Sara Simmonds 🧬

Computational Biologist | PhD Biology | Follow for the latest in #compio related to #cellbio #AIxBio

[Sara Simmonds 🧬 @SeSimmonds]

If something comes to mind, a role, a team, a conversation or you just want to connect, I'd genuinely love to hear from you.

[Sara Simmonds 🧬 @SeSimmonds]

I'm looking for my next mission.

My time at the CZ Biohub has been one of the most rewarding chapters of my career. I got to build AI models and platforms that served researchers around the world and worked alongside some of the most brilliant and wonderful people I've ever met.

[Sara Simmonds 🧬 @SeSimmonds]

I love hard problems at the intersection of AI and biology, mission-driven teams, and work that moves science forward in a real way. That said, I'm keeping my mind wide open.

[Chan Zuckerberg Initiative @ChanZuckerberg]

🚨 Just dropped: A powerful AI model to explore cells. Meet TranscriptFormer — trained on 112M cells from 12 species. It uncovers gene expression patterns across evolution and can simulate biology it’s never seen before. Learn more at: https://t.co/5ks2u46OkE

[Sara Simmonds 🧬 @SeSimmonds]

What a great summary!

[Kyle Tretina, Ph.D. @AllThingsApx]

The first cross-kingdom “GPT for cells.” 🤖🦠

TranscriptFormer reframes a single-cell atlas as a generative, cross-species language model that jointly predicts which genes appear and how much they’re expressed.

[Sara Simmonds 🧬 @SeSimmonds]

📢 Exciting update from CZ CELLxGENE now supports data from an expanded range of organisms beyond human and mouse.

This is just the beginning—we're continuously adding support for more organisms. 🪰🐟🪱🐷🐰🐵🦍

https://t.co/o94HMiIIBc

[biohub @biohub]

“The Billion Cells Project will help clarify our understanding of the fundamental biology underpinning human health + disease while supercharging efforts at the intersection of AI & biology.” - @JCoolScience

Learn more about the project https://t.co/YaP800otuT

[Stephen Quake @StephenQuake]

Virtual cell models have the potential to transform biological research. Today @ChanZuckerberg released an initial set of models, including scGenePT and SubCell, designed to be easy to run and build upon. This is a really exciting time in biology. https://t.co/3Jv3wxWlqG

[Kirk Lohmueller @lohmueller]

I'm excited to announce a tenure track faculty position in conservation genomics in EEB @UCLA! We're looking for candidates who use genomic tools to study evolutionary processes related to conservation. Note, the actual application deadline is Nov 29. https://t.co/HlP7npjCOu

[Loïc A. Royer 💻🔬⚗️ @loicaroyer]

🚨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.
https://t.co/mItTD6clYv

Explore the datasets here:
https://t.co/F7bhDmfDJD

Led by @Merlin_Lange with key contributions by @ale_agranados, @Shruthi94Vijay, @jobragantini, @Sarah_E_Ancheta and @yangjoonkim

#zebrahub #devbio #cell #Biology #imaging @CellCellPress @czbbiohub #CZBiohubS

[Loïc A. Royer 💻🔬⚗️ @loicaroyer]

📡🧵 Excited to release two #bioRxiv preprints!
The first preprint is: "Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis"
https://t.co/5wBZ6XAYaa

We present a comprehensive time-resolved single-cell multiomic atlas of zebrafish development. Integrating scATAC-seq and scRNA-seq from 94,000+ cells, we map gene regulatory networks across six key stages of embryogenesis (10 to 24 hpf).

A major accomplishment by @yangjoonkim co-led by @Merlin_Lange with experiments by @Shruthi94Vijay #Zebrahub-Multiome is a sequel to https://t.co/hPFARKa8Oi, our transcriptomic and imaging atlas of zebrafish development.

#zebrafish #development #ATACseq #cell #biology #sequencing @czbiohub #CZBiohubSF @cziscience

Note: We sent two preprints simultaneously yesterday, and this is the first one to come out... I will append to this thread when the second one is out...

[Loïc A. Royer 💻🔬⚗️ @loicaroyer]

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales

https://t.co/KN5Hw3BpI0

A tour-de-force by @jobragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor datasets. It has convenient @napari_imaging and @FijiSc plugin interfaces and built-in HPC cluster support.

https://t.co/DvKyowFbbi

#cell_tracking #microscopy #devbio @czbiohub

[biohub @biohub]

Spatial mapping provides key insights into tissue architecture, gene expression + key patterning events in development & disease.

Explore spatial transcriptomics datasets in seconds with CZ #CellxGene by applying the Visium and/or Slide-seqV2 filters https://t.co/dHzgCtiMvK

[Aaron Pomerantz, PhD @AaronPomerantz]

Exciting to see this out! A collaborative effort with @cziscience and @nanopore to offer the research community a free, easy-to-use pipeline for metagenomic analysis of complex microbial communities without the need for coding or computing resources
https://t.co/YE9tcrhsXx

[biohub @biohub]

🚨 New preprint 🚨

Our CZ ID team + @czbiohub highlight the platform’s new antimicrobial resistant (AMR) module, which enables the detection of microbes & AMR genes in mNGS + whole-genome sequencing data 🧵

[Rui Costa @ruimcosta]

Yesterday I had the pleasure of sitting down with @StephenQuake, Amy Herr, @PepperMarion, and @JShendure for a special panel celebrating the launch of the Seattle Hub for Synthetic Biology. The passion, optimism, and commitment to open science was shared by the entire panel. Together, we will understand life and advance health. Watch the conversation here: https://t.co/57IAYJX7YF

I'd also like to thank the scientists who shared their own passion during yesterday's tour - Hina Iftikhar, Emily Cliff, Sudarshan Pinglay, and @FloChardon.

Photos by Dale Ramos/@ChanZuckerberg

@UWMedicine #SeaSynBio

[Chan Zuckerberg Biohub Network @czbiohub]

📢Announcing the first-ever Chicago BioEngineering Conference! #CZBiohubCHI will bring together scientists in advanced sensing technologies, tissue & cell engineering, new omics approaches, and more. Don't miss it: Sept 30-Oct 1. (1/2)

Learn more ⤵️ https://t.co/MNLcT3iLSe

[Chan Zuckerberg Biohub Network @czbiohub]

The CZ Biohub Network is pleased to welcome the biomedical & AI expertise of 3 new members to our Board of Directors:
🌟Sam Altman/@sama, @OpenAI CEO
🌟Sam Hawgood, @UCSF Chancellor
🌟Mike Schroepfer/@schrep, Partner @Gigascale

View the full Board:
https://t.co/B8pZiOm7x0

[biohub @biohub]

#SingleCell researchers: did you know you can download + visually explore data from 1200+ datasets, spanning 789+ cell types through CZ #CellxGene Discover? https://t.co/mjjrpH5p6D