Publications
Selected
At the end of this page, you can find the full list of publications and patents.
Simultaneous testing of multiple genes is important for applications such as pathogen identification. Such testing has primarily relied on fluorescence labeling that are complicated and costly. To achieve that in a label-free manner, here we report a method, named StratoLAMP, using the inherently generated precipitate in isothermal amplification as the detecting feature. By specially designing the amplification system, droplets encapsulating different nucleic acid targets exhibited different levels of precipitates, which were accurately stratified to infer the encapsulated targets using deep learning image analysis. We demonstrated the capability of the StratoLAMP in simultaneous quantification of two nucleic acid targets within the samples. By eliminating the need for fluorescence, the StratoLAMP holds great application potential for nucleic acid quantification in resource-limited settings.
Meichi Jin,# Jingyi Ding,# Yu Zhou, Jiazhao Chen, Yi Wang, and Zida Li*
Proc. Natl. Acad. Sci. U.S.A., 121(2), e2314030121, 2024
Multiplex, digital nucleic acid tests have important biomedical applications, but existing methods mostly use fluorescent probes that are target-specific and difficult to optimize, limiting their widespread applications. Here, we report color-encoded, intelligent digital loop-mediated isothermal amplification (CoID-LAMP) for the coidentification of multiple nucleic acid targets. CoID-LAMP supplements different primer solutions with different dyes, generates primer droplets and sample droplets, and collectively pairs these two types of droplets in a microwell array device to perform LAMP. After imaging, the droplet colors were analyzed to decode the primer information, and the precipitate byproducts within droplets were detected to determine the target occupancy and calculate the concentrations. We first established an image analysis pipeline based on a deep learning algorithm for reliable droplet detection and validated the analytical performance in nucleic acid quantification. We then implemented CoID-LAMP using fluorescent dyes as the coding materials and established an 8-plex digital nucleic acid assay, confirming the reliable coding performance and the capability of multiplex nucleic acid quantification. We further implemented CoID-LAMP using brightfield dyes for a 4-plex assay, suggesting that the assay could be realized solely by brightfield imaging with minimal demand on the optics. Leveraging the advantages of droplet microfluidics in multiplexing and deep learning in intelligent image analysis, CoID-LAMP offers a useful tool for multiplex nucleic acid quantification.
Kai Wu,# Qi Fang,# Zhantao Zhao, and Zida Li*
Anal. Chem. 95(11), 5069–5078 (2023)
Combinatorial drug therapy reduces drug resistance and disease relapse, but informed drug combinations are lacking due to the high scale of possible combinations and the relatively simple phenotyping strategies. Here we report combinatorial perturbation sequencing (CP-seq) on single cells using microwell-base droplet random pairing. CP-seq uses oligonucleotides to barcode drugs, encapsulates drugs and cells in separate droplets, and pairs cell droplets with two drug droplets randomly on a microwell array chip to complete combinatorial drug treatment and barcode-tagging on cells. The subsequent single-cell RNA sequencing simultaneously detects the single-cell transcriptomes and drug barcodes to demultiplex the corresponding drug treatment. The microfluidic droplet operations had robust performance, with the overall utilization rate of the microwells being up to 83%. We then progressively validated the CP-seq by performing single-drug treatments and then combinatorial-drug treatments, confirming the CP-seq’s capability in the collection and analysis of drug-perturbed transcriptomes. Leveraging the advantage of droplet microfluidics in massive multiplexing, the CP-seq represents a great technology for combinatorial perturbation screening with high throughput and comprehensive profiling.
Run Xie,# Yang Liu,# Shiyu Wang, Xuyang Shi, Zhantao Zhao, Longqi Liu, Ya Liu,* and Zida Li*
Biosens. Bioelectron. 220, 114913 (2023)
Digital nucleic acid amplification tests enable absolute quantification of nucleic acids, but the generation of uniform compartments and reading of the fluorescence requires specialized instruments that are costly, limiting their widespread applications. Here, the authors report deep learning-enabled polydisperse emulsion-based digital loop-mediated isothermal amplification (deep-dLAMP) for label-free, low-cost nucleic acid quantification. deep-dLAMP performs LAMP reaction in polydisperse emulsions and uses a deep learning algorithm to segment and determine the occupancy status of each emulsion in images based on precipitated byproducts. The volume and occupancy data of the emulsions are then used to infer the nucleic acid concentration based on the Poisson distribution. deep-dLAMP can accurately predict the sizes and occupancy status of each emulsion and provide accurate measurements of nucleic acid concentrations with a limit of detection of 5.6 copies µl-1 and a dynamic range of 37.2 to 11000 copies µl-1. In addition, deep-dLAMP shows robust performance under various parameters, such as the vortexing time and image qualities. Leveraging the state-of-the-art deep learning models, deep-dLAMP represents a significant advancement in digital nucleic acid tests by significantly reducing the instrument cost. We envision deep-dLAMP would be readily adopted by biomedical laboratories and be developed into a point-of-care digital nucleic acid test system.
Linzhe Chen,# Jingyi Ding,# Hao Yuan, Chi Chen,* and Zida Li*
Adv. Sci. 9(9), 2105450 (2022)
Monitoring of the coagulation function has applications in many clinical settings. Routine coagulation assays in the clinic are sample-consuming and slow in turnaround. Microfluidics provides the opportunity to develop coagulation assays that are applicable in point-of-care settings, but reported works required bulky sample pumping units or costly data acquisition instruments. In this work, we developed a microfluidic coagulation assay with a simple setup and easy operation. The device continuously generated droplets of blood sample and buffer mixture and reported the temporal development of blood viscosity during coagulation based on the color appearance of the resultant droplets. We characterized the relationship between blood viscosity and color appearance of the droplets and performed experiments to validate the assay results. In addition, we developed a prototype analyzer equipped with simple fluid pumping and economical imaging module and obtained similar assay measurements. This assay showed great potential to be developed into a point-of-care coagulation test with practical impact.
Linzhe Chen, Donghao Li, Xinyu Liu, Yihan Xie, Jieying Shan, Haofan Huang, Xiaxia Yu, Yudan Chen, Weidong Zheng, and Zida Li*
ACS Sens. 7(8), 2170–2177 (2022)
Patents
Zida Li, Tao Wang, Yongjin Zhou, Zengtong Chen
A system and method for single cell isolation using droplet microfluidics
China Invention Patent Provisional Application, CN113477282A (2021)
Zida Li, Jingyi Ding, Linzhe Chen, Chi Chen
A nucleic acid quantification method based on non-uniform droplets and image analysis
China Invention Patent Provisional Application, CN114540469A (2022)
Zida Li, Qi Fang, Yujun Chai, Xiaoxiang Hu
A Droplet Digital Enzyme-Linked Immunosorbent Assay Method, Device, and Related Medium
China Invention Patent Application, ZL202410149722.7 (2024)
Zida Li, Donghao Li, Yujuan Chai, Xinyu Liu, Weidong Zheng
A detection system and method for point-of-care blood clotting function assessment
China Invention Patent Application, ZL202111620552.9 (2025)
Zida Li, Linzhe Chen, Weidong Zheng, Jieying Shan, Yihan Xie, Xinyu Liu
A device and method for the assessement of blood viscosity using microfluidics
China Invention Patent Application, ZL202110639057.6 (2021)
Zida Li, Meichi Jin, Jingyi Ding, Yi Wang, Yu Zhou
The Multiplex Nucleic Acid Quantification Method, Device, and Medium Based on Precipitation Bright Field Image Processing
China Invention Patent Application, ZL202310028332.X (2022)
Zida Li, Zhantao Zhao
An image-activated picoinjection method, system, and equipment
China Invention Patent Application, ZL202211449260.8 (2023)
Zida Li, Qi Fang, Kai Wu
Method, device, and medium for multiple digital detection of nucleic acid with deep learning
China Invention Patent Application, ZL202211516857.X (2023)
Zida Li, Xiaxia Yu, Xinyu Liu, Jieying Shan, Yihan Xie
Simulation system and method of in vitro diagnostics
China Invention Patent Application, ZL202110750662.0 (2023)
Zida Li, Lanzhu Huang, Weidong Zheng
A fabrication method and application of soft post rings for clot retraction testing
China Invention Patent Application, ZL202010260648.8 (2022)
Jianping Fu, Kevin Ward, Zida Li, Xiang Li
A microscale device for blood coagulation assay
U.S. Patent Application, 62/304,385 (2018)
Ho Cheung Shum, Alban Sauret, Zida Li, Yang Song
System and method for generation of emulsions with low interfacial tension and measuring frequency vibrations in the system
U.S. Patent Application, 13/839,072 (2013)
Full List of publications
Flow-LAMP: Label-free Digital LAMP using Scatter-based Flow Cytometry on Vortex-Generated Polydisperse Gel Beads
Wanjun Yao, Weidong Zheng, Zida Li, et al.
In Preparation
Precipitate-informed deep learning enables label-free multiplex digital nucleic acid testing in polydisperse droplets
Jiazhao Chen, Jingyi Ding, Rui Deng, Meichi Jin, Yi Wang, Zida Li, et al.
In Preparation
Materials-Driven Innovations in Digital Nucleic Acid Amplification Technologies: Transforming Molecular Diagnostics
Jiazhao Chen, Kai Wu, Jingyi Ding, Zida Li, et al.
In Revision
Reimagining POCT assays: Automated digital microfluidics for multiplex in vitro diagnostics
Wenkai Fan, Donghao Li, Jingyi Ding, Zida Li*
Talanta, 294, 128270 (2025)
Droplet digital PCR-based single aptamer selection
Zerui Wu,# Wanjun Yao,# Jinyu Chen, Yonghao Chen, Zida Li, Weiping Ding,* Liqun He,* and Peng Hu*
Talanta, 292, 127924 (2025)
Embracing Poisson encapsulation statistics for improved droplet digital immunoassay
Yujuan Chai, Xiaoxiang Hu, Qi Fang, Yuanyuan Guo, Binmao Zhang, Hangjia Tu, and Zida Li*
Anal. Chem. 97(1), 444–453 (2025)
StratoLAMP: Label-free, multiplex digital loop-mediated isothermal amplification based on visual stratification of precipitate
Meichi Jin,# Jingyi Ding,# Yu Zhou, Jiazhao Chen, Yi Wang, and Zida Li*
Proc. Natl. Acad. Sci. U.S.A., 121(2), e2314030121, 2024
Image-activated pico-injection for single cell analysis
Zhantao Zhao, Heng Zhai, Peng Zuo, Tao Wang, Run Xie, Mu Tian, Ruyuan Song, Xiaonan Xu, and Zida Li*
Talanta 272, 125765 (2024)
CoID-LAMP: Color-encoded, intelligent digital LAMP for multiplexed nucleic acid quantification
Kai Wu,# Qi Fang,# Zhantao Zhao, and Zida Li*
Anal. Chem. 95(11), 5069–5078 (2023)
Combinatorial perturbation sequencing on single cells using microwell-based droplet random pairing
Run Xie,# Yang Liu,# Shiyu Wang, Xuyang Shi, Zhantao Zhao, Longqi Liu, Ya Liu,* and Zida Li*
Biosens. Bioelectron. 220, 114913 (2023)
High resolution, multiplex antibody patterning using micropillar-focused droplet printing and microcontact printing
Meichi Jin, Kai Wu, Mengzhen Wang, Yang Zhang, Chengbin Yang, and Zida Li*
Adv. Biol. 7(8), 2300111 (2023)
Bone-on-a-chip platforms and integrated biosensors: towards advanced in vitro bone models with real-time biosensing
Yang Zhang, Taozhao Yu, Jingyi Ding, and Zida Li*
Biosens. Bioelectron. 219, 114798 (2023)
deep-dLAMP: deep learning-enabled polydisperse emulsion-based digital loop-mediated isothermal amplification
Linzhe Chen,# Jingyi Ding,# Hao Yuan, Chi Chen,* and Zida Li*
Adv. Sci. 9(9), 2105450 (2022)
Point-of-care blood coagulation assay based on dynamic monitoring of blood viscosity using droplet microfluidics
Linzhe Chen, Donghao Li, Xinyu Liu, Yihan Xie, Jieying Shan, Haofan Huang, Xiaxia Yu, Yudan Chen, Weidong Zheng, and Zida Li*
ACS Sens. 7(8), 2170–2177 (2022)
Generation and Screening of Antigen-Specific Nanobodies from Mammalian Cells Expressing the BCR Repertoire Library Using Droplet-Based Microfluidics
Menghua Lyu,# Xuyang Shi,# Xiaopan Liu,# Yang Liu, Xijun Zhu, Lijuan Liao, Hongyan Zhao, Na Sun, Shiyu Wang, Linzhe Chen, Linyuan Fan, Qumiao Xu, Qianqian Zhu, Kai Gao, Huaying Chen, Yonggang Zhu, Zida Li, Weijin Guo, Yue Zheng, Ying Gu, Longqi Liu,* Meiniang Wang,* and Ya Liu*
Anal. Chem. 94(22), 7970–7980 (2022)
Point-of-care blood coagulation assay enabled by printed circuit board-based digital microfluidics
Donghao Li,# Xinyu Liu,# Yujuan Chai,# Jieying Shan, Yihan Xie, Yong Liang, Susu Huang, Weidong Zheng, and Zida Li*
Lab Chip 22(4), 709-716 (2022)
Single-cell sequencing to unveil the mystery of embryonic development
Zida Li,#,* Feng Lin,# Chu-Han Zhong, Shue Wang, Xufeng Xue, and Yue Shao*
Adv. Biol. 6(2), 2101151 (2022)
High-throughput functional screening of antigen-specific T-cells based on droplet microfluidics on single-cell level
Shiyu Wang,# Yang Liu,# Yijian Li, Menghua Lv, Kai Gao, Ying He, Wenbo Wei, Yonggang Zhu, Xuan Dong, Xun Xu, Zida Li,* Longqi Liu,* and Ya Liu*
Anal. Chem. 94(2), 918–926 (2022)
Emerging biosensing technologies for improved diagnostics of COVID-19 and future pandemics
Linzhe Chen, Guoliang Zhang, Longqi Liu, and Zida Li
Talanta 225, 121986 (2021)
Micro-engineered flexural post rings for effective blood sample fencing and high throughput measurement of clot retraction force
Lanzhu Huang,# Xinyu Liu,# Yuanbin Ou, Haofan Huang, Xia Zhang, Yize Wang, Yong Liang, Xiaxia Yu, Weidong Zheng, Huisheng Zhang, and Zida Li*
ACS Sens. 5(12), 3949-3955 (2020)
Recent advances in solar-driven evaporation system
Zhourui Xu, Zida Li, Yihang Jiang, Gaixia Xu, Mingwei Zhu, Wing-Cheung Law, Ken-Tye Yong, Yanshuai Wang, Chengbin Yang, Biqin Dong, and Feng Xing*
J. Mater. Chem. A 8, 25571-25600 (2020)
Stretchable supercapacitors as emergent energy storage units for health monitoring bioelectronics
Xue Chen, Nicolo Simone Villa, Yanfeng Zhuang, Linzhe Chen, Tianfu Wang, Zida Li, and Tiantian Kong
Adv. Energy Mater. 10(4), 1902769 (2020)
Dean flow assisted single cell and bead encapsulation for high performance single cell expression profiling
Luoquan Li,# Ping Wu,# Zhaofeng Luo, Lei Wang, Weiping Ding, Tao Wu, Jinyu Chen, Jinlong He, Yi He, Heran Wang, Ying Chen, Guibo Li, Zida Li,* and Liqun He*
ACS Sens. 4(5), 1299-1305 (2019)
Multiple splitting of droplets using multi-furcating microfluidic channels
Zida Li, Luoquan Li, Meixiang Liao, Liqun He, and Ping Wu
Biomicrofluidics 13(2), 024112 (2019)
Controlled modeling of human epiblast and amnion development using stem cells
Yi Zheng, Xufeng Xue, Yue Shao, Sicong Wang, Sajedeh Nasr Esfahani, Zida Li, Jonathon M. Muncie, Johnathon N. Lakins, Valerie M. Weaver, Deborah L. Gumucio, and Jianping Fu*
Nature 573(7774), 421-425 (2019)
Dorsal-ventral patterned neural cyst from human pluripotent stem cells in a neurogenic niche
Yuanyuan Zheng,# Xufeng Xue,# Agnes M. Resto Irizarry, Zida Li, Yue Shao, Yi Zheng, Gang Zhao,* and Jianping Fu*
Sci. Adv. 5(12), eaax5993 (2019)
Microengineered human amniotic ectoderm tissue array for high-content developmental phenotyping
Sajedeh Nasr Esfahani, Yue Shao, Agnes M Resto Irizarry, Zida Li, Xufeng Xue, Deborah L Gumucio, and Jianping Fu*
Biomaterials 216, 119244 (2019)
Biophysical phenotypes and determinants of anterior vs. posterior primitive streak cells derived from human pluripotent stem cells
Feng Lin, Yue Shao, Xufeng Xue, Yi Zheng, Zida Li, Chunyang Xiong, and Jianping Fu
Acta Biomater. 86, 125-134 (2019)
Carbon nanotube strain sensor based hemoretractometer for blood coagulation testing
Zida Li, Yize Wang, Xufeng Xue, Brendan McCracken, Kevin Ward, and Jianping Fu*
ACS Sens. 3(3), 670-676 (2018)
Capillary assisted deposition of carbon nanotube film for strain sensing
Zida Li, Xufeng Xue, Feng Lin, Yize Wang, Kevin Ward, and Jianping Fu*
Appl. Phys. Lett. 111(17), 173105 (2017)
Tracking the tumor invasion front using long-term fluidic tumoroid culture
Koh Meng Aw Yong, Zida Li, Sofia D. Merajver, and Jianping Fu*
Sci. Rep. 7, (2017)
Acoustic tweezing cytometry enhances osteogenesis of human mesenchymal stem cells through cytoskeletal contractility and YAP activation
Xuefeng Xue, Xiaowei Hong, Zida Li, Cheri X. Deng, and Jianping Fu*
Biomaterials 134, 22-30 (2017)
Controlled tubular unit formation from collagen film for modular tissue engineering
Jianming Sang, Xiang Li, Yue Shao, Zida Li, and Jianping Fu*
ACS Biomater. Sci. Eng. 3(11), 2860-2868 (2016)
A miniaturized hemoretractometer for blood clot retraction testing
Zida Li, Xiang Li, Brendan McCracken, Yue Shao, Kevin Ward, and Jianping Fu*
Small 12, 3926–3934 (2016)
Musical interfaces: visualization and reconstruction of music with a microfluidic two-phase flow
Sze Yi Mak, Zida Li, Arnaud Frere, Tat Chuen Chan, and Ho Cheung Shum*
Sci. Rep. 4, 6675 (2014)
Syringe-pump-induced fluctuation in all-aqueous microfluidic system implications for flow rate accuracy
Zida Li, Sze Yi Mak, Alban Sauret, and Ho Cheung Shum*
Lab Chip 14(4), 744-749 (2014)
Emerging microengineered tools for functional analysis and phenotyping of blood cells
Xiang Li, Weiqiang Chen, Zida Li, Ling Li, Hongchen Gu, and Jianping Fu*
Trends Biotechnol. 32(11), 586-594 (2014)
Dynamics for dense packing of colloids
Liqun He*, Ping Wu, Zida Li, and Lili Feng
Adv. Mater. Res. 165, 248-254 (2012)