Jian Shu

VIP-OT introduces a new direction in building AI virtual cell. It couples high-dimensional, low-cost, nondestructive vibrational (chemical) imaging with optimal transport to infer single cell biochemical state dynamics and perturbation response trajectories and combinations.

VIP-OT: When perturbation meets vibrational imaging and optimal transport | After introducing optimal transport to single-cell genomics in 2019, we’re excited to bring OT to the field of vibrational imaging for the first time. 🥳 biorxiv.org/content/10.648…

We are excited to share RamanOmics, the first multimodal framework integrating snRNA-seq, spatial transcriptomics, and label-free Raman imaging to map the spatial biochemical–molecular architecture of aging, senescence, and tissue repair. #NIH SenNet biorxiv.org/content/10.648…

Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings nature.com/articles/s4146…

When cellular reprogramming meets AI: towards de novo cell design | Nature Reviews Genetics nature.com/articles/s4157…

Excited to share an update on our collaboration with Aviv Regev and Collin Stultz, led by Charles Comiter: predicting single-cell spatial transcriptomics from H&E images using SCHAF. New models, new datasets, and new discoveries. biorxiv.org/content/10.110…

The placenta is one of the most complex and fascinating, yet least studied, human organs. A wonderful collaboration with the amazing members of the Haider and Chen @insitubiology labs. #placenta #HCA #Hiring

We are excited to publish a spatially resolved single-cell multi-omic census of the placenta, contributing to the @humancellatlas project. The placenta plays an essential role in maintaining a healthy pregnancy, yet its function remains poorly understood. nature.com/articles/s4159…

The Human Cell Atlas initiative has the monumentally ambitious goal of cataloguing every cell type in the human body, from development to old age, and it is remarkable go.nature.com/411zuwx

We are thrilled to share an HCA Collection of 40+ peer-reviewed papers in @NaturePortfolio shedding light on human development, healthy and disease biology and vital analytical tools. #HCA2024NatureCollection #HumanCellAtlas nature.com/immersive/d428…

Excited to share VIBRANT, a new modality and platform for drug discovery using infrared imaging⚡️#drugdiscovery #imaging #ai

Excited to share our latest collaborative work, Raman2RNA (R2R)! 🚀 Our long-term mission: Build AI models to 'generate' and 'predict' single-cell multi-omics data, evolving biology from 'mapping' to 'mapping+generation and prediction'. 🧬🤖 #DigitalBiology #TeamScience #Hiring

We're excited to share Bering, a graph neural network that harnesses subcellular gene colocalization graphs and transfer embeddings for joint cell segmentation and annotation for spatial transcriptomics. @Kang_Jin__ @Oxer22 @tangjianpku @brucearonow We welcome your feedback.

Come join Charles @cscomiter on a venture to build novel generative models to “generate” single-cell multi-omics data from various imaging modalities and more. #Hiring

The creativity behind SCHAF will set the stage for a slew of works relating imaging and omics data. Come join Charles on a new venture to build a “DALL-E” for biology to generate multi-omics data from various novel imaging modalities for large-scale tissue mapping. We are hiring.

I am ecstatic to share the most recent work of my first PhD student Charles Comiter with Aviv Regev. Charles started this challenging work with Aviv when he was an undergraduate student at Yale.

Thrilled to share my primary PhD work: a Transcription Factor Atlas for understanding gene regulation and cell engineering @CellCellPress. We created a comprehensive TF ORF library and applied it to profile resulting expression changes. A thread 1/X sciencedirect.com/science/articl…

Congrats to Jian Shu, PhD, of the Department of Dermatology, who received an NIH New Innovator Award DP2 with the HEAL Initiative for his project, Scale Up Single-Cell Technologies to Map Pain-Associated Genes and Cells Across the Lifespan! reporter.nih.gov/search/45hB3hO…

Interested in decoding and reprogramming cellular senescence/aging? Join us: 👉 jianshulab.org/copy-of-careers