Kun Zhang
@KunZhangBioE
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Bioengineering professor at UCSD; Principal Investigator at Altos Labs
San Diego, CA
Joined January 2022
Excited to share PerturBench from Altos ( https://t.co/9aox6Bhw6J), a platform for building and benchmarking Virtual Cell models that will be presented at NeurIPS 2025.
arxiv.org
We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes...
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Happy to share the results and data of Human Kidney Atlas V2 covering over 350 patients, resulting from a team effort by KPMP and HuBMAP.
biorxiv.org
Building upon a foundational Human Kidney resource, we present a comprehensive multi-modal atlas that defines spatially resolved versus unresolved repair states and mechanisms in human kidney...
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Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation https://t.co/hF56Sxbj82
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🧬 BREAKING: Our CRISPR-GPT paper is out TODAY in Nature Biomedical Engineering @natBME ! 🤯 We built an AI agent that turns ANYONE into a gene-editing expert in 1 DAY instead of months. An undergrad with ZERO experience achieved 90%+ editing efficiency on their FIRST attempt. 🧵
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What if the blueprint for youth is never truly lost, just inaccessible? Today, we're excited to announce the publication of our "Cell Annealing" model in which cells can be rebooted to restore their optimal, youthful state and escape ageing. https://t.co/ulEESqffsP
nature.com
Cell Research - Escaping ageing through Cell Annealing—a phenomenological model
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DNA methylation goes spatial! Introducing Spatial-DMT: a technology that co-profiles DNA methylation and transcriptome in the same tissue section. A fantastic collaboration with @zhouwanding lab. Kudos to Chin Nien Lee @ChinNLee2021 and Hongxiang Fu!
biorxiv.org
The spatial resolution of omics dynamics is fundamental to understanding tissue biology. Spatial profiling of DNA methylation, which is a canonical epigenetic mark extensively implicated in transcr...
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Happy to share our results on the largest multi-modal lung cell atlas, resulting from the HuBMAP lung cell mapping center:
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This is pretty cool, a creative use of AI.
I am organizing a seminar/conference + recruiting speakers. In this blog post, I walk through how I use #AI to augment my intelligence in identifying diverse speakers (+ prevent manels). Try it out yourself: https://t.co/AXb4jS6MSf
#AcademicTwitter #DEI #Rstats #creativecoding
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Free scientific illustrations for biologists! 😍 @NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations! all freely available in the public domain. Retweet and spread the message! https://t.co/p1bD1kxO7H
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🔬💔Discovery of a novel mechanism of cardiac inflammation that may expand therapeutic opportunities from our very own Dr. Kevin King! He is a senior author of the study and faculty in the Shu Chien Gene Lay Department of Bioengineering.
A new mechanism that triggers inflammation after heart attacks: work by @UCSanDiego researchers in @Nature: https://t.co/OHGAddbBWw
@UCSDHealth @UCSDHealthSci @ucsdbe #Cardiology #heartattack #inflammation
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🔬✨ Congrats to Kian Kalhor, nominated by Dr. Kun Zhang, for receiving the 2023-2024 Engelson Ph.D. Thesis Award! To learn more about his work, check out Kian’s thesis, "Mapping Human Tissues with Spatial Transcriptomics"!
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PDACatch, a NGS DNA methylation test for pancreatic cancer, received the FDA Breakthrough Device Designation in 2023, and is currently being offered as a Laboratory Developed Test in the US through Singlera's clinical partner BT Genomics:
btreveal.com
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HepaAiQ, another DNA methylation-based test for liver cancer developed by Singlera, has shown very strong performance on clinical samples in a publication came out this week:
onlinelibrary.wiley.com
The HepaAiQ assay integrates the most effective HCC-specific methylation biomarkers using multilocus quantitative PCR. In multicentre studies, the HepaAiQ model accurately distinguishes HCC from...
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In addition to early screening, ColonAiQ was also found effective in monitoring relapses after surgery:
jamanetwork.com
This cohort study investigates the effectiveness of circulating tumor DNA methylation in early detection of colorectal cancer recurrence.
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In 2014 I co-founded Singlera Genomics with several partners. In 2024 a blood-based methylation test for colon cancer, ColonAiQ, received the Chinese FDA approval. Congratulations to the team who developed the test, took it through the approval, and ran it on 200k+ patients.
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For the most part, life gives you so many decisions to make and so many opportunities to recover from your mistakes that, if you handle them well, you can have a terrific life. Of course, sometimes there are major influences on the quality of our lives that come from things
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Our spatial RNA mapping method is out. We first conceived the idea more than 10 years ago:
link.springer.com
Nature Communications - Application of multiplexed RNA in situ mapping techniques to human tissues remains challenging. Here, the authors report DART-FISH, a padlock probe-based technology capable...
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Our latest out today in @Nature. We profiled 12 million single cells from mouse embryos spanning gastrulation to birth, defined cell type tree from zygote to birth, and unexpectedly found crazy fast changes within first hour of extrauterine life. OA PDF:
Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab. We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup. Preprint: https://t.co/GDS65Qf58X 1/n
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.@UCSDJacobs and @ucsdbe's Biotechnology & Bioinformatics undergraduate majors are ranked #2 by @usnews! Thanks to all faculty, staff, and students for their hard work. https://t.co/J7wbm8bav0
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