com/articles/s4158… & scverse.org

By learning a joint representation using deep generative modeling, MultiVI integrates multimodal and single modality single-cell datasets which enhances multiple functionalities. Yosef Lab Tal Ashuach Mariano Gabitto OA paper: nature.com/articles/s4159…

In this resource Streets and colleagues provide a timeline of CD4+ and CD8+ T cell lineage commitment, identifying sequential waves of TCR signaling that initiate CD4+ T cell then CD8+ T cells lineage differentiation. Read it here: rdcu.be/djHe5 nature.com/articles/s4159…

veloVI enhances RNA velocity analysis with uncertainty quantification and extensibility by deep generative modeling of gene-specific transcriptional dynamics. Adam Gayoso Philipp Weiler Fabian Theis Yosef Lab OA paper: nature.com/articles/s4159…

Excited that veloVI is out Nature Methods! Led by Adam Gayoso & Philipp Weiler w awesome Yosef Lab, we combine deep generative modeling with a mechanistic single-cell transcriptional model for better RNA velocity analysis with uncertainty quantification. nature.com/articles/s4159…

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

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/10.110…

🚨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

Excited to share our study on how aging affects the human immune system at different tissues, with single cell genomics. Fantastic teamwork with Peter Sims, Jo Jones, Donna Farber and Teichlab; and with Cambridge CBTM and LiveOn NY. Fresh on bioRxiv: doi.org/10.1101/2024.0…

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.post2…

Are you an international PhD graduate interested in doing a postdoc at Weizmann Institute ? 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!

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 consortium and beyond! linkedin.com/jobs/view/3869…

The lab is in full bloom as we gather in Berkeley and Israel to toast the arrival of spring and joyous Purim! Celebrating our collective achievements over delicious food and great company ☀️🎉

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/10.110…

SCG2024 program is now online! 🔥 conferences.weizmann.ac.il/SCG2024/program Continuing our tradition with never heard before-unpublished work in the leading edge of single cell biology, analysis and technology.

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

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/biKowkrPhFVPo8… Looking forward to seeing you Sept, 26th, 10AM ELSC Brain, Givat Ram, JLM.