2020年发表论文


Accurate loop calling for 3D genomic data with cLoops.

Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, and Jing-Dong J Han .

Bioinformatics, 2020. 36(3): p. 666-675 .[Html]


scRMD: imputation for single cell RNA-seq data via robust matrix decomposition.

Chong Chen, Changjing Wu, Linjie Wu, Xiaochen Wang, Minghua Deng, and Ruibin Xi .

Bioinformatics, 2020a. 36(10): p. 3156-3161 .[Html]


Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm.

Liang Chen, Weinan Wang, Yuyao Zhai, and Minghua Deng .

Front Genet, 2020b. 11: p. 295 .[Html]


Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-Seq Data.

Weilai Chi, and Minghua Deng .

Genes (Basel), 2020. 11(5).[Html]


Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast.

Marco Di Stefano, Francesca Di Giovanni, Vasilisa Pozharskaia, Merc猫 Gomar-Alba, Davide Bau, Lucas B. Carey, Marc A. Marti-Renom, and Marti-Renom Mendoza .

Genetics, 2020. 214(3): p. 651-667 .[Html]


PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning.

Zhencheng Fang, Jie Tan, Shufang Wu, Mo Li, Chunhui Wang, Yongchu Liu, and Huaiqiu Zhu .

Bioinformatics, 2020. 36(10): p. 3239-3241 .[Html]


Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach.

Shuo Gu, and Luhua Lai .

Acta Pharmacol Sin, 2020. 41(3): p. 432-438 .[Html]


Pathways connecting two opposed bilayers with a fusion pore: a molecularly-informed phase field approach.

Yucen Han, Zirui Xu, An-Chang Shi, and Lei Zhang .

Soft Matter, 2020. 16(2): p. 366-374 .[Html]


Allostery of multidomain proteins with disordered linkers.

Qiaojing Huang, Maodong Li, Luhua Lai, and Zhirong Liu .

Curr Opin Struct Biol, 2020. 62: p. 175-182 .[Html]


Budding yeast complete DNA synthesis after chromosome segregation begins.

Tsvetomira Ivanova, Michael Maier, Alus Missarova, C茅line Ziegler-Birling, Monica Dam, Merc猫 Gomar-Alba, Lucas B. Carey, and Manuel Mendoza .

Nature Communications, 2020. 11(1).[Html]


Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals.

Dapeng Ju, Wei Zhang, Jiawei Yan, Haijiao Zhao, Wei Li, Jiawen Wang, Meimei Liao, Zhancong Xu, Zhiqiang Wang, Guanshen Zhou, Long Mei, Nannan Hou, Shuhua Ying, Tao Cai, She Chen, Xiaowen Xie, Luhua Lai, Chao Tang, Noheon Park, Joseph S Takahashi, Niu Huang, Xiangbing Qi, and Eric Erquan Zhang .

Sci Transl Med, 2020. 12(542).[Html]


Circulating re-entrant waves promote maturation of hiPSC-derived cardiomyocytes in self-organized tissue ring.

Junjun Li, Lu Zhang, Leqian Yu, Itsunari Minami, Shigeru Miyagawa, Marcel Horning, Ji Dong, Jing Qiao, Xiang Qu, Ying Hua, Nanae Fujimoto, Yuji Shiba, Yang Zhao, Fuchou Tang, Yong Chen, Yoshiki Sawa, Chao Tang, and Li Liu .

Commun Biol, 2020. 3(1): p. 122 .[Html]


Automatic retrosynthetic route planning using template-free models.

Kangjie Lin, Youjun Xu, Jianfeng Pei, and Luhua Lai .

Chem Sci, 2020. 11(12): p. 3355-3364 .[Html]


Editorial overview: Allosteric assemblies.

Jin Liu, and Luhua Lai .

Curr Opin Struct Biol, 2020.[Html]


A combined computational and experimental strategy identifies mutations conferring resistance to drugs targeting the BCR-ABL fusion protein.

Jinxin Liu, Jianfeng Pei, and Luhua Lai .

Commun Biol, 2020. 3(1): p. 18 .[Html]


H2A.Z facilitates licensing and activation of early replication origins.

Haizhen Long, Liwei Zhang, Mengjie Lv, Zengqi Wen, Wenhao Zhang, Xiulan Chen, Peitao Zhang, Tongqing Li, Luyuan Chang, Caiwei Jin, Guozhao Wu, Xi Wang, Fuquan Yang, Jianfeng Pei, Ping. Chen, Raphael.Deng Margueron, Haiteng., Mingzhao. Zhu, and Guohong. Li .

Nature, 2020. 577(7791): p. 576-581 .[Html]


Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding.

Xiao Luo, Xinming Tu, Yang Ding, Ge Gao, and Minghua Deng .

Bioinformatics, 2020. 36(5): p. 1405-1412 .[Html]


Noise control and utility: From regulatory network to spatial patterning.

Qing Nie, Lingxia Qiao, Yuchi Qiu, Lei Zhang, and Wei Zhao .

Sci China Math, 2020. 63(3): p. 425-440 .[Html]


A Catalog of GAL4 Drivers for Labeling and Manipulating Circadian Clock Neurons in Drosophila melanogaster.

Manabu Sekiguchi, Kotaro Inoue, Tian Yang, Dong-Gen Luo, and Taishi Yoshii .

J Biol Rhythms, 2020. 35(2): p. 207-213 .[Html]


Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure.

Yuxiu Shao, Jiwei Zhang, and Louis Tao .

PLoS Comput Biol, 2020. 16(6): p. e1007265 .[Html]


Protein Fibrils Formed by Rationally Designed alpha-Helical Peptides.

Xiangyu Sun, and Luhua Lai .

Langmuir, 2020. 36(22): p. 6126-6131 .[Html]


Tuning Cell Motility via Cell Tension with a Mechanochemical Cell Migration Model.

Kuan Tao, Jing Wang, Xiangyu Kuang, Weikang Wang, Feng Liu, and Lei Zhang .

Biophys J, 2020.[Html]


Why and how the nematode's early embryogenesis can be precise and robust: a mechanical perspective.

Binghui Tian, Guoye Guan, Lei-Han Tang, and Chao Tang .

Phys Biol, 2020a. 17(2): p. 026001 .[Html]


DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B.

Xiaoyu Tian, Pengli Zheng, Chenqian Zhou, Xurui Wang, Hua Ma, Wei Ma, Xiaokai Zhou, Junlin Teng, and Jianguo Chen .

Autophagy, 2020b. 16(5): p. 797-810 .[Html]


Phosphorylation-dependent conformational changes of arrestin in the rhodopsin-arrestin complex.

Dali Wang, Xiangdong Liu, Jianqiang Liu, and Chen Song .

Phys Chem Chem Phys, 2020. 22(17): p. 9330-9338 .[Html]


Activation Mechanism of the Mechanosensitive OSCA Channel: A Molecular Dynamics Study.

Dali Wang, and Chen Song .

Biophysical Journal, 2020. 118(3): p. 419a-419a .[Html]


A neuropeptide regulates fighting behavior in Drosophila melanogaster.

Fengming Wu, Bowen Deng, Na Xiao, Tao Wang, Yining Li, Rencong Wang, Kai Shi, Dong-Gen Luo, Yi Rao, and Chuan Zhou .

Elife, 2020a. 9.[Html]


Evidence for rate-dependent filtering of global extrinsic noise by biochemical reactions in mammalian cells.

Jiegen Wu, Xu Han, Haotian Zhai, Tingyu Yang, and Yihan Lin .

Mol Syst Biol, 2020b. 16(5): p. e9335 .[Html]


Protein topology and allostery.

Juan Xie, and Luhua Lai .

Curr Opin Struct Biol, 2020. 62: p. 158-165 .[Html]


High-throughput cell migration assay under combinatorial chemical environments by a novel 24-well-plate based device.

Jian. Xu, Xudong Wang, Xiao Li, Gen Yang, and Chunxiong Luo .

Biomed Microdevices, 2020. 22(2): p. 40 .[Html]


The dynamic transmission of positional information in stau-mutants during Drosophila embryogenesis.

Zhe Yang, Hongcun Zhu, Kakit Kong, Xiaoxuan Wu, Jiayi Chen, Peiyao Li, Jialong Jiang, Jinchao Zhao, Bofei Cui, and Feng Liu .

Elife, 2020. 9.[Html]


Construction of a Pathway Map on a Complicated Energy Landscape.

Jianyuan Yin, Yiwei Wang, Jeff Z Y Chen, Pingwen Zhang, and Lei Zhang .

Phys Rev Lett, 2020. 124(9): p. 090601 .[Html]


LigBuilder V3: A Multi-Target de novo Drug Design Approach.

Yaxia Yuan, Jianfeng Pei, and Luhua Lai .

Front Chem, 2020. 8: p. 142 .[Html]


Characterization of functional transposable element enhancers in acute myeloid leukemia.

Yingying Zeng, Yaqiang Cao, Rivka Sukenik Halevy, Picard Nguyen, Denghui Liu, Xiaoli Zhang, Nadav Ahituv, and Jing-Dong J Han .

Sci China Life Sci, 2020. 63(5): p. 675-687 .[Html]


The Atomistic Details of the Ca2+ Permeation through the Open-State Ryanodine Receptor 1.

Aihua Zhang, Hua Yu, Chunhong Liu, and Chen Song .

Biophysical Journal, 2020a. 118(3): p. 272a-272a .[Html]


The Ca(2+) permeation mechanism of the ryanodine receptor revealed by a multi-site ion model.

Aihua Zhang, Hua Yu, Chunhong Liu, and Chen Song .

Nat Commun, 2020b. 11(1): p. 922 .[Html]


Physiochemical Mechanisms of Biomolecular Liquid-Liquid Phase Separation.

Changsheng Zhang, and Luhua Lai .

Acta Phys-Chim Sin, 2020. 36(1).[Html]


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The energy cost and optimal design for synchronization of coupled molecular oscillators.

Dongliang Zhang, Yuansheng Cao, Qi Ouyang, and Yuhai Tu .

Nat Phys, 2020c. 16(1): p. 95-+ .[Html]


Analysis of Circulating Waves in Tissue Rings derived from Human Induced Pluripotent Stem Cells.

Lu Zhang, Junjun Li, Li Liu, and Chao Tang .

Sci Rep, 2020d. 10(1): p. 2984 .[Html]


AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms.

Shuwen Zhang, and Youdong Mao .

Biomolecules, 2020. 10(4).[Html]


Visualization of Ligand-Bound Ectodomain Assembly in the Full-Length Human IGF-1 Receptor by Cryo-EM Single-Particle Analysis.

Xi Zhang, Daqi Yu, Jingchuan Sun, Yujie Wu, Junyuan Gong, Xuemei Li, Li Liu, Shan Liu, Jianbo Liu, Yulan Wu, Dongyang Li, Yinping Ma, Xu Han, Yanan Zhu, Zhaolong Wu, Yihua Wang, Qi Ouyang, and Tao Wang .

Structure, 2020e. 28(5): p. 555-561 e554 .[Html]


Upconversion Nanoparticles-Based Multiplex Protein Activation to Neuron Ablation for Locomotion Regulation.

Yan Zhang, Wanmei Zhang, Kanghua Zeng, Yanxiao Ao, Mengdie Wang, Zhongzheng Yu, Fukang Qi, Weiwei Yu, Heng Mao, Louis Tao, Cuntai Zhang, Timothy Thatt Yang Tan, Xiangliang Yang, Kanyi Pu, and Shangbang Gao .

Small, 2020f. 16(8): p. e1906797 .[Html]


Vertically Transported Graphene Oxide for High-Performance Osmotic Energy Conversion.

Zhenkun Zhang, Wenhao Shen, Linxin Lin, Mao Wang, Ning Li, Zhifeng Zheng, Feng Liu, and Liuxuan Cao .

Adv Sci, 2020g.[Html]


Critical slowing down and attractive manifold: A mechanism for dynamic robustness in the yeast cell-cycle process.

Yao Zhao, Dedi Wang, Zhiwen Zhang, Ying Lu, Xiaojing Yang, Qi Ouyang, Chao Tang, and Fangting Li .

Phys Rev E, 2020. 101(4-1): p. 042405 .[Html]


[Clinical characteristics and gene expression profiles in children with ETV6-RUNX1 acute lymphoblastic leukemia].

Xueling Zheng, Ziyang Wang, Yanran Sun, Han Zhang, Chao Gao, Ruidong Zhang, Yi Liu, Yaguang Peng, Jing-Dong J Han, and Huyong Zheng .

Zhonghua Xue Ye Xue Za Zhi, 2020. 41(5): p. 405-411 .[Html]