Wei Li

323 posts

Wei Li

Wei Li

@davidliwei

Computational biologist working on gene editing and cancer biology. Associate Professor, University of Maryland School of Medicine. Views are my own.

Rockville, MD شامل ہوئے Haziran 2009
655 فالونگ938 فالوورز
پن کیا گیا ٹویٹ
Wei Li
Wei Li@davidliwei·
Our most recent Nature Cell Biology paper describes an innovative Perturbation-response Score (PS) method to decode heterogeneous responses of cells to perturbations at single-cell level. Particularly helpful for analyzing Perturb-seq data. nature.com/articles/s4155…
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Austin Hartman
Austin Hartman@AustinMHartman·
4/6 We also found that off-target seed alignments closer to off-target TSSs tended to lead to stronger repression and candidate off-target guides were enriched for Gs
Austin Hartman tweet media
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Austin Hartman
Austin Hartman@AustinMHartman·
1/6 I was reanalyzing Perturb-seq data and stumbled into what I thought was a new TCR signaling regulator, only to realize it was an off-target effect. The guide ‘seed’ aligned near a canonical pathway member's TSS leading to off-target repression and association with the pathway
Austin Hartman tweet media
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Wei Li
Wei Li@davidliwei·
Also, especially shout out to the scGPT tool built by @BoWang87. It would be much more difficult to build our model without the wonderful, open-source scGPT!
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Wei Li
Wei Li@davidliwei·
Perturbation-prediction AI models are critical for building virtual cells. Many models exist, but what is next? What is the critical gap to application? Our pertTF preprint shows the next step: cross-system prediction, and beyond gene expression. biorxiv.org/content/10.648…
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Wei Li
Wei Li@davidliwei·
@xinjin @NVIDIAHealth Really incredible resource to understand brain function and great for the AI community. Thanks for releasing all these wonderful datasets!!
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Xin Jin, PhD
Xin Jin, PhD@xinjin·
📢 Preprint: we present a whole-mouse-brain in vivo Perturb-seq atlas, 7.7 million cells, 1947 disease-associated perturbations, moving toward direct readout of how human genetics rewires cell states & circuits in vivo. Grateful for the Team! @NVIDIAHealth biorxiv.org/content/10.648…
Xin Jin, PhD tweet media
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Yarui Diao
Yarui Diao@YaruiDiao·
Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.
Nature Biotechnology@NatureBiotech

Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR go.nature.com/4rZqimf

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Wei Li
Wei Li@davidliwei·
Perturb2026 is an exciting conference about generating perturbation data, building AI models, and interacting with academic and industry attendees. Great lineup of speakers. Come and join us on March 18-19, Vienna, Austria! perturb2026.bio
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Bo Wang
Bo Wang@BoWang87·
🧬 Building the Virtual Cell starts with data. Today, we’re making the X-Atlas/Orion Perturb-seq dataset even more accessible — now live on Hugging Face @huggingface 🤗 📊 One of the largest & highest-quality perturbation datasets ever released, it provides the foundation for training AI models that can simulate and reason about cellular behavior. 👉 Explore here: huggingface.co/datasets/Xaira… Fewer barriers. More models. A step closer to the virtual cell. 🌌 #VirtualCell #FoundationModels #AIinBiology #HuggingFace
Bo Wang@BoWang87

🚀 Xaira Therapeutics has just dropped a game-changer for AI-driven biology. Today, we unveiled X-Atlas/Orion, the largest publicly available genome-wide Perturb-seq dataset to date—spanning 8.4 million single cells with perturbations across all ~20,000 human protein-coding genes. This release is not just about scale—it’s about enabling a new era of causal, mechanistic foundation models for biology. 📝 Preprint on bioRxiv: biorxiv.org/content/10.110… 📂 Dataset on Figshare: doi.org/10.25452/figsh… 🔍 What makes X-Atlas/Orion special: 📈 Unprecedented scale & quality: Each cell profiled with deep (~16k UMIs) transcriptomics and rich metadata 🧪 Quantitative dose-response modeling: Thanks to high-fidelity sgRNA detection and ~4 guides per gene, allowing continuous modeling of genetic effects 🧬 FiCS platform: A fully industrialized single-cell perturbation system enabling rapid, reproducible experiments at massive throughput 🧠 This isn’t just “data.” It’s the biological substrate for building virtual cell models that can generalize, predict, and ultimately power AI-native drug discovery. 💬 My final take: This is a foundational moment for the field. The ability to model how genes affect cell state—quantitatively, causally, and at scale—is what we need to unlock predictive biology. Kudos to the incredible team at Xaira for open-sourcing this resource so the entire community can build on it. #PerturbSeq #SingleCell #Genomics #VirtualCell #FoundationModels #AIForBiology #Xaira #DrugDiscovery #SyntheticBiology #CausalAI More press release: Press release : 🔗 GEN article : genengnews.com/topics/artific… 🔗 BusinessWire: businesswire.com/news/home/2025…

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Yarui Diao
Yarui Diao@YaruiDiao·
Following 2023 paper, our new study on TE regulation is out today @NatureCellBio! nature.com/articles/s4155…
Yarui Diao@YaruiDiao

Out now @NatureGenet!!! Dive into the interplay of RNA m6A/DNA 5mC that controls transposable elements (TEs) chromatin activation and hESC fate! Kudos to our brilliant postdoc, Tongyu Sun, who developed CARGO-BioID for TE-centered proteome analysis to unearth all these findings!

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Wei Li
Wei Li@davidliwei·
Application is still open until Aug 25. Great for trainees of all levels. Come and join us!
Cold Spring Harbor Asia@CSHANews

#CSHAsia Course on #CRISPR #Genome Engineering: Basics, Applications and Future Directions ⌛️Application is still available by Aug. 25 📍Suzhou, China 📅October 9-19, 2025 🎯Undergrad/graduate students, postdoctoral fellows, scientists and professors

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Peng Jiang
Peng Jiang@PengJiang20·
Our Cell paper is online (doi.org/10.1016/j.cell…)! We present the CIDE framework, broadly applicable to cancer research and oncology. Also, we highlight AOAH as a promising new immunotherapy.
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Wei Li
Wei Li@davidliwei·
@BaoxuP Also immediately after this course (Oct 9-19) is the CSHA "Systems Biology of Gene Regulation and Genome Editing" conference (Oct 20-24). Great opportunity to attend both events in one place! @CSHANews
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Wei Li
Wei Li@davidliwei·
We are delighted to organize this CSHA inaugural CRISPR course, this October, at the beautiful Suzhou City, China. Great opportunity for trainees/researchers to learn everything about genome engineering and interact with top scientists in the field. App ddl Aug 8.
Wei Li tweet media
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Jingyi Jessica Li (李婧翌)
Jingyi Jessica Li (李婧翌)@jsb_ucla·
I’m honored to join Fred Hutch as Professor and Program Head of Biostatistics, and as the Donald and Janet K. Guthrie Endowed Chair in Statistics. Excited to be part of a deeply collaborative and scientifically vibrant community with a rich legacy of impact.
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دریافت کریں

@AustinMHartman @BoWang87 @DanweiHuangfu @hon_lab @YaruiDiao @hanrui_zhang @Xaira_Thera @perturbai_tx