Research

Our research integrates cutting-edge single-cell multi-omics, lineage tracing, spatial transcriptomics, bioinformatics, artificial intelligence, and organoid technologies. We are driven by the goal to map and model the functional and regulatory dynamics of cells within living systems—from embryos to adult tissues—and to translate these insights into novel strategies for tissue repair, organ reconstruction, and regenerative medicine.

Highlighted

Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development

Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Li Wang, …, Minhan Wang, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng

Nature Methods  ·  31 Jul 2023  ·  doi:10.1038/s41592-023-01884-1

GitHub

spatial-rna+atac-seq brain-development

Three-dimensional molecular architecture of mouse organogenesis

Fangfang Qu, Wenjia Li, Jian Xu, Ruifang Zhang, Jincan Ke, …, Duanqing Pei, Jiekai Chen, Guizhong Cui, Shengbao Suo, Guangdun Peng

Nature Communications  ·  03 Apr 2023  ·  doi:10.1038/s41467-023-40155-7

3d-architecture organogenesis

Dual-nuclease single-cell lineage tracing by Cas9 and Cas12a

Cheng Chen, Yuanxin Liao, Miao Zhu, Li Wang, Xinran Yu, Meishi Li, Guangdun Peng

Cell Reports  ·  28 Jan 2025  ·  doi:10.1016/j.celrep.2024.115105

lineage-tracing crispr/cas

All

2026

Divergent stem cell mechanisms govern the primary body axis and appendage regeneration in the axolotl

Liqun Wang, Li Song, Chao Yi, Jing Zhou, Zhouying Yong, …, Guangdun Peng, Elly M. Tanaka, Hanbo Li, Yanmei Liu, Ji-Feng Fei

Science Advances  ·  06 Feb 2026  ·  doi:10.1126/sciadv.adx5697

A single-cell time-series atlas of endothelial cell embryonic development

Lihui Lin, Jing Zhong, Fuqing Jiang, Yu-xiang Wang, Lan-yue Ma, …, Shangtao Cao, Yang Liu, Guangdun Peng, Jiekai Chen, Qi Chen

Cell  ·  01 Feb 2026  ·  doi:10.1016/j.cell.2026.01.002

Spatial Chromatin Accessibility Analysis of Intratumor Heterogeneity in Breast Cancer

Yingying Qian, Miao Zhu, Chongyang Ren, Yeyong Zhou, Jian Xu, …, Jiaoyi lv, Qiaorui Xing, Guochun Zhang, Guangdun Peng, Ning Liao

Genomics, Proteomics & Bioinformatics  ·  12 Jan 2026  ·  doi:10.1093/gpbjnl/qzag001

breast-cancer spatial-atac

Nat10-mediated ac4C epitranscriptomics orchestrates hematopoietic stem/progenitor cell fate determination via translation control

Feng Huang, Yushuai Wang, Weiwei Gao, Xiuxin Zhang, Jiajia Zhou, …, Qi Chen, Guangdun Peng, Jianjun Chen, Huilin Huang, Hengyou Weng

Science Advances  ·  09 Jan 2026  ·  doi:10.1126/sciadv.ady0301

2025

Spatial and single-cell transcriptomics landscape of adenomyosis

Xing Yang, Chunjie Li, Junxian He, Bingbing Xie, Linyan Lv, …, Guizhong Cui, Guihua Liu, Shengbao Suo, Guangdun Peng, Xiaoyan Liang

Journal of Advanced Research  ·  26 Dec 2025  ·  doi:10.1016/j.jare.2025.12.042

adenomyosis transcriptomics-landscape

SPHENIC: Topology-Aware Multi-View Clustering for Spatial Transcriptomics

Chenkai Guo, Yikai Zhu, Renxiang Guan, Jinli Ma, Siwei Wang, Ke Liang, Guangdun Peng, Dayu Hu

arXiv  ·  16 Oct 2025  ·  arxiv:2508.10646

persistent-homology multi-view-clustering

Dissecting the Spatial and Single‐Cell Transcriptomic Architecture of Cancer Stem Cell Niche Driving Tumor Progression in Gastric Cancer

Guangyu Zhang, Xin Zhang, Wenting Pan, Xizhao Chen, Lingfei Wan, …, Xinhui Wang, Guangdun Peng, Xinlong Yan, Yanchun Wang, Min Zhang

Advanced Science  ·  14 Aug 2025  ·  doi:10.1002/advs.202413019

gastric-cancer single-cell-rna-seq

A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells

Huanhuan Li, Wei Guan, Jiahui Huang, Penglei Shen, Jinyi Wu, …, Guangming Wu, Jiekai Chen, Jian Zhang, Naihe Jing, José C.R. Silva

Cell  ·  15 Jul 2025  ·  doi:10.1016/j.cell.2025.07.018

embryogenesis stem-cells

High-resolution mapping of single cells in spatial context

Jincan Ke, Jian Xu, Jia Liu, Yumeng Yang, Chenkai Guo, Bingbing Xie, Guizhong Cui, Guangdun Peng, Shengbao Suo

Nature Communications  ·  15 Jul 2025  ·  doi:10.1038/s41467-025-61667-4

GitHub

high-resolution-scrna-seq-mapping spatial-deconvolution

Spatiotemporal transcriptome atlas of developing mouse lung

Xiaogao Meng, Wenjia Li, Jian Xu, Yao Yao, An Gong, …, Chenkai Guo, Hui Zheng, Guizhong Cui, Shengbao Suo, Guangdun Peng

Science Bulletin  ·  10 Mar 2025  ·  doi:10.1016/j.scib.2025.03.012

spatiotemporal-atlas lung-development

Learning Phenotype Associated Signature in Spatial Transcriptomics with PASSAGE

Chen‐Kai Guo, Chen‐Rui Xia, Guangdun Peng, Zhi‐Jie Cao, Ge Gao

Small Methods  ·  04 Feb 2025  ·  doi:10.1002/smtd.202401451

GitHub

multi-slice-spatial-analysis graph-attention-network

Dual-nuclease single-cell lineage tracing by Cas9 and Cas12a

Cheng Chen, Yuanxin Liao, Miao Zhu, Li Wang, Xinran Yu, Meishi Li, Guangdun Peng

Cell Reports  ·  28 Jan 2025  ·  doi:10.1016/j.celrep.2024.115105

lineage-tracing crispr/cas

Leveraging spatial multiomics to unravel tissue architecture in embryo development

Fuqing Jiang, Haoxian Wang, Zhuxia Li, Guizhong Cui, Guangdun Peng

Trends in Genetics  ·  28 Jan 2025  ·  doi:10.1016/j.tig.2024.11.007

spatial-multiomics embryo-development

2024

Surface-Functionalizing Strategies for Multiplexed Molecular Biosensing: Developments Powered by Advancements in Nanotechnologies

Shangjie Zou, Guangdun Peng, Zhiqiang Ma

Nanomaterials  ·  14 Dec 2024  ·  doi:10.3390/nano14242014

nanotechnology molecular-biosensing

A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2

Zeqing Wang, Zhuxia Li, Tianle Luan, Guizhong Cui, Shunpan Shu, …, Wei Yu, Jihong Cui, Ang Li, Guangdun Peng, Yanshan Fang

Developmental Cell  ·  21 Oct 2024  ·  doi:10.1016/j.devcel.2024.06.016

spinal-cord-injury astrocyte-atlas

Learning phenotype associated signature in spatial transcriptomics with PASSAGE

Chen-Kai Guo, Chen-Rui Xia, Guangdun Peng, Zhi-Jie Cao, Ge Gao

openRxiv  ·  11 Sep 2024  ·  doi:10.1101/2024.09.06.611564

Systematic comparison of sequencing-based spatial transcriptomic methods

Yue You, Yuting Fu, Lanxiang Li, Zhongmin Zhang, Shikai Jia, …, Guangdun Peng, Abhishek Sampath Kumar, Matthew E. Ritchie, Xiaodong Liu, Luyi Tian

Nature Methods  ·  04 Jul 2024  ·  doi:10.1038/s41592-024-02325-3

benchmarking spatial-technology

Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration

Yue Fan, Xuzhao Bian, Xiaogao Meng, Lei Li, Laiyi Fu, …, Dalong Gao, Xiong Guo, Mikko Juhani Lammi, Guangdun Peng, Shiquan Sun

Annals of the Rheumatic Diseases  ·  01 Jul 2024  ·  doi:10.1136/ard-2023-224420

osteoarthritis cartilage-degeneration

Dual nuclease single-cell lineage tracing by Cas9 and Cas12a

Cheng Chen, Yuanxin Liao, Miao Zhu, Li Wang, Xinran Yu, Meishi Li, Guangdun Peng

openRxiv  ·  30 May 2024  ·  doi:10.1101/2024.05.27.596125

2023

Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation

Ran Wang, Xianfa Yang, Jiehui Chen, Lin Zhang, Jonathan A. Griffiths, …, Jinsong Li, Liantang Wang, John C. Marioni, Patrick P. L. Tam, Naihe Jing

Nature Communications  ·  14 Sep 2023  ·  doi:10.1038/s41467-023-41482-5

Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development

Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Li Wang, …, Minhan Wang, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng

Nature Methods  ·  31 Jul 2023  ·  doi:10.1038/s41592-023-01884-1

GitHub

spatial-rna+atac-seq brain-development

Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedding of Transcriptomic Networks

Yuxuan Zhao, Shiqiang Zhang, Jian Xu, Yangyang Yu, Guangdun Peng, Carlo Vittorio Cannistraci, Jing‐Dong J. Han

Advanced Science  ·  15 Jun 2023  ·  doi:10.1002/advs.202206307

Time, Space and Single-Cell Resolved Molecular Trajectory of Cell Populations and the Laterality of the Body Plan at Gastrulation

Ran Wang, Xianfa Yang, Jiehui Chen, Lin Zhang, Jonathan A. Griffiths, …, Jinsong Li, Liantang Wang, John C. Marioni, Patrick P.L. Tam, Naihe Jing

openRxiv  ·  21 Apr 2023  ·  doi:10.1101/2023.04.19.537134

Lung development and regeneration: newly defined cell types and progenitor status

Xiaogao Meng, Guizhong Cui, Guangdun Peng

Cell Regeneration  ·  03 Apr 2023  ·  doi:/10.1186/s13619-022-00149-0

lung-regeneration progenitor-status

Three-dimensional molecular architecture of mouse organogenesis

Fangfang Qu, Wenjia Li, Jian Xu, Ruifang Zhang, Jincan Ke, …, Duanqing Pei, Jiekai Chen, Guizhong Cui, Shengbao Suo, Guangdun Peng

Nature Communications  ·  03 Apr 2023  ·  doi:10.1038/s41467-023-40155-7

3d-architecture organogenesis

Lung development and regeneration: newly defined cell types and progenitor status

Xiaogao Meng, Guizhong Cui, Guangdun Peng

Cell Regeneration  ·  03 Apr 2023  ·  doi:10.1186/s13619-022-00149-0

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

He Jax Xu, Yao Yao, Fenyong Yao, Jiehui Chen, Meishi Li, …, Fangru Lu, Ping Hu, Shuijin He, Guangdun Peng, Naihe Jing

Cell Regeneration  ·  23 Mar 2023  ·  doi:10.1186/s13619-023-00159-6

motor-neurons neural-progenitors

Distinct reward processing by subregions of the nucleus accumbens

Gaowei Chen, Shishi Lai, Guo Bao, Jincan Ke, Xiaogao Meng, …, Fang Xu, Guo-Qiang Bi, Guangdun Peng, Kuikui Zhou, Yingjie Zhu

Cell Reports  ·  01 Feb 2023  ·  doi:10.1016/j.celrep.2023.112069

Genome Editing by Dual Nucleases Records Deep Lineage Hierarchy with High Fidelity

Cheng Chen, Yuanxin Liao, Miao Zhu, Li Wang, Xinran Yu, Meishi Li, Guangdun Peng

Elsevier BV  ·  01 Jan 2023  ·  doi:10.2139/ssrn.4502778

2022

Three-dimensional molecular architecture of mouse organogenesis

Fangfang Qu, Wenjia Li, Jian Xu, Ruifang Zhang, Jincan Ke, …, Duanqing Pei, Jiekai Chen, Guizhong Cui, Shengbao Suo, Guangdun Peng

openRxiv  ·  17 Nov 2022  ·  doi:10.1101/2022.11.17.516228

Three-dimensional molecular architecture of mouse organogenesis

Guangdun Peng, Fangfang QU, Jian Xu, Wenjia Li, Ruifang Zhang, …, Guangming Wu, Duanqing Pei, Jiekai Chen, Guizhong Cui, Shengbao Suo

Springer Science and Business Media LLC  ·  17 Nov 2022  ·  doi:10.21203/rs.3.rs-2230279/v1

Spatial molecular anatomy of germ layers in the gastrulating cynomolgus monkey embryo

Guizhong Cui, Su Feng, Yaping Yan, Li Wang, Xiechao He, …, Ping Zheng, Patrick P.L. Tam, Wei Si, Naihe Jing, Guangdun Peng

Cell Reports  ·  08 Nov 2022  ·  doi:10.1016/j.celrep.2022.111285

primate-embryo germ-layers

Activation of Wnt/β-catenin signaling by Zeb1 in endothelial progenitors induces vascular quiescence entry

Qing Cissy Yu, Ajun Geng, Christopher B. Preusch, Yujie Chen, Guangdun Peng, …, Weijun Pan, Jianfeng Chen, K. Christopher Garcia, Tom H. Cheung, Yi Arial Zeng

Cell Reports  ·  01 Nov 2022  ·  doi:10.1016/j.celrep.2022.111694

Spatiotemporal orchestration of multicellular transcriptional programs and communications in the early stage of spinal cord injury

Zeqing Wang, Zhuxia Li, Tianle Luan, Guizhong Cui, Shunpan Shu, …, Wei Yu, Jihong Cui, Ang Li, Guangdun Peng, Yanshan Fang

openRxiv  ·  07 Oct 2022  ·  doi:10.1101/2022.10.07.511269

Single-cell technologies: From research to application

Lu Wen, Guoqiang Li, Tao Huang, Wei Geng, Hao Pei, …, Guangdun Peng, Xianwen Ren, Nan Jiang, Caihuan Tian, Zi-Jiang Chen

The Innovation  ·  30 Aug 2022  ·  doi:10.1016/j.xinn.2022.100342

single-cell-technologies clinical-application

Integration of Computational Analysis and Spatial Transcriptomics in Single-Cell Studies

Ran Wang, Guangdun Peng, Patrick P.L. Tam, Naihe Jing

Genomics, Proteomics & Bioinformatics  ·  25 Jul 2022  ·  doi:10.1016/j.gpb.2022.06.006

Profiling spatial gene activity in marmoset embryos

Guangdun Peng, Patrick P. L. Tam

Cell Research  ·  20 Jul 2022  ·  doi:10.1038/s41422-022-00703-0

Spatial transcriptomics: new dimension of understanding biological complexity

Zhuxia Li, Guangdun Peng

Biophysics reports  ·  30 Jun 2022  ·  pmc:PMC10189652

spatial-transcriptomics biological-complexity

Connecting past and present: single-cell lineage tracing

Cheng Chen, Yuanxin Liao, Guangdun Peng

Protein & Cell  ·  30 Jun 2022  ·  doi:10.1007/s13238-022-00913-7

lineage-tracing review

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Jax H. Xu, Yao Yao, Fenyong Yao, Jiehui Chen, Meishi Li, …, Fangru Lu, Ping Hu, Shuijin He, Guangdun Peng, Naihe Jing

openRxiv  ·  27 Jun 2022  ·  doi:10.1101/2022.06.26.495599

Embryonic vascular establishment requires protein C receptor-expressing endothelial progenitors

Qing Cissy Yu, Lanyue Bai, Yingying Chen, Yujie Chen, Guangdun Peng, Daisong Wang, Guowei Yang, Guizhong Cui, Naihe Jing, Yi Arial Zeng

Development  ·  15 Jun 2022  ·  doi:10.1242/dev.200419

Simultaneous profiling of spatial gene expression and chromatin accessibility for mouse brain development

Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Li Wang, …, Qingmei Shen, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng

openRxiv  ·  23 Mar 2022  ·  doi:10.1101/2022.03.22.485333

Spatial and molecular anatomy of germ layers in the gastrulating Cynomolgus monkey embryo

Guizhong Cui, Su Feng, Yaping Yan, Li Wang, Xiechao He, …, Ke Tang, Ping Zheng, Wei Si, Naihe Jing, Guangdun Peng

openRxiv  ·  28 Jan 2022  ·  doi:10.1101/2022.01.26.474719

Spatial transcriptomics: new dimension of understanding biological complexity

Li Zhuxia, Peng Guangdun

Biophysics Reports  ·  01 Jan 2022  ·  doi:10.52601/bpr.2021.210037

2021

Base editing‐mediated perturbation of endogenous PKM1/2 splicing facilitates isoform‐specific functional analysis in vitro and in vivo

Jianxiang Lin, Susu Wu, Qingmei Shen, Jie Liu, Shisheng Huang, Guangdun Peng, Yunbo Qiao

Cell Proliferation  ·  09 Jul 2021  ·  doi:10.1111/cpr.13096

base-editing isoform-analysis

RNA helicase DDX5 acts as a critical regulator for survival of neonatal mouse gonocytes

Qing Xia, Guizhong Cui, Ye Fan, Xiuqin Wang, Gongcheng Hu, …, Wei Li, Jiayu Chen, Huayu Qi, Guangdun Peng, Hongjie Yao

Cell Proliferation  ·  05 Mar 2021  ·  doi:10.1111/cpr.13000

rna-helicase neonatal-gonocytes

2020

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

Woo Jun Shim, Enakshi Sinniah, Jun Xu, Burcu Vitrinel, Michael Alexanian, …, Michael Piper, Lionel Christiaen, Quan Nguyen, Mikael Bodén, Nathan J. Palpant

Cell Systems  ·  01 Dec 2020  ·  doi:10.1016/j.cels.2020.11.001

Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development

Guangdun Peng, Guizhong Cui, Jincan Ke, Naihe Jing

Annual Review of Genomics and Human Genetics  ·  31 Aug 2020  ·  doi:10.1146/annurev-genom-120219-083220

lineage-specification review

Imbalance of Excitatory/Inhibitory Neuron Differentiation in Neurodevelopmental Disorders with an NR2F1 Point Mutation

Ke Zhang, Fang Yu, Jian Zhu, Sue Han, Jiehui Chen, …, Jinsong Li, Guangdun Peng, Shuijin He, Naihe Jing, Ke Tang

Cell Reports  ·  01 Apr 2020  ·  doi:10.1016/j.celrep.2020.03.085

C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors

Di Demi He, Xinyu Thomas Tang, Wenjie Dong, Guizhong Cui, Guangdun Peng, Xiujuan Yin, Yujie Chen, Naihe Jing, Bo O. Zhou

Stem Cell Reports  ·  01 Apr 2020  ·  doi:10.1016/j.stemcr.2020.03.001

2019

Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning

Hani Jieun Kim, Pierre Osteil, Sean J Humphrey, Senthilkumar Cinghu, Andrew J Oldfield, …, Guangdun Peng, Shengbao Suo, Raja Jothi, Patrick P L Tam, Pengyi Yang

Nucleic Acids Research  ·  19 Dec 2019  ·  doi:10.1093/nar/gkz1179

Comments on ‘Molecular architecture of lineage allocation and tissue organization in early mouse embryo’

Guizhong Cui, Naihe Jing, Guangdun Peng

Journal of Molecular Cell Biology  ·  22 Nov 2019  ·  doi:10.1093/jmcb/mjz101

commentary mouse-embryo

Dissecting primate early post-implantation development using long-term in vitro embryo culture

Yuyu Niu, Nianqin Sun, Chang Li, Ying Lei, Zhihao Huang, …, Guizhong Cui, Guangdun Peng, Juan Carlos Izpisúa Belmonte, Weizhi Ji, Tao Tan

Science  ·  15 Nov 2019  ·  doi:10.1126/science.aaw5754

primate-development post-implantation

AutoGenome: An AutoML Tool for Genomic Research

Denghui Liu, Chi Xu, Wenjun He, Zhimeng Xu, Wenqi Fu, …, Jie Yang, Guangdun Peng, Dali Han, Xiaolong Bai, Nan Qiao

openRxiv  ·  15 Nov 2019  ·  doi:10.1101/842526

A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing

Yifei Zhou, Xueqing Wang, Mengjiao Song, Zhidong He, Guizhong Cui, Guangdun Peng, Christoph Dieterich, Adam Antebi, Naihe Jing, Yidong Shen

Nature Communications  ·  23 Oct 2019  ·  doi:10.1038/s41467-019-12821-2

Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development

Xianfa Yang, Boqiang Hu, Jiaoyang Liao, Yunbo Qiao, Yingying Chen, …, Ran Wang, Guangdun Peng, Jinsong Li, Fuchou Tang, Naihe Jing

Cell Research  ·  07 Oct 2019  ·  doi:10.1038/s41422-019-0234-8

Molecular architecture of lineage allocation and tissue organization in early mouse embryo

Guangdun Peng, Shengbao Suo, Guizhong Cui, Fang Yu, Ran Wang, …, Guoyu Chen, Yun Qian, Patrick P. L. Tam, Jing-Dong J. Han, Naihe Jing

Nature  ·  22 Aug 2019  ·  doi:10.1038/s41586-019-1469-8

lineage-allocation mouse-embryo

Conserved epigenetic regulatory logic infers genes governing cell identity

Woo Jun Shim, Enakshi Sinniah, Jun Xu, Burcu Vitrinel, Michael Alexanian, …, Michael Piper, Lionel Christiaen, Quan Nguyen, Mikael Bodén, Nathan J. Palpant

openRxiv  ·  12 May 2019  ·  doi:10.1101/635516

Dynamics of Wnt activity on the acquisition of ectoderm potency in epiblast stem cells

Pierre Osteil, Josh B. Studdert, Hwee Ngee Goh, Emilie E. Wilkie, Xiaochen Fan, …, Hilary Knowles, Jing-Dong J. Han, Naihe Jing, Nicolas Fossat, Patrick P. L. Tam

Development  ·  01 Apr 2019  ·  doi:10.1242/dev.172858

A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis

Yuanyuan Xue, Denghui Liu, Guizhong Cui, Yanyan Ding, Daosheng Ai, …, Xingwei Chen, Guangdun Peng, Naihe Jing, Jing-Dong J. Han, Feng Liu

Cell Reports  ·  01 Apr 2019  ·  doi:10.1016/j.celrep.2019.04.030

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development

Shangli Cheng, Yu Pei, Liqun He, Guangdun Peng, Björn Reinius, Patrick P.L. Tam, Naihe Jing, Qiaolin Deng

Cell Reports  ·  01 Mar 2019  ·  doi:10.1016/j.celrep.2019.02.031

VGLL4 plays a critical role in heart valve development and homeostasis

Wei Yu, Xueyan Ma, Jinjin Xu, Andreas Wilhelm Heumüller, Zhaoliang Fei, …, Zhiqiang Lin, Yun Zhao, Zuoyun Wang, Bin Zhou, Lei Zhang

PLOS Genetics  ·  21 Feb 2019  ·  doi:10.1371/journal.pgen.1007977

Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction

Qiaozhen Liu, Kuo Liu, Guizhong Cui, Xiuzhen Huang, Shun Yao, …, Yi Arial Zeng, Naihe Jing, Guangdun Peng, Hongbin Ji, Bin Zhou

Nature Genetics  ·  18 Feb 2019  ·  doi:10.1038/s41588-019-0346-6

Hormones induce the formation of luminal-derived basal cells in the mammary gland

Wenqian Song, Ran Wang, Weimin Jiang, Qi Yin, Guangdun Peng, …, Jianfeng Chen, Jingsong Li, Tom H. Cheung, Naihe Jing, Yi Arial Zeng

Cell Research  ·  10 Jan 2019  ·  doi:10.1038/s41422-018-0137-0

2018

Author Correction: Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation

Neophytos Christodoulou, Christos Kyprianou, Antonia Weberling, Ran Wang, Guizhong Cui, Guangdun Peng, Naihe Jing, Magdalena Zernicka-Goetz

Nature Cell Biology  ·  19 Nov 2018  ·  doi:10.1038/s41556-018-0245-6

Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation

Neophytos Christodoulou, Christos Kyprianou, Antonia Weberling, Ran Wang, Guizhong Cui, Guangdun Peng, Naihe Jing, Magdalena Zernicka-Goetz

Nature Cell Biology  ·  15 Oct 2018  ·  doi:10.1038/s41556-018-0211-3

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

Clayton E. Friedman, Quan Nguyen, Samuel W. Lukowski, Abbigail Helfer, Han Sheng Chiu, …, Hannele Ruohola-Baker, Ziv Bar-Joseph, Patrick P.L. Tam, Joseph E. Powell, Nathan J. Palpant

Cell Stem Cell  ·  01 Oct 2018  ·  doi:10.1016/j.stem.2018.09.009

Mouse gastrulation: Attributes of transcription factor regulatory network for epiblast patterning

Guizhong Cui, Shengbao Suo, Ran Wang, Yun Qian, Jing‐Dong J. Han, Guangdun Peng, Patrick P. L. Tam, Naihe Jing

Development, Growth & Differentiation  ·  01 Oct 2018  ·  doi:10.1111/dgd.12568

Regulatory network characterization in development: challenges and opportunities

Guangdun Peng, Jing-Dong J. Han

F1000Research  ·  17 Sep 2018  ·  doi:10.12688/f1000research.15271.1

A gene regulatory network anchored by LIM homeobox 1 for embryonic head development

Tennille Sibbritt, Chi K. Ip, Poh‐Lynn Khoo, Emilie Wilkie, Vanessa Jones, …, Naihe Jing, Pierre Osteil, Mirana Ramialison, Patrick P. L. Tam, Nicolas Fossat

genesis  ·  01 Sep 2018  ·  doi:10.1002/dvg.23246

Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells

Chang Liu, Ran Wang, Zhisong He, Pierre Osteil, Emilie Wilkie, …, Wenke Guo, Yingying Chen, Guangdun Peng, Patrick P.L. Tam, Naihe Jing

Stem Cell Reports  ·  01 Jul 2018  ·  doi:10.1016/j.stemcr.2018.05.019

Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development

Xue Han, Sai Luo, Guangdun Peng, J Yuyang Lu, Guizhong Cui, …, Zai Chang, Jie Na, Aibin He, Naihe Jing, Xiaohua Shen

Journal of Molecular Cell Biology  ·  09 Mar 2018  ·  doi:10.1093/jmcb/mjy003

Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages

Xianfa Yang, Boqiang Hu, Yu Hou, Yunbo Qiao, Ran Wang, …, Jun Chen, Chang Liu, Guangdun Peng, Fuchou Tang, Naihe Jing

Cell Research  ·  20 Feb 2018  ·  doi:10.1038/s41422-018-0010-1

TGF-β signaling pathway in early mouse development and embryonic stem cells

Chang Liu, Guangdun Peng, Naihe Jing

Acta Biochimica et Biophysica Sinica  ·  01 Jan 2018  ·  doi:10.1093/abbs/gmx120

Single-Cell Rna-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X-Chromosome Dynamics During Early Postimplantation Mouse Development

Shangli Cheng, Yu Pei, Liqun He, Guangdun Peng, Björn Reinius, Patrick P. L. Tam, Naihe Jing, Qiaolin Deng

SSRN Electronic Journal  ·  01 Jan 2018  ·  doi:10.2139/ssrn.3231846

Direct Reprogramming of Astrocytes into Functional Serotonergic Neurons

Sue Han, Yi Wang, Yueguang Liu, Guangdun Peng, Guizhong Cui, …, Feng Zhu, Jiacheng Yuan, Junlan Geng, Naihe Jing, Leping Cheng

SSRN Electronic Journal  ·  01 Jan 2018  ·  doi:10.2139/ssrn.3264941

Cardiac Directed Differentiation Using Small Molecule WNT Modulation at Single-Cell Resolution

Clayton E. Friedman, Quan Nguyen, Samuel W. Lukowski, Abbigail Helfer, Han Sheng Chiu, …, James Hudson, Ziv Bar-Joseph, Patrick P. L. Tam, Joseph E. Powell, Nathan J. Palpant

SSRN Electronic Journal  ·  01 Jan 2018  ·  doi:10.2139/ssrn.3155757

2017

Analysis of cardiac differentiation at single cell resolution reveals a requirement of hypertrophic signaling for HOPX transcription

Clayton E Friedman, Quan Nguyen, Samuel W Lukowski, Han Sheng Chiu, Abbigail Helfer, …, Hannele Ruohola-Baker, Ziv Bar-Joseph, Patrick P L Tam, Joseph E Powell, Nathan J Palpant

openRxiv  ·  07 Dec 2017  ·  doi:10.1101/229294

Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells

Yuanyuan Li, Ran Wang, Nan Qiao, Guangdun Peng, Ke Zhang, Ke Tang, Jing-Dong J. Han, Naihe Jing

Journal of Biological Chemistry  ·  01 Dec 2017  ·  doi:10.1074/jbc.m117.796383

Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

Guangdun Peng, Patrick P. L. Tam, Naihe Jing

National Science Review  ·  01 Jul 2017  ·  doi:10.1093/nsr/nwx093

CRISPR-Cas9-mediated genome editing in one blastomere of two-cell embryos reveals a novel Tet3 function in regulating neocortical development

Lingbo Wang, Min-Yin Li, Chao Qu, Wan-Ying Miao, Qi Yin, …, Catherine CL Wong, Guoliang Xu, Naihe Jing, Xiang Yu, Jinsong Li

Cell Research  ·  21 Apr 2017  ·  doi:10.1038/cr.2017.58

Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta

Lyad Zamir, Reena Singh, Elisha Nathan, Ralph Patrick, Oren Yifa, …, Yuliang Wang, Nathan Palpant, Patrick PL Tam, Richard P Harvey, Eldad Tzahor

eLife  ·  08 Mar 2017  ·  doi:10.7554/elife.20994

The genome-wide molecular regulation of mouse gastrulation embryo

Guangdun Peng, Naihe Jing

Science China Life Sciences  ·  27 Feb 2017  ·  doi:10.1007/s11427-016-0285-3

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

Jun Chen, Shengbao Suo, Patrick PL Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing

Nature Protocols  ·  16 Feb 2017  ·  doi:10.1038/nprot.2017.003

geo-seq protocol

2016

Dynamic Heterogeneity of Brachyury in Mouse Epiblast Stem Cells Mediates Distinct Response to Extrinsic Bone Morphogenetic Protein (BMP) Signaling

Lu Song, Jun Chen, Guangdun Peng, Ke Tang, Naihe Jing

Journal of Biological Chemistry  ·  01 Jul 2016  ·  doi:10.1074/jbc.m115.705418

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

Guangdun Peng, Shengbao Suo, Jun Chen, Weiyang Chen, Chang Liu, …, Guizhong Cui, Lu Song, Patrick P.L. Tam, Jing-Dong J. Han, Naihe Jing

Developmental Cell  ·  01 Mar 2016  ·  doi:10.1016/j.devcel.2016.02.020

2015

Genome-wide analysis of histone acetylation dynamics during mouse embryonic stem cell neural differentiation

Pingyu Liu, Xiaoyang Dou, Guangdun Peng, Jing-Dong Jackie Han, Naihe Jing

Genomics Data  ·  01 Sep 2015  ·  doi:10.1016/j.gdata.2015.05.001

Genome-wide ChIP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent stem cell neural fate commitment

Lu Song, Na Sun, Guangdun Peng, Jun Chen, Jing-Dong Jackie Han, Naihe Jing

Genomics Data  ·  01 Sep 2015  ·  doi:10.1016/j.gdata.2015.06.028

Ectodermal progenitors derived from epiblast stem cells by inhibition of Nodal signaling

Lingyu Li, Lu Song, Chang Liu, Jun Chen, Guangdun Peng, Ran Wang, Pingyu Liu, Ke Tang, Janet Rossant, Naihe Jing

Journal of Molecular Cell Biology  ·  19 May 2015  ·  doi:10.1093/jmcb/mjv030

Histone deacetylation promotes mouse neural induction by restricting Nodal-dependent mesendoderm fate

Pingyu Liu, Xiaoyang Dou, Chang Liu, Lingbo Wang, Can Xing, …, Chunmei Yue, Jinsong Li, Jing-Dong J. Han, Ke Tang, Naihe Jing

Nature Communications  ·  23 Apr 2015  ·  doi:10.1038/ncomms7830

Intrinsic regulations in neural fate commitment

Ke Tang, Guangdun Peng, Yunbo Qiao, Lu Song, Naihe Jing

Development, Growth & Differentiation  ·  01 Feb 2015  ·  doi:10.1111/dgd.12204

2014

The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

Qingqing Zhu, Lu Song, Guangdun Peng, Na Sun, Jun Chen, …, Yunbo Qiao, Ke Tang, Jing-Dong Jackie Han, Jinsong Li, Naihe Jing

eLife  ·  14 Jun 2014  ·  doi:10.7554/eLife.02224

2012

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

Gang Li, Jae Hoon Bahn, Jae-Hyung Lee, Guangdun Peng, Zugen Chen, Stanley F. Nelson, Xinshu Xiao

Nucleic Acids Research  ·  28 Mar 2012  ·  doi:10.1093/nar/gks280

2011

Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

Jae-Hyung Lee, Chen Gao, Guangdun Peng, Christopher Greer, Shuxun Ren, Yibin Wang, Xinshu Xiao

Circulation Research  ·  09 Dec 2011  ·  doi:10.1161/CIRCRESAHA.111.249433

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

Jae Hoon Bahn, Jae-Hyung Lee, Gang Li, Christopher Greer, Guangdun Peng, Xinshu Xiao

Genome Research  ·  29 Sep 2011  ·  doi:10.1101/gr.124107.111

Expression of the IgSF protein Kirre in the rat central nervous system

Lingwei Kong, Roy C.Y. Choi, Heidi Q. Xie, Xidao Wang, Guangdun Peng, Zhiqin Xie, Karl W.K. Tsim, Naihe Jing

Life Sciences  ·  01 Mar 2011  ·  doi:10.1016/j.lfs.2011.01.014

2009

Role of SIP30 in the development and maintenance of peripheral nerve injury-induced neuropathic pain

Yu-Qiu Zhang, Ning Guo, Guangdun Peng, Mei Han, Jeremy Raincrow, …, Lique M. Coolen, Robert J. Wenthold, Zhi-Qi Zhao, Naihe Jing, Lei Yu

Pain  ·  01 Nov 2009  ·  doi:10.1016/j.pain.2009.07.011

SIP30 Is Regulated by ERK in Peripheral Nerve Injury-induced Neuropathic Pain

Guangdun Peng, Mei Han, Yimin Du, Anning Lin, Lei Yu, Yuqiu Zhang, Naihe Jing

Journal of Biological Chemistry  ·  01 Oct 2009  ·  doi:10.1074/jbc.m109.036756