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435 results on '"Zou, Xudong"'

107. CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference

Author

Tian, Shuye, primary, Zhang, Bin, additional, He, Yuhao, additional, Sun, Zhiyuan, additional, Li, Jun, additional, Li, Yisheng, additional, Yi, Hongyang, additional, Zhao, Yan, additional, Zou, Xudong, additional, Li, Yunfei, additional, Cui, Huanhuan, additional, Fang, Liang, additional, Gao, Xin, additional, Hu, Yuhui, additional, and Chen, Wei, additional

Published
2022
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112. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

Author

Zou, Xudong, primary, Schaefke, Bernhard, additional, Li, Yisheng, additional, Jia, Fujian, additional, Sun, Wei, additional, Li, Guipeng, additional, Liang, Weizheng, additional, Reif, Tristan, additional, Heyd, Florian, additional, Gao, Qingsong, additional, Tian, Shuye, additional, Li, Yanping, additional, Tang, Yisen, additional, Fang, Liang, additional, Hu, Yuhui, additional, and Chen, Wei, additional

Published
2021
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116. Design and Simulation Study of an Optical Mode-Localized MEMS Accelerometer.

Author

Feng, Yu, Yang, Wuhao, and Zou, Xudong

Subjects
DIRECTIONAL couplers, FINITE element method, OPTICAL sensors, ACCELEROMETERS, EXPERIMENTAL design, RESONATORS
Abstract

In this paper, we demonstrate a novel photonic integrated accelerometer based on the optical mode localization sensing mechanism, which is designed on an SOI wafer with a device layer thickness of 220 nm. High sensitivity and large measurement range can be achieved by integrating coupled ring resonators with a suspended directional coupler on a proof mass. With the help of FEA simulation and numerical analysis, the proposed optical mode-localized sensor presents a sensitivity of 10/g (modal power ratio/acceleration) and an inertial displacement of from −8 to 10 microns corresponding to a range from −23.5 to 29.4 g. The free spectral range is 4.05 nm around 1.55 microns. The acceleration resolution limited by thermomechanical noise is 4.874 μg. The comprehensive performance of this design is competitive with existing MEMS mode localized accelerometers. It demonstrates the potential of the optical mode-localized inertial sensors as candidates for state-of-the-art sensors in the future. [ABSTRACT FROM AUTHOR]

Published
2023
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132. DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

Author

Li, Zhongxiao, Li, Yisheng, Zhang, Bin, Li, Yu, Long, Yongkang, Zhou, Juexiao, Zou, Xudong, Zhang, Min, Hu, Yuhui, Chen, Wei, and Gao, Xin

Subjects
Polyadenylation, Computer science, Machine learning, computer.software_genre, Biochemistry, Task (project management), Deep Learning, Genetic variation, Genetics, Code (cryptography), Molecular Biology, 3' Untranslated Regions, Gene, Sequence, business.industry, Deep learning, Computational Biology, Regression, Computational Mathematics, Binary classification, Ranking, Gene Expression Regulation, Pairwise comparison, Neural Networks, Computer, Artificial intelligence, business, computer, psychological phenomena and processes
Abstract

Alternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic works have mainly focused on the recognition of polyadenylation sites (PAS) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PAS in a same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PAS into account. To address this, here we propose a deep learning architecture, DeeReCT-APA, to quantitatively predict the usage of all alternative PAS of a given gene. To accommodate different genes with potentially different numbers of PAS, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a CNN-LSTM architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PAS, and outputs percentage scores representing the usage levels of all PAS of a gene. In addition to the fact that only our method can predict quantitatively the usage of all the PAS within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and shed light on future mechanistic understanding in APA regulation. Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.

Published
2020

144. Pan‐tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation

Author

Li, Yisheng, primary, Schaefke, Bernhard, additional, Zou, Xudong, additional, Zhang, Min, additional, Heyd, Florian, additional, Sun, Wei, additional, Zhang, Bin, additional, Li, Guipeng, additional, Liang, Weizheng, additional, He, Yuhao, additional, Zhou, Juexiao, additional, Li, Yunfei, additional, Fang, Liang, additional, Hu, Yuhui, additional, and Chen, Wei, additional

Published
2020
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148. Dynamic behaviours of double-ended tuning fork based comb-driven microelectromechanical resonators for modulating magnetic flux synchronously.

Author

Liu, Zhenxi, Chen, Jiamin, Yang, Wuhao, Zheng, Tianyi, Jiao, Qifeng, and Zou, Xudong

Subjects
MAGNETIC flux, RESONATORS, TUNING forks, MEMS resonators, FREQUENCIES of oscillating systems, MICROELECTROMECHANICAL systems, WHEATSTONE bridge
Abstract

Microelectromechanical system (MEMS) resonators have been widely used in the magneto-resistive (MR) sensor for modulating the magnetic flux to enhance the detection limit. However, the manufacturing tolerances in MEMS fabrication processes make it challenging to fabricate the identical resonators with the same vibration frequency, which greatly decreases the detection limit of the MR sensor. To synchronize the MEMS resonators and improve the performance of the MR sensor, the double-ended tuning fork (DETF) based comb-driven MEMS resonators is proposed in this paper, making the system operate at the out-of-phase mode to complete the synchronization. The dynamic behaviour of the resonators is investigated through theoretical analysis, numerical solution based on MATLAB code and Simulink, and experimental verification. The results show that the transverse capacitances in the comb will significantly affect the resonance frequency due to the second-order electrostatic spring constant. It is the first time to observe the phenomenon that the resonant frequency increases with the increase of the bias, and it can also decrease with increasing the bias through adjusting the initial space between the fixed finger and the moving mass, they are different from the model about spring softening and spring hardening. Besides, the proposed DETF based comb-driven resonators can suppress the in-phase and out-of-phase mode through adjusting the driving and sensing ports, and sensing method, meanwhile make the magnetic flux modulation fully synchronized, and maximize the modulation efficiency, and minimize the detection limit. These characteristics are appropriate for the MR sensor, even other devices that need to adjust the resonance frequency and vibration amplitude. Furthermore, the model and the design can also be extended to characteristic the single end tuning fork based MEMS resonator and other MEMS-based MR sensors. [ABSTRACT FROM AUTHOR]

Published
2022
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149. High resolution resonant accelerometer based on MEMS technology

Author

Zou, Xudong

Abstract

This thesis is not available on this repository until the author agrees to make it public. If you are the author of this thesis and would like to make your work openly available, please contact us: thesis@repository.cam.ac.uk., The Library can supply a digital copy for private research purposes; interested parties should submit the request form here: http://www.lib.cam.ac.uk/collections/departments/digital-content-unit/ordering-images, Please note that print copies of theses may be available for consultation in the Cambridge University Library's Manuscript reading room. Admission details are at http://www.lib.cam.ac.uk/collections/departments/manuscripts-university-archives

Published
2018
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