2021 Published
Uncovering de novo gene birth in yeast using deep transcriptomics.
W. R. Blevins, J. Ruiz-Orera, X. Messeguer, B. Blasco-Moreno, J. L. Villanueva-Canas, L. Espinar, J. Diez, L. B. Carey, and M. M. Alba .
Nat Commun, 2021. 12(1): p. 604 .[Html]
Model Reduction Captures Stochastic Gamma Oscillations on Low-Dimensional Manifolds.
Yuhang Cai, Tianyi Wu, Louis Tao, and Zhuocheng Xiao .
Front Comput Neurosc, 2021. 15.[Html]
USP19 promotes hypoxia-induced mitochondrial division via FUNDC1 at ER-mitochondria contact sites.
Peiyuan Chai, Yiru Cheng, Chuyi Hou, Lei Yin, Donghui Zhang, Yingchun Hu, Qingzhou Chen, Pengli Zheng, Junlin Teng, and Jianguo Chen .
J Cell Biol, 2021. 220(7).[Html]
A novel two-layer-integrated microfluidic device for high-throughput yeast proteomic dynamics analysis at the single-cell level.
Kaiyue Chen, Nan Rong, Shujing Wang, and Chunxiong Luo .
Integr Biol-Uk, 2021a. 13(10): p. 258-258 .[Html]
Stress response capacity analysis during aging and possible new insights into aging studies.
Kaiyue Chen, Wenting Shen, Ziqing Gao, and Chunxiong Luo .
Curr Genet, 2021b. 67(3): p. 417-420 .[Html]
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation.
Liang Chen, Qiuyan He, Yuyao Zhai, and Minghua Deng .
Bioinformatics, 2021c. 37(6): p. 775-784 .[Html]
Ligand-based optimization and biological evaluation of N-(2,2,2-trichloro-1-(3-phenylthioureido)ethyl)acetamide derivatives as potent intrinsically disordered protein c-Myc inhibitors.
Limin Chen, Beiming Cheng, Qi Sun, and Luhua Lai .
Bioorg Med Chem Lett, 2021d. 31.[Html]
A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance.
Lufeng Dan, Yuze Li, Shuhua Chen, Jingbo Liu, Yu Wang, Fangting Li, Xiangwei He, and Lucas B Carey .
P Natl Acad Sci USA, 2021. 118(43).[Html]
VirionFinder: Identification of Complete and Partial Prokaryote Virus Virion Protein From Virome Data Using the Sequence and Biochemical Properties of Amino Acids.
Zhencheng Fang, and Hongwei Zhou .
Front Microbiol, 2021a. 12.[Html]
A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data.
Zhencheng Fang, and Hongwei Zhou .
Jove-J Vis Exp, 2021b(175).[Html]
High-throughput Method for Detecting Siderophore Production by Rhizosphere Bacteria.
Shaohua Gu, Wen Wan, Zhengying Shao, and Wei Zhong .
Bio Protoc, 2021. 11(9): p. e4001 .[Html]
Volume segregation programming in a nematode's early embryogenesis.
Guoye Guan, Mingkin Wong, Zhongying Zhao, Lei-Han Tang, and Chao Tang .
Phys Rev E, 2021. 104(5).[Html]
Gut Microbiota-Related Effects of Tanhuo Decoction in Acute Ischemic Stroke.
Qian Guo, Xiaoqing Jiang, Can Ni, Linjing Li, Li Chen, Yaqi Wang, Mo Li, Chunhui Wang, Li Gao, Huaiqiu Zhu, and Juexian Song .
Oxid Med Cell Longev, 2021a. 2021.[Html]
Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic.
Qian Guo, Mo Li, Chunhui Wang, Jinyuan Guo, Xiaoqing Jiang, Jie Tan, Shufang Wu, Peihong Wang, Tingting Xiao, Man Zhou, Zhencheng Fang, Yonghong Xiao, and Huaiqiu Zhu .
Sci Rep-Uk, 2021b. 11(1).[Html]
Solution landscapes of the simplified Ericksen-Leslie model and its comparison with the reduced Landau-de Gennes model.
Yucen Han, Jianyuan Yin, Yucheng Hu, Apala Majumdar, and Lei Zhang .
P Roy Soc a-Math Phy, 2021a. 477(2253).[Html]
Solution landscape of a reduced Landau-de Gennes model on a hexagon.
Yucen Han, Jianyuan Yin, Pingwen Zhang, Apala Majumdar, and Lei Zhang .
Nonlinearity, 2021b. 34(4): p. 2048-2069 .[Html]
Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation.
Jiayin Hong, Julius Palme, Bo Hua, and Michael Springer .
Plos Comput Biol, 2021. 17(9).[Html]
Allosteric Type and Pathways Are Governed by the Forces of Protein-Ligand Binding.
Qiaojing Huang, Pengbo Song, Yixin Chen, Zhirong Liu, and Luhua Lai .
J Phys Chem Lett, 2021. 12(22): p. 5404-5412 .[Html]
Development of a One-Step Multiplex PCR Assay for Differential Detection of Four species (Enterobacter cloacae, Enterobacter hormaechei, Enterobacter roggenkampii, and Enterobacter kobei) Belonging to Enterobacter cloacae Complex With Clinical Significance.
Yang Ji, Peihong Wang, Tingting Xu, Yanzi Zhou, Rongchang Chen, Huaiqiu Zhu, and Kai Zhou .
Front Cell Infect Mi, 2021. 11.[Html]
A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences.
Zhisheng Jiang, Serena F Generoso, Marta Badia, Bernhard Payer, and Lucas B Carey .
Plos Comput Biol, 2021. 17(11).[Html]
Fast whole-body motor neuron calcium imaging of freely moving Caenorhabditis elegans without coverslip pressed.
Haiwen Li, Fan Feng, Muyue Zhai, Jiazhi Zhang, Jingyuan Jiang, Yifan Su, Liangyi Chen, Shangbang Gao, Louis Tao, and Heng Mao .
Cytom Part A, 2021a. 99(11): p. 1143-1157 .[Html]
Numerical Discretization of Variational Phase Field Model for Phase Transitions in Ferroelectric Thin Films.
Ruotai Li, Qiang Du, and Lei Zhang .
Commun Comput Phys, 2021b. 29(3): p. 729-746 .[Html]
A synergetic effect of BARD1 mutations on tumorigenesis.
Wenjing Li, Xiaoyang Gu, Chunhong Liu, Yanyan Shi, Pan Wang, Na Zhang, Rui Wu, Liang Leng, Bingteng Xie, Chen Song, and Mo Li .
Nature Communications, 2021c. 12(1).[Html]
Heritability Enrichment of Immunoglobulin G N-Glycosylation in Specific Tissues.
Xingang Li, Hao Wang, Yahong Zhu, Weijie Cao, Manshu. Song, Youxin Wang, Haifeng Hou, Minglin Lang, Xiuhua Guo, Xuerui Tan, Jing-Dong J Han, and Wei Wang .
Front Immunol, 2021d. 12.[Html]
Structure-based de novo drug design using 3D deep generative models.
Yibo Li, Jianfeng Pei, and Luhua Lai .
Chemical Science, 2021e. 12(41): p. 13664-13675 .[Html]
De novo generation of macrophage from placenta-derived hemogenic endothelium.
Guixian Liang, Chunyu Zhou, Xiangxiang Jiang, Yifan Zhang, Baofeng Huang, Suwei Gao, Zhixin Kang, Dongyuan Ma, Fengchao Wang, Berthold Gottgens, Hongmei Wang, Jing-Dong J Han, and Feng Liu .
Dev Cell, 2021. 56(14): p. 2121-+ .[Html]
Disentangling Intrinsic and Extrinsic Gene Expression Noise in Growing Cells.
Jie Lin, and Ariel Amir .
Phys Rev Lett, 2021. 126(7): p. 078101 .[Html]
An efficient and label-free LC-MS/MS method for assessing drug's activity at dopamine and serotonin transporters using transporter-transfected HEK293T cells.
Zebin Lin, Chenyang Liu, Enshan Fanr, Yurong Zhang, Shuiqing Zheng, and Yulan Rao .
J Psychopharmacol, 2021. 35(6): p. 693-700 .[Html]
Atomistic Details of Charge/Space Competition in the Ca2+ Selectivity of Ryanodine Receptors.
Chunhong Liu, Aihua Zhang, Nieng Yan, and Chen Song .
J Phys Chem Lett, 2021b. 12(17): p. 4286-4291 .[Html]
Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro.
Hongbo Liu, Fei Ye, Qi Sun, Hao Liang, Chunmei Li, Siyang Li, Roujian Lu, Baofeng Huang, Wenjie Tan, and Luhua Lai .
J Enzym Inhib Med Ch, 2021c. 36(1): p. 497-503 .[Html]
A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation.
Yanyan Liu, Pu Ke, Yichun Kuo, Yuxiao Wang, Xuewu Zhang, Chen Song, and Yibing Shan .
Elife, 2021d. 10.[Html]
Short-Term Plasticity Regulates Both Divisive Normalization and Adaptive Responses in Drosophila Olfactory System.
Yuxuan Liu, Qianyi Li, Chao Tang, Shanshan Qin, and Yuhai Tu .
Front Comput Neurosc, 2021e. 15.[Html]
Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics.
Liang Ma, Zeyue Gao, Jiegen Wu, Bijunyao Zhong, Yuchen Xie, Wen Huang, and Yihan Lin .
Mol Cell, 2021. 81(8): p. 1682-+ .[Html]
Structure, Dynamics and Function of the 26S Proteasome.
Youdong Mao .
Subcell Biochem, 2021. 96: p. 1-151 .[Html]
BACH1 recruits NANOG and histone H3 lysine 4 methyltransferase MLL/SET1 complexes to regulate enhancer-promoter activity and maintains pluripotency.
Cong Niu, Siqing Wang, Jieyu Guo, Xiangxiang Wei, Mengping Jia, Zhaoxiong Chen, Wenxuan Gong, Yue Qin, Xinhong Wang, Xiuling Zhi, Meng Lu, Sifeng Chen, Mingxia Gu, Jianyi Zhang, Jing-Dong J Han, Fei Lan, and Dan Meng .
Nucleic Acids Res, 2021. 49(4): p. 1972-1986 .[Html]
Multiple Target Drug Design Using LigBuilder 3.
Xiaoyu Qing, Shiwei Wang, Yaxia Yuan, Jianfeng Pei, and Luhua Lai .
Methods Mol Biol, 2021. 2266: p. 279-298 .[Html]
New regulators of Drosophila eye development identified from temporal transcriptome changes.
Manon Quiquand, Gerard Rimesso, Nan Qiao, Shengbao Suo, Chunyu Zhao, Matthew Slattery, Kevin P White, Jing-Dong J Han, and Nicholas E Baker .
Genetics, 2021. 217(4).[Html]
Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway.
Hao Ruan, Chen Yu, Xiaogang Niu, Weilin Zhang, Hanzhong Liu, Limin Chen, Ruoyao Xiong, Qi Sun, Changwen Jin, Ying Liu, and Luhua Lai .
Chemical Science, 2021. 12(8): p. 3004-3016 .[Html]
Finding gene network topologies for given biological function with recurrent neural network.
Jingxiang Shen, Feng Liu, Yuhai Tu, and Chao Tang .
Nature Communications, 2021. 12(1).[Html]
Bardoxolone and bardoxolone methyl, two Nrf2 activators in clinical trials, inhibit SARS-CoV-2 replication and its 3C-like protease.
Qi Sun, Fei Ye, Hao Liang, Hongbo Liu, Chunmei Li, Roujian Lu, Baoying Huang, Li Zhao, Wenjie Tan, and Luhua Lai .
Signal Transduct Tar, 2021. 6(1).[Html]
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Harnessing peak transmission around symptom onset for non-pharmaceutical intervention and containment of the COVID-19 pandemic.
Liang Tian, Xuefei Li, Fei Qi, Qian-Yuan Tang, Viola Tang, Jiang Liu, Zhiyuan Li, Xingye Cheng, Xuanxuan Li, Yingchen Shi, Haiguang Liu, and Lei-Han Tang .
Nature Communications, 2021a. 12(1).[Html]
New insights regarding SNARE proteins in autophagosome-lysosome fusion.
Xiaouy Tian, Junlin Teng, and Jianguo Chen .
Autophagy, 2021b. 17(10): p. 2680-2688 .[Html]
Lipid Contact Probability - an Essential and Predictive Property for the Structural and Functional Studies of (Membrane) Proteins.
Lei Wang, Jiangguo Zhang, Dali Wang, and Chen Song .
Biophys J, 2021a. 120(3): p. 83a-83a .[Html]
Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume.
Qirun Wang, and Jie Lin .
Nature Communications, 2021. 12(1).[Html]
Non-muscle myosin heavy chain 9 maintains intestinal homeostasis by preventing epithelium necroptosis and colitis adenoma formation.
Shan Wang, Siqi Li, Yehua Li, Quanlong Jiang, Xintong Li, Yalong Wang, Jing-Dong J Han, Yuan Liu, and Yeguang Chen .
Stem Cell Rep, 2021b. 16(5): p. 1290-1301 .[Html]
A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2.
Shiwei Wang, Qi Sun, Youjun Xu, Jianfeng Pei, and Luhua Lai .
Brief Bioinform, 2021c. 22(6).[Html]
Modelling and computation of liquid crystals.
Wei Wang, Lei Zhang, and Pingwen Zhang .
Acta Numer, 2021d. 30: p. 765-851 .[Html]
Atomistic and Dynamic Details of the Gating Mechanism of the Tethered Mechanosensitive Ion Channel Nompc.
Yang Wang, Yifeng Guo, Guanluan Li, Chunhong Liu, Lei Wang, Aihua Zhang, Zhiqiang Yan, and Chen Song .
Biophys J, 2021e. 120(3): p. 335a-336a .[Html]
The push-to-open mechanism of the tethered mechanosensitive ion channel NompC.
Yang Wang, Yifeng Guo, Guanluan Li, Chunhong Liu, Lei Wang, Aihua Zhang, Zhiqiang Yan, and Chen Song .
Elife, 2021f. 10.[Html]
Charge Segregation in the Intrinsically Disordered Region Governs VRN1 and DNA Liquid-like Phase Separation Robustness.
Yanyan Wang, Huabin Zhou, Xiangyu Sun, Qiaojing Huang, Siyang Li, Zhirong Liu, Changsheng Zhang, and Luhua Lai .
J Mol Biol, 2021g. 433(22).[Html]
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.
Shufang Wu, Zhencheng Fang, Jie Tan, Mo Li, Chunhui Wang, Qian Guo, Congmin Xu, Xiaoqing Jiang, and Huaiqiu Zhu .
Gigascience, 2021a. 10(9).[Html]
Attractive internuclear force drives the collective behavior of nuclear arrays in Drosophila embryos.
Xiaoxuan Wu, Kakit Kong, Wenlei Xiao, and Feng Liu .
Plos Comput Biol, 2021b. 17(11).[Html]
Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs.
Yan Wu, Jiaqi Wu, Minghua Deng, and Yihan Lin .
Nature Communications, 2021c. 12(1).[Html]
A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish.
Jun Xia, Zhixin Kang, Yuanyuan Xue, Yanyan Ding, Suwei Gao, Yifan. Zhang, Peng Lv, Xinyu Wang, Dongyuan Ma, Lu Wang, Jing-Dong J Han, and Feng Liu .
P Natl Acad Sci USA, 2021a. 118(14).[Html]
Assessing the rate of aging to monitor aging itself.
Xian Xia, Yiyang Wang, Zhengqing Yu, Jiawei Chen, and Jing-Dong J Han .
Ageing Res Rev, 2021b. 69.[Html]
LightCUD: a program for diagnosing IBD based on human gut microbiome data.
Congmin Xu, Man Zhou, Zhongjie Xie, Mo Li, Xi Zhu, and Huaiqiu Zhu .
Biodata Min, 2021a. 14(1).[Html]
Dimerization of PHGDH via the catalytic unit is essential for its enzymatic function.
Hanyu Xu, Xiaoyu Qing, Qian Wang, Chunmei Li, and Luhua Lai .
J Biol Chem, 2021b. 296.[Html]
Quantitative investigation reveals distinct phases in Drosophila sleep.
Xiaochan Xu, Wei Yang, Binghui Tian, Xiuwen Sui, Weilai Chi, Yi Rao, and Chao Tang .
Commun Biol, 2021c. 4(1).[Html]
Solution landscapes of the diblock copolymer-homopolymer model under two-dimensional confinement.
Zhen Xu, Yucen Han, Jianyuan Yin, Bing Yu, Yasumasa Nishiura, and Lei Zhang .
Phys Rev E, 2021d. 104(1-1): p. 014505 .[Html]
Transition pathways connecting crystals and quasicrystals.
Jianyuan Yin, Kai Jiang, Anchang Shi, Pingwen Zhang, and Lei Zhang .
P Natl Acad Sci USA, 2021. 118(49).[Html]
Global Optimization-Based Dimer Method for Finding Saddle Points.
Bing Yu, and Lei Zhang .
Discrete Cont Dyn-B, 2021. 26(1): p. 741-753 .[Html]
The STING phase-separator suppresses innate immune signalling.
Xiaoyu Yu, Liyuan Zhang, Jingxiang Shen, Yanfang Zhai, Qifei Jiang, Mengran Yi, Xiaobing Deng, Ziran Ruan, Run Fang, Zhaolong Chen, Xiaohan Ning, and Zhengfan Jiang .
Nat Cell Biol, 2021. 23(4): p. 330-U325 .[Html]
Nonequilibrium Thermodynamics in Biochemical Systems and Its Application.
Dongliang Zhang, and Qi Ouyang .
Entropy-Switz, 2021. 23(3).[Html]
Red- and Far-Red-Emitting Zinc Probes with Minimal Phototoxicity for Multiplexed Recording of Orchestrated Insulin Secretion.
Junwei Zhang, Xiaohong Peng, Yunxiang Wu, Huixia Ren, Jingfu Sun, Shiyan Tong, Tianyan Liu, Yiwen Zhao, Shusen Wang, Chao Tang, Liangyi Chen, and Zhixing Chen .
Angew Chem Int Edit, 2021a. 60(49): p. 25846-25855 .[Html]
Urinary Molecular Pathology for Patients with Newly Diagnosed Urothelial Bladder Cancer.
Ruiyun Zhang, Jingyu Zang, Feng Xie, Yue Zhang, Yiqiu Wang, Ying Jing, Yi Zhang, Zhaoxiong Chen, Akezhouli Shahatiaili, Meichun Cai, Zhixin Zhao, Pan Du, Shidong Jia, Guanglei Zhuang, and Haige Chen .
J Urology, 2021b. 206(4): p. 873-883 .[Html]
Asymmetric Structures and Conformational Plasticity of the Uncleaved Full-Length Human Immunodeficiency Virus Envelope Glycoprotein Trimer.
Shijian Zhang, Kunyu Wang, Weili Wang, Hanh T Nguyen, Shuobing Chen, Maolin Lu, Eden P Go, Haitao Ding, Robert T Steinbock, Heather Desaire, John C Kappes, Joseph Sodroski, and Youdong Mao .
J Virol, 2021c. 95(24).[Html]
Cabazitaxel suppresses colorectal cancer cell growth via enhancing the p53 antitumor pathway.
Wen Zhang, Ruiqian Sun, Yongjun Zhang, Rong Hu, Qian Li, Weili Wu, Xinyu Cao, Jiajian Zhou, Jianfeng Pei, and Ping Yuan .
Febs Open Bio, 2021d. 11(11): p. 3032-3050 .[Html]
The Impact of Mutation L138F/L210F on the Orai Channel: A Molecular Dynamics Simulation Study.
Xiaoqian Zhang, Hua Yu, Xiangdong. Liu, and Chen Song .
Front Mol Biosci, 2021e. 8.[Html]
Paired dCas9 design as a nucleic acid detection platform for pathogenic strains.
Yihao Zhang, Yu Wang, Luze Xu, Chunbo Lou, Qi Ouyang, and Long Qian .
Methods, 2021f. 203: p. 70-77 .[Html]
Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin.
Wei Zhao, Lingxia Qiao, Shiyu Yan, Qing Nie, and Lei Zhang .
Iscience, 2021. 24(7).[Html]
Auxin guides germ-cell specification in Arabidopsis anthers.
Yafeng Zheng, Donghui Wang, Sida Ye, Wenqian Chen, Guilan Li, Zhihong Xu, Shunong Bai, and Feng Zhao .
P Natl Acad Sci USA, 2021. 118(22).[Html]
Stochasticity Triggers Activation of the S-phase Checkpoint Pathway in Budding Yeast.
Peijie Zhou, Xin Gao, Xiaoli Li, Linxi Li, Caoyuan Niu, Qi Ouyang, Huiqiang Lou, Tiejun Li, and Fangting Li .
Phys Rev X, 2021a. 11(1).[Html]
A virtual sequencer reveals the dephasing patterns in error-correction code DNA sequencing.
Wenxiong Zhou, Li Kang, Haifeng Duan, Shuo Qiao, Louis Tao, Zitian. Chen, and Yanyi Huang .
Natl Sci Rev, 2021b. 8(5).[Html]
Single-molecule Imaging of EWS-FLI1 Condensates Assembling on DNA.
Linyu Zuo, Jiawei Ding, and Zhi Qi .
Jove-J Vis Exp, 2021a(175).[Html]
Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription.
Linyu Zuo, Guanwei Zhang, Matthew Massett, Jun Cheng, Zicong Guo, Liang Wang, Yifei Gao, Ru Li, Xu Huang, Pilong Li, and Zhi Qi .
Nature Communications, 2021b. 12(1).[Html]
