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1/6 The CZI Science team’s preprint on how CZ #CellxGene Discover serves as a centralized hub for standardized, interoperable and openly available #SingleCell matrices is out! Really proud of what we’re building to address the community’s needs bit.ly/40kFX2W 🧵

MS2 in zebrafish! Elizabeth Eck, Bruno Moretti and Brandon Schlomann, in collaboration with Loïc A. Royer 💻🔬⚗️ and oaties labs, discovered that smooth protein oscillations in the segmentation clock are the result of discrete transcriptional pulses. doi.org/10.1101/2024.0…

1/6 🍍🍕🧬 What do a photo of Italians savoring pineapple pizza and a synthetic DNA sequence have in common? Both can be intricately crafted by generative AI! Introducing DNA-Diffusion, our AI model set to advance #SyntheticBiology and #GeneRegulation: biorxiv.org/content/10.110…

Excited to share our manuscript on single-cell and spatial multi-omics of anti-integrin therapy in ulcerative colitis (UC) nature.com/articles/s4146…. This work was led by Elvira Mennillo, in collaboration with Alexis Combes, @GabiFragiadaks, and Angela Oliveira Pisco 1/8

We are very happy to see that our manuscript, 'Joint Genotypic and Phenotypic Outcome Modeling Improves Base Editing Variant Effect Quantification,' is now published in Nature Genetics. Read it for free here: rdcu.be/dFBBC, original twittorial below!

We built CZ #CellxGene to provide the community with curated, interoperable single-cell data. Today, the platform has 85M+ cells & tools like Census that are being used to train new analysis models. Proud to see nature highlight our work & collaborators nature.com/articles/d4158…

🔬🤖Excited to share our new preprint on robust virtual staining of key organelles! biorxiv.org/content/10.110… ✨ Virtual staining and segmentation of nuclei and cell membranes in phase images can significantly accelerate image-based screens and developmental studies. 🔍 Current

1/ 📡Exciting news! 🚀 Our #Omega paper has been accepted at @NatureMethods! Omega is a napari🔬 plugin that uses Large Language Models to assist users with bioimage processing and analysis tasks! Check out our original project announcement (see below), read the paper:

Chan Zuckerberg Biohub Network Li-Hao Yeh ORC Southampton This is one of those projects that has taken several iterations and years to finish - look at the timestamps! Special thanks to Rita Strack for being an amazing editor throughout this process. 13/n

1/8 Excited to share our preprint on RNA velocity! 🚀🧬 In this study, we compare 5 RNA velocity methods across 3 datasets. Check out our findings! #scRNAseq #RNAvelocity 📄 biorxiv.org/content/10.110…

Exciting job opportunity! 🚀 My team at Chan Zuckerberg Biohub Network SF is hiring a motivated and ambitious Research Assistant! (Bachelor or Master level) Join us to work at the intersection of developmental biology🥚, cutting-edge imaging🔬, and molecular biology & genomics🧬. You will learn a

The Physics of Life Symposium at #CZBiohubSF is coming up! We invite early-career researchers, postdocs & students to share their science and esp encourage #WomeninSTEM #underrepresented groups to submit abstracts. Abstracts due: Thu, 8/15 Learn more ⤵️ czbiohub.org/events/physics…

We are excited to share work led by Han Chen and Madhavan Venkatesh developing a quantized multitask learning strategy for network biology, built on a foundation model pretrained on ~95M single-cell transcriptomes. Manuscript: tinyurl.com/qmtl-gf Model: huggingface.co/ctheodoris/Gen…

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales doi.org/10.1101/2024.0… A tour-de-force by Jordão Bragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor

Thrilled to share our latest research on zebrafish development using single-cell multi-omics (RNA+ATAC) approaches! Check out the interactive data visualizations to explore gene regulatory dynamics across embryogenesis.

🚨Big news! Five years in the making, our Zebrahub paper is now published in #Cell 🎉. We’ve built a timecourse atlas of zebrafish embryonic development, combining #scRNAseq data and #lightsheet live imaging, and delved deep into the dynamics of key progenitors.

Honored to be part of this great team effort! Please check out this resource on live imaging and single-cell transcriptomics, a Google Earth of zebrafish development!

We're finally out at Nature Communications. Congrats to Jiaxi (Jake) Zhao, Nick Lammers, YangJoon Kim, Simon Alamos and @gabrimartini_ny ! nature.com/articles/s4146…

A dream come true: in 2004 I started thinking about counting microstates to predict gene expression with Jane Kondev Rob Phillips Hernan Garcia. 20 years later we can measure them: nature.com/articles/s4158… Thank you William J. Greenleaf Benjamin Doughty Michaela Hinks Julia and all co-authors!

🔊 Exciting AI Research Opportunity! my team at Chan Zuckerberg Biohub Network SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠 #AIJobs #ML job-boards.greenhouse.io/chanzuckerberg… Think of it as a "postdoc on steroids" in