Jekyll2026-02-23T21:26:19+00:00https://rchenlab.github.io/feed.xmlChen LabWelcome to the laboratory of Dr. Rui Chen at the University of California, Irvine!Mapping the Human Retina Fast-Tracks Vision Research2026-01-23T00:00:00+00:002026-01-23T00:00:00+00:00https://rchenlab.github.io/2026/01/23/NG-HRCA

Our lab has built the most detailed map of the human retina ever created, offering a powerful new tool for understanding vision and eye disease. By analyzing nearly four million individual retinal cells from 125 donors and combining data from studies around the world, we identified more than 130 distinct types of cells that make up the retina.

Developed as part of the global Human Cell Atlas initiative, the new atlas shows how retinal cells differ across age, ancestry, and different regions of the eye. This detailed view helps researchers better understand how the healthy retina works, how it changes with age, and how genetic factors contribute to vision disorders.

Published in Nature Genetics, the study was led by researchers including Rui Chen, Jin Li, Jun Wang and Yumei Li in collaboration with an international team. The atlas is expected to speed up discoveries that could lead to improved diagnosis and treatment of eye diseases.

The research was supported primarily by the Chan Zuckerberg Initiative.

]]>Our Lab Becomes First U.S. Site to Deploy Pyxa™ 3D Spatial Transcriptomics System2025-12-03T00:00:00+00:002025-12-03T00:00:00+00:00https://rchenlab.github.io/2025/12/03/3D-spatial-transcriptomics-siteWe are pleased to announce that our lab (the laboratory of Dr. Rui Chen at UC Irvine) has been selected as the first U.S. installation site for the Pyxa™ platform, a next-generation 3D spatial transcriptomics system developed by Stellaromics. This installation expands Stellaromics’ global beta program, following the inaugural deployment at the University of Glasgow in October 2025.

Advancing 3D Spatial Multi-omics at UCI

The Pyxa platform enables high-resolution, multiplexed 3D spatial transcriptomics in intact tissue sections up to 100 µm thick. By capturing hundreds of molecular targets with subcellular precision, Pyxa preserves native tissue architecture—allowing researchers to map cell–cell interactions, molecular gradients, and complex structural features that cannot be resolved using traditional 2D or dissociated single-cell methods.

Our team will apply Pyxa to generate comprehensive 3D spatial atlases of the human eye and trigeminal ganglion, providing new insights into sensory function and disease mechanisms.

A Milestone for Spatial Biology at UCI

This deployment brings cutting-edge 3D spatial multi-omics to UC Irvine and strengthens our role in driving innovative technologies for vision research, sensory neuroscience, and cell atlas development.

]]>HCA Nature Collection2024-11-20T00:00:00+00:002024-11-20T00:00:00+00:00https://rchenlab.github.io/2024/11/20/nature-cell-atlas-collectionOur lab’s research, Zhen’s publication titled “Single cell dual-omic atlas of the human developing retina” has been selected for inclusion in the HCA Nature Collection, “The Human Cell Atlas: towards a first draft atlas”

In this study, we offer a detailed single-nuclei dual-omic atlas of the human developing retina, examining around 220,000 nuclei from 14 human embryos and fetuses aged 8 to 23 weeks post-conception. This atlas encompasses both macular and peripheral tissues, capturing all major retinal cell types, as well as a significant number of progenitors and cell-type-specific precursors. Our analysis of cell trajectories reveals a shift from continuous progression in early progenitors to a more hierarchical development during later stages of cell type specification. We identify both established and novel candidate transcription factors, along with gene regulatory networks that guide the transitions of various cell fates. Notably, comparisons between macular and peripheral retinae show both consistent and distinct developmental patterns. This atlas offers unparalleled insight into the transcriptional and chromatin accessibility landscapes during retinal development, providing valuable information on retinal development and related diseases.

This collection including our manuscript exemplifies the pioneering efforts of the HCA community, showcasing groundbreaking datasets, computational tools, and biomedical discoveries. These contributions lay a strong foundation for the first draft of the Human Cell Atlas, developed by the 18 HCA Biological Networks in collaboration with the core HCA data integration team. More broadly, this collection illustrates how single-cell genomics is revolutionizing our understanding of human biology and driving both experimental and computational innovation.

This achievement has been celebrated globally, with coverage from BBC News, El Pais, CNN, The FT, Reuters, GenomeWeb, The Economist, Yahoo News, among others. The collection has generated significant excitement on social media and at scientific meetings.

]]>Zhen’s Public Defense2024-08-30T00:00:00+00:002024-08-30T00:00:00+00:00https://rchenlab.github.io/2024/08/30/zhen-graduationWe have a new PhD: Congratulations to Dr. Zhen Zuo! We are so proud of you!

]]>Lab Relocation2024-08-01T00:00:00+00:002024-08-01T00:00:00+00:00https://rchenlab.github.io/2024/08/01/UCI

Our lab is relocating to the University of California, Irvine. We will begin a new chapter at Irvine in Ophthalmology and Genetics Research.

]]>CZI Data Insights Cycle 3 Grantee Announcement2024-07-23T00:00:00+00:002024-07-23T00:00:00+00:00https://rchenlab.github.io/2024/07/23/CZI-cycle3The Chan Zuckerberg Initiative (CZI) Data Insights Cycle 3 grantee announcement is now available! These projects aim to support researchers and computational experts in developing tools and resources to extract deeper insights into health and disease from existing single-cell biology datasets.

Our lab will continue collaborating with Dr. Ken Chen’s team from the University of Texas MD Anderson Cancer Center on the project “Insights into the Somatic Mutation Landscape of Single-Cell Omics.” This project aims to explore the somatic mutation landscape across various human normal tissues using diverse sources of single-cell omics data.

]]>Grant awarded to Dr. Hafiz Muhammad Jafar Hussain2024-04-01T00:00:00+00:002024-04-01T00:00:00+00:00https://rchenlab.github.io/2024/04/01/jafar-grant

We are enthusiastic to share the news about the Career-Starter Research Grant awarded to Dr. Hafiz Muhammad Jafar Hussain by The Knights Templar Eye Foundation.

Dr. Hafiz Muhammad Jafar Hussain, a Postdoctoral Associate at our lab, has been awarded a substantial grant of $90,000 from The Knights Templar Eye Foundation to support his research on retinal diseases. This funding is part of the Foundation’s commitment to backing researchers dedicated to the treatment and prevention of vision-impairing conditions in infants and children. Dr. Jafar’s research is set to advance the understanding and potential treatment options for inherited retinal diseases (IRDs) through the exploration and functional analysis of novel candidate genes.

]]>New Postdoctoral Associate2024-03-04T00:00:00+00:002024-03-04T00:00:00+00:00https://rchenlab.github.io/2024/03/04/new-postdoc-jinjingWe welcome new postdoctoral researcher Jinjing Jian Ph.D.!

]]>New Bioinformatics Programmer II2024-02-26T00:00:00+00:002024-02-26T00:00:00+00:00https://rchenlab.github.io/2024/02/26/new-programmer-tingtingWe welcome new bioinformatics programmer Tingting Yang Ph.D.!

]]>Lunar New Year Party2024-02-10T00:00:00+00:002024-02-10T00:00:00+00:00https://rchenlab.github.io/2024/02/10/lab-lunarnewyear-partyWe have a wonderful lab party to celebrate the Lunar New Year of 2024. We enjoy the games and food and have a lot of fun. Happy Spring Festival to everyone!!!

]]>