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My first-author PhD thesis work is published in nature ! 🧬🔬🎉 I’m beyond grateful for this moment and for everyone who supported me! UCSF Neurosurgery Okada Lab @ UCSF Joe Costello Klebanoff_Lab RNA Splicing aberrations generate tumor-wide neoantigens! nature.com/articles/s4158…

Thrilled to share our UM SVI LAB work published today in Journal of Clinical Investigation focused on harnessing viral mimicry to activate immunotherapy for #GBM. Thanks to all of my Sylvester Comprehensive Cancer Center UM Neurosurgery colleagues for their invaluable contributions! jci.org/articles/view/…

Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day on Friday 4/25. All talks will be live-streamed (no registration required) at satijalab.org/scgd25

CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type! nature.com/articles/s4158…

Happy to share our recent take on #Tcell #exhaustion in #cancer and #infection, now out at Nature Rev Immunol. Kudos to Cell Stress & Immunity (CSI) Lab for taking the lead here, and to our co-authors offtwitter(?)!! Available at rdcu.be/ehm67 Fox Chase Cancer Center

Excited to share our exploration Nature Methods into new horizons opening up in the era of low cost sequencing! 🔥 Deeper sequencing at WGS scale for PPM sensitivity of tumor informed MRD 🔥Duplex sequencing at WGS scale for plasma only exploration of ctDNA Check out thread 👇

Delighted to share a step-by-step protocol for spatially resolved epigenome-transcriptome co-sequencing to map tissue development, aging & disease. Fully committed to open science!! ⁦SenNet Consortium⁩ ⁦Human BioMolecular Atlas Program (HuBMAP)⁩ ⁦NIH Common Fund⁩ @NCIHTAN nature.com/articles/s4159…

🚀 Our perspective is out in nature! We present a roadmap for Multimodal Foundation Models (MFMs) — large AI models pretrained across multi-omics and multi-timepoint data — to serve as the computational backbone for building virtual cells. Read the full paper in Nature:

Navigating established and emerging biomarkers for immune checkpoint inhibitor therapy dlvr.it/TKC1Nr

"Mathematics for Computer Science" from MIT. The entire book of 1048 pages is now FREE.

What if LLMs could “read” & “write” biology? 🤔 Introducing C2S‑Scale—a Yale University + Google AI Google DeepMind collab: we scaled LLMs (up to 27 B!) to analyze & generate single‑cell insights by turning transcriptomes into text 🧬➡️📝 🔗 Blog: research.google/blog/teaching-… 🔗 Preprint:

scMultiSim is a comprehensive single-cell and spatial data simulator generating realistic multi-omics data based on modeling gene regulatory networks, cell-cell interactions, and other biological and technical factors nature.com/articles/s4159…

Topography Aware Optimal Transport for Alignment of Spatial Omics Data biorxiv.org/content/10.110…

Our Single Cell Genomics Day - highlighting our favorite new sc/spatial methods - starts Friday at 10AM ET! The most common question we get: is this open to anyone? Yes! Talks are free and live-streamed (no registration required) on Youtube and satijalab.org/scgd

Online Now: Brain metastasis: From etiology to ecotypes dlvr.it/TKjkbd

14/ Want to learn more? Read our regulatory paper biorxiv.org/content/10.110… and companion spatial multi-omics study biorxiv.org/content/10.110… Watch out for a separate 🧵from Omer Ali Bayraktar on conserved spatiotemporal trajectories in GB

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

Detecting and quantifying clonal selection in somatic stem cells | Nature Genetics. So pleased to share this work. It is one of the most important pieces of work we have done. Huge thanks to all. More improvements on SCIFER to come! nature.com/articles/s4158…

1/11 Our study on subclonal immune evasion in non-small cell lung cancer has just been published in Cancer Cell cell.com/cancer-cell/fu…

Excited to share a milestone published in Nature Medicine from our decade-long effort to build The Human Phenotype Project, a unique longitudinal cohort with unmatched depth of clinical and multi-omic profiling, enabling truly predictive, personalized medicine. Led together with