ORCID: https://orcid.org/0000-0003-0188-6256

2025年

[37] Mengying Ye, Xinyin Li, Lu Huang, Xinru Mei, Huahang Yu, Ke Cao, Feng Chen* and Yongxi Zhao*. Biophysical-to-DNA catalytic cumulative birecorder for measuring continuous membrane fluidity. Journal of the American Chemical Society, 2025, 147, 51, 47523-47536. 

[36] Huan Liu#, Lu Huang#, Jiahui Wang, Jintao Hu, Xinyin Li, Yingying Guo, Feng Chen* and Yongxi Zhao*. UPBAS-Net: An Upsampling-Powered Boundary-Aware Segmentation Network for Fluorescent Spots in Microscopy Images. Analytical Chemistry, 2025, 97, 40, 22200-22210. The platform is available at http://cellpropack.com.

[35] Xiaofei Ma#, Yuanbin Guo#, Haotian Li, Chen Zhao, Xuran Dai, Mo Ma, Pinyi Ma, Daqian Song, Yongxi Zhao,Feng Chen* and Ying Sun*. Microneedle-Based DNA Tension Gauge Tethers Enable In Vivo Monitoring of Cell Mechanics during Skin Tissue Regeneration. JACS Au, 2025, 5, 9, 4560-4569. The first method to monitor cell mechanics in vivo instead of in cultured cells. In collaboration with Prof. Ying Sun at Jilin University.

[34] Zhu Li#, Xinyin Li#, Mengying Ye, Wenjing Shu, Yan He, Haotian Li, Feng Chen* and Yongxi Zhao*. Location-Differentiated DNA Hierarchical Cyclic Construction Demarcating Identical Biomolecules Across Cell Membrane Microenvironments. Angewandte Chemie International Edition, 2025, 64, 31, e202505249. Propose and prove the concept of spatial molecule differentiation to distinguish the identical molecules at different cellular locations without super-resolution microscope. 

[33] Huahang Yu, Mengying Ye, Yingying Guo, Yating Sun, Ke Cao, Feng Chen* and Yongxi Zhao*. ABC-seq Expands Small RNAs Profiling with Successive Nucleic Acid Structure-differentiated Enzymatic Recognition. Angewandte Chemie International Edition, 2025, 64, 31, e202423208.

[32] Siyue Fan#, Xinyin Li#, Huan Liu, Mengying Ye, Yan He, Wenhao Fu, Feng Chen* and Yongxi Zhao*. Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments Below Spatial Resolution. Angewandte Chemie International Edition, 2025, 64, 21, e202425136. Propose the concept of molecule differentiation inspired by well-known cell differentiation, which enables digital counting of identical molecules by different signals below spatial resolution. Three months later, a similar article entitled “Ångström-resolution imaging of cell-surface glycans” was published on Nature Nanotechnology. https://www.nature.com/articles/s41565-025-01966-5

[31] Xiaowen Cao, Yuheng Zhu, Siyue Fan, Feng Chen* and Yongxi Zhao*. Accurate counting of RNA in tissues with highly denoising amplified imaging. Chinese Chemical Letters, 2025, 36, 12, 111091.

[30] Xiaowen Cao, Wenhao Fu, Xinyin Li, Feng Chen* and Yongxi Zhao*. DNA-encoded fluorescence signals for imaging analysis. Small Methods, 2025, 9, 6, 2401303.

[29] Ying Sun*, Yuchuan Liu, Daqian Song, Feng Chen*. DNA-assisted separation of nanoparticles. Small Methods, 2025, 9, 6, 2401389. In collaboration with Prof. Ying Sun at Jilin University.

[28] Feng Chen, Xinyin Li, Min Bai, and Yongxi Zhao*. Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING. Nature Protocols, 2025, 20, 220-247. The first protocol to visualize spatial proximities between different chromatin modifications.

Before 2024

[27] Xiaowen Cao, Feng Chen*, Jing Xue, Yue Zhao, Min Bai and Yongxi Zhao*. Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging. Nucleic Acids Research, 2023, 51, 3, e13. Two years later, a similar method also based on DNA-encoded fluorescence intensity channels, entitled “High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes”, was published on Nature Biotechnology (Published: 30 October 2025). https://www.nature.com/articles/s41587-025-02883-7

[26] Jing Xue, Youlan Fu, Siyue Fan, Xiaowen Cao, Wei Huang, Jin Zhang, Yongxi Zhao and Feng Chen*. Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations. Chemical Communications, 2022, 58, 10020-10023.

[25] Feng Chen#, Jing Xue#, Min Bai, Chunhai Fan and Yongxi Zhao*. Lighting up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification. Accounts of Chemical Research, 2022, 55, 2248-2259. 

[24] Fengjiao Zhao#, FengChen#, Huahang Yu, Siyue Fan, Min Bai, Jing Xue, Yue Zhao, Xiaolei Zuo, Chunhai Fan and Yongxi Zhao*. CRISPR/Cas system-guided plasmid mutagenesis without sequence restriction. Fundamental Research, 2025, 5, 4, 1481-1487. https://doi.org/10.1016/j.fmre.2022.06.017. Three years later, a similar article entitled “PCR-Free Site-Directed Mutagenesis on Repetitive Sequences Using Single-Stranded DNA-Assisted Double-Stranded DNA Nicking by DNAzymes” was published on Angewandte Chemie International Edition. https://onlinelibrary.wiley.com/doi/10.1002/anie.202509127.

[23] Li Su#, Feng Chen#, Huahang Yu, Hao Yan, Fengjiao Zhao, Chunhai Fan, and Yongxi Zhao*. Addition–Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling. Analytical Chemistry, 2021, 93, 13974-13980. The first RNA dynamics sequencing method by Chinese.

[22] Feng Chen#, Min Bai#, Xiaowen Cao, Jing Xue, Yue Zhao, Na Wu, Lei Zhang, Dexin Zhang, and Yongxi Zhao*. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications. Nature Communications, 2021, 12, 1965. Selected as Research Highlight by Nature Methods. Walking through chromatin modifications, Nature Methods, 2021, 18: 446.

[21] Jing Xue#, Feng Chen#, Li Su#, Xiaowen Cao, Min Bai, Yue Zhao, Chunhai Fan, and Yongxi Zhao*.Pairwise Proximity-differentiated Visualization of Single-cell DNA Epigenetic Marks.Angewandte Chemie International Edition,2021, 60, 7, 3428-3432.

[20]Feng Chen#, Jing Xue#, Jin Zhang, Min Bai, Xu Yu, Chunhai Fan and Yongxi Zhao*. Differentiated Visualization of Single-Cell 5-Hydroxymethylpyrimidines with Microfluidic Hydrogel Encoding. Journal of the American Chemical Society, 2020, 142, 6, 2889-2896. 

Highlighted by 科技日报http://digitalpaper.stdaily.com/http_www.kjrb.com/kjrb/html/2020-03/16/content_441516.htm?div=-1

[19] Xiaowen Cao, Huahang Yu, Jing Xue, Min Bai, Yue Zhao, Youjun Li, Yongxi Zhao and Feng Chen*. RNA-primed Amplification for Noise-suppressed Visualization of Single-cell Splice Variants. Analytical Chemistry,2020, 92, 13, 9356-9361.

[18] Min Bai#, Feng Chen#, Xiaowen Cao, Yue Zhao, Jing Xue, Xu Yu, Chunhai Fan, and Yongxi Zhao*. Intracellular Entropy-driven Multi-bit DNA Computing for Tumor Progression Discrimination. Angewandte Chemie International Edition, 2020, 59, 32, 13267-13272.

Highlighted by 国家自然科学基金委员会,http://www.nsfc.gov.cn/csc/20340/20343/53227/index.html

[17] Feng Chen#, Min Bai#, Xiaowen Cao, Yue Zhao, Jing Xue, and Yongxi Zhao*. Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures. Nucleic Acids Research, 2019, 47, 22, e145.

[16] Jing Xue#, Feng Chen#, Min Bai, Xiaowen Cao, Ping Huang,  and Yongxi Zhao*.All-in-one Synchronized DNA Nanodevices Facilitating Multiplexed Cell Imaging.Analytical Chemistry, 2019, 91, 7, 4696-4701.

[15] Feng Chen#, Jing Xue#, Min Bai, Jing Qin,  and Yongxi Zhao*.Programming in situ accelerated DNA walkers in diffusion-limited microenvironments.Chemical Science, 2019, 10，3103-3109.

[14] Jing Wei#, Gen Wang#, Feng Chen#, Min Bai, Yan Liang, Huanting Wang, Dongyuan Zhao,  Yongxi Zhao*. Sol-gel Synthesis of Metal-Phenolic Coordination Spheres and Their Derived Carbon Composites.Angewandte Chemie International Edition, 2018, 57, 9838 –9843.

[13] Feng Chen#, Min Bai#, Yue Zhao, Ke Cao, Xiaowen Cao and Yongxi Zhao*. MnO2-Nanosheet-Powered Protective Janus DNA Nanomachines Supporting Robust RNA Imaging. Analytical Chemistry, 2018, DOI: 10.1021/acs.analchem.7b04634.

[12] Feng Chen#, Min Bai#, Ke Cao, Yue Zhao, Xiaowen Cao, Jing Wei, Na Wu, Jiang Li, Lihua Wang, Chunhai Fan, and Yongxi Zhao* .Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells. ACS Nano, 2017,11: 11908-11914.(ESI热点论文)

[11] Feng Chen, Min Bai, Ke Cao, Yue Zhao, Jing Wei, Yongxi Zhao*. Fabricating MnO2 Nanozymes as Intracellular Catalytic DNA Circuit Generators for Versatile Imaging of  Base-Excision Repair in Living Cell.Advanced Functional Materials, 2017, 27, 1702748.

[10] Feng Chen#, Xuyao Wang#, Xiaowen Cao , Yongxi Zhao*.  Accurate Electrochemistry Analysis of Circulation Methylated DNA from Clinical Plasma Based on Paired-End Tagging and Amplifications. Analytical Chemistry, 2017, 89: 10468-10473.

[9] Xuyao Wang#, Feng Chen#, Dexin Zhang, Yue Zhao, Jing Wei, Lihua Wang, Shiping Song, Chunhai Fan,Yongxi Zhao*. Single copy-sensitive electrochemical assay for circulating methylated DNA in clinical samples with ultrahigh specificity based on a sequential discrimination-amplification strategy. Chemical Science, 2017, 8: 4764-4770. (Outside Back Cover, RSC优秀论文)

[8] Feng Chen#, Manli Lin#, Yue Zhao, Yongxi Zhao*. Catalase-functionalized SiO2 nanoparticles mediate growth of gold nanoparticles for plasmonic biosensing of attomolar microRNA with the naked eye. RSC Advances, 2016, 6: 15709-15715. 

[7] Feng Chen, Dexin Zhang, Qing Zhang, Xiaolei Zuo, Chunhai Fan, Yongxi Zhao*. Zero-background helicase-dependent amplification and its application to reliable assay of telomerase activity in cancer cell by eliminating primer-dimer artifacts. ChemBioChem, 2016, 17: 1171-1176. 

[6] Yongxi Zhao*, Feng Chen, Qian Li, Lihua Wang, Chunhai Fan*. Isothermal amplification of nucleic acids.Chemical Reviews, 2015 , 115, 12491-12545.(ESI高被引论文)

[5] Feng Chen, Chunhai Fan,Yongxi Zhao*. Inhibitory impact of 3′-terminal 2′-O-methylated small silencing RNA on target-primed polymerization and unbiased amplified quantification of the RNA in arabidopsis thaliana. Analytical Chemistry, 2015, 87: 8758-8764.

[4] Feng Chen,Yue Zhao,Chunhai Fan,Yongxi Zhao*. Mismatch extension of DNA polymerases and high-accuracy single nucleotide polymorphism diagnostics by gold nanoparticle-improved isothermal amplification. Analytical Chemistry, 2015, 87: 8718-8723.

[3] Qing Zhang#, Feng Chen#, Feng Xu, Yongxi Zhao*, Chunhai Fan. Target-triggered three-way junction structure and polymerase/nicking enzyme synergetic isothermal quadratic DNA machine for highly specific, one-step, and rapid microRNA detection at attomolar level. Analytical Chemistry,2014, 86 (16):8098-8105.

[2] Feng Chen, Yongxi Zhao*, Lin Qi, Chunhai Fan. One-step highly sensitive florescence detection of T4 polynucleotide kinase activity and biological small molecules by ligation-nicking coupled reaction-mediated signal amplification. Biosensors and Bioelectronics, 2013,47:218-224.

[1] Feng Chen, Yongxi Zhao*. Methylation-blocked enzymatic recycling amplification for highly sensitive fluorescence sensing of DNA methyltransferase activity. Analyst,2013,138:284-289.