2019 published
Network Clustering Analysis Using Mixture Exponential-Family Random Graph Models and Its Application in Genetic Interaction Data.
Yishu Wang,Huaying Fang,Dejie Yang,Hongyu Zhao,Minghua Deng.
IEEE-Acm Transactions on Computational Biology and Bioinformatics, 2019. 16(5): p. 1743-1752 . [Html]
How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain-an atomic level characterization.
Likun Zhao,Luhua Lai,Zhuqing Zhang.
Physical Chemistry Chemical Physics, 2019. 21(36): p. 19795-19804 . [Html]
Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation.
Lingxia Qiao,Wei Zhao,Chao Tang,Qing Nie,Lei Zhang.
Cell Syst, 2019. 9(3): p. 271-285 e7 . [Html]
Discrimination of indoor versus outdoor environmental state with machine learning algorithms in myopia observational studies.
Bin Ye,Kangping Liu,Siting Cao,Padmaja Sankaridurg,Wayne Li,Mengli Luan,Bo Zhang,Jianfeng Zhu,Haidong Zou,Xun Xu,Xiangui He.
J Transl Med, 2019. 17(1): p. 314 . [Html]
CCDC74A/B are K-fiber crosslinkers required for chromosomal alignment.
Haining Zhou,Tao Zheng,Tianning Wang,Qi Li,Fulin Wang,Xin Liang,Jianguo Chen,Junlin Teng.
BMC Biol, 2019. 17(1): p. 73 . [Html]
Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination.
Justin B. Steinfeld,Ondrej Beláň,Youngho Kwon,Tsuyoshi Terakawa,Amr Al-Zain,Michael J. Smith,J. Brooks Crickard,Zhi Qi,Weixing Zhao,Rodney Rothstein,Lorraine S. Symington,Patrick Sung,Simon J. Boulton,Eric C. Greene.
Genes Dev, 2019. 33(17-18): p. 1191-1207 . [Html]
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.
Haicang Zhang,Qi Zhang,Fusong Ju,Jianwei Zhu,Yujuan Gao,Ziwei Xie,Minghua Deng,Shiwei Sun,Wei-Mou Zheng,Dongbo Bu.
BMC Bioinformatics, 2019. 20(1): p. 537 . [Html]
Cell Cycle Inhibitor Whi5 Records Environmental Information to Coordinate Growth and Division in Yeast.
Yimiao Qu,Jun Jiang,Xiang Liu,Ping Wei,Xiaojing Yang,Chao Tang.
Cell Rep, 2019. 29(4): p. 987-994 e5 . [Html]
Identification of Cancer-associated metabolic vulnerabilities by modeling multi-objective optimality in metabolism.
Ziwei Dai,Shiyu Yang,Liyan Xu,Hongrong Hu,Kun Liao,Jianghuang Wang,Qian Wang,Shuaishi Gao,Bo Li,Luhua Lai.
Cell Commun Signal, 2019. 17(1): p. 124 . [Html]
Expectation pooling: An effective and interpretable pooling method for predicting DNA-protein binding.
Xiao Luo,Xinming Tu,Yang Ding,Ge Gao,Minghua Deng.
Bioinformatics, 2019. [Html]
Optimal compressed sensing strategies for an array of nonlinear olfactory receptor neurons with and without spontaneous activity.
Shanshan Qin,Qianyi Li,Chao Tang,Yuhai Tu.
Proc Natl Acad Sci U S A, 2019. 116(41): p. 20286-20295 . [Html]
DNA Origami as Scaffolds for Self-Assembly of Lipids and Proteins.
Yuanchen Dong,Youdong Mao.
Chembiochem, 2019. 20(19): p. 2422-2431 . [Html]
A Mechanism for Synaptic Copy Between Neural Circuits.
Yuxiu Shao,Binxu Wang,Andrew T. Sornborger,Louis Tao.
Neural Comput, 2019. 31(10): p. 1964-1984 . [Html]
The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A.
Xiaoyang Dou,Jerome D. Boyd-Kirkup,Joseph McDermott,Xiaoli Zhang,Fang Li, Bowen Rong,Rui Zhang,Bisi Miao,Peilin Chen,Hao Cheng,Jianhuang Xue,David Bennett,Jiemin Wong,Fei Lan,Jing-Dong J. Han.
Genome Res, 2019. 29(10): p. 1622-1634 . [Html]
CCDC84 Acetylation Oscillation Regulates Centrosome Duplication by Modulating HsSAS-6 Degradation.
Tianning Wang,Yuhong Zou,Ning Huang,Junlin Teng,Jianguo Chen.
Cell Rep, 2019. 29(7): p. 2078-+ . [Html]
Structure and Dynamics of Cinnamycin-Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids.
Mikkel Vestergaard,Nils Anton Berglund,Pin-Chia Hsu,Chen Song,Heidi Koldsø,Birgit Schiøtt*,Mark S. P. Sansom.
Acs Omega, 2019. 4(20): p. 18889-18899 . [Html]
Transition pathways between defect patterns in confined nematic liquid crystals.
Yucen Han,Yucheng Hu,Pingwen Zhang,Lei Zhang.
Journal of Computational Physics, 2019. 396: p. 1-11 . [Html]
A Novel Noninvasive Program for Staging Liver Fibrosis in Untreated Patients With Chronic Hepatitis B.
Chen Yan,Wang Yongji,Chen Yongping,Yu Zujiang,Chi Xiaoling, Hu Ke-Qin,Li Qin,Tan Lin,Xiang, Dedong,Shang Qinghua,Lei Chunliang,Chen Liang,Hu Xiaoyu,Wang, Jing,Liu Huabao,Lu Wei,Chi Weilai,Dong Zheng,Wang Xiaodong,Li Zhiqin,Xiao Huanming,Chen Da,Bai Wenlin,Zhang Changjiang,Xiao Guangming,Qi Xun,Chen Jing,Zhou Li,Sun Huiwei,Deng Minghua,Qi Xiaolong,Zhang Zheng,Qi Xingshun,Yang Yongping.
Clin Transl Gastroenterol, 2019. 10(5): p. 1-12 . [Html]
Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics.
Xing Shi,Changjun Shao,Chunxiong Luo,Yanan Chu,Jian Wang,Qingren Meng,Jun Yu,Zhancheng Gao,Yu Kang.
mSystems, 2019. 4(4). [Html]
Efficient ligand discovery from natural herbs by integrating virtual screening, affinity mass spectrometry and targeted metabolomics.
Zhihua Wang,Hao Liang,Haijie Cao,Bingjie Zhang,Jun Li,Wenqiong Wang,Shanshan Qin,Yuefei Wang,Lijiang Xuan,Luhua Lai,Wenqing Shui.
Analyst, 2019. 144(9): p. 2881-2890 . [Html]
Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel.
Chen Song，Bert L. de Groot，Mark S.P. Sansom.
Biophys J, 2019. 116(9): p. 1658-1666 . [Html]
Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions.
William R. Blevins,Lucas B. Carey,M. Mar Albà.
BMC Res Notes, 2019. 12(1): p. 250 . [Html]
Mechanosensory circuits coordinate two opposing motor actions in Drosophila feeding.
Yao Zhou,Li-Hui Cao,Xiu-Wen Sui,Xiao-Qing Guo,Dong-Gen Luo.
Sci Adv, 2019. 5(5): p. eaaw5141 . [Html]
Expanding the phenotypic and genetic spectrum of Chinese patients with congenital absence of vas deferens bearing CFTR and ADGRG2 alleles.
P. Yuan,Z. K. Liang,H. Liang,L. Y. Zheng,D. Li,J. Li,J. Zhang,J. Tian,L. H. Lai,K. Zhang,Z. Y. He,Q. X. Zhang,W. J. Wang.
Andrology, 2019. 7(3): p. 329-340 . [Html]
Growth strategy of microbes on mixed carbon sources.
Wang, X., et al. .
Nat Commun, 2019. 10. [Html]
Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects.
Miao Yu,Yixin Chen,Zi-Le Wang,Zhirong Liu.
Physical Chemistry Chemical Physics, 2019. 21(9): p. 5200-5214 . [Html]
ATL3 Is a Tubular ER-Phagy Receptor for GABARAP-Mediated Selective Autophagy.
Qingzhou Chen,Ya Xiao,Peiyuan Chai,Pengli Zheng,Junlin Teng,Jianguo Chen.
Current Biology, 2019. 29(5): p. 846-+ . [Html]
Protein dynamic analysis of the budding yeast sporulation process at the single-cell level in an air-enriched microfluidic device.
Xiang Zhao,Chunxiong Luo,Hongli Wang.
Integrative Biology, 2019. 11(3): p. 79-86 . [Html]
Deep learning for molecular generation.
Youjun Xu,Kangjie Lin,Shiwei Wang,Lei Wang,Chenjing Cai,Chen Song,Luhua Lai,Jianfeng Pei.
Future Med Chem, 2019. 11(6): p. 567-597 . [Html]
Systematically investigating the key features of the DNase deactivated Cpf1 for tunable transcription regulation in prokaryotic cells.
Chensi Miao,Huiwei Zhao,Long Qian,Chunbo Lou.
Synthetic and Systems Biotechnology, 2019. 4(1): p. 1-9 . [Html]
Visualization of Genomic Loci in Living Cells with BiFC-TALE.
Huan Hu,Xiaojing Yang,Chao Tang.
Curr Protoc Cell Biol, 2019. 82(1): p. e78 . [Html]
Legionella effector SetA as a general O-glucosyltransferase for eukaryotic proteins.
Ling Gao,Qitao Song,Hao Liang,Yuntao Zhu,Tiantian Wei,Na Dong,Junyu Xiao,Feng Shao,Luhua Lai,Xing Chen.
Nat Chem Biol, 2019. 15(3): p. 213-216 . [Html]
Investigating targets for neuropharmacological intervention by molecular dynamics simulations.
Giulia Rossetti,Achim Kless,Luhua Lai,Tiago F. Outeiro,Paolo Carloni.
Biochemical Society Transactions, 2019. 47: p. 909-918 . [Html]
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.
Zhencheng Fang,Jie Tan,Shufang Wu,Mo Li,Congmin Xu,Zhongjie Xie,Huaiqiu Zhu.
Gigascience, 2019. 8(6). [Html]
Computational design and optimization of novel d-peptide TNFalpha inhibitors.
Wei Yang,Qi Zhang,Changsheng Zhang,Annan Guo,Yanyan Wang,Hantian You,Xiaoling Zhang,Luhua Lai.
FEBS Lett, 2019. 593(12): p. 1292-1302 . [Html]
Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.
Humayun Sharif,Li Wang,Wei Li Wang,Venkat Giri Magupalli,Liudmila Andreeva,Qi Qiao,Arthur V. Hauenstein,Zhaolong Wu,Gabriel Núñez,Youdong Mao,Hao Wu.
Nature, 2019. 570(7761): p. 338-343 . [Html]
Sequencing of the MHC region defines HLA-DQA1 as the major genetic risk for seropositive rheumatoid arthritis in Han Chinese population.
Jianping Guo,Tao Zhang,Hongzhi Cao,Xiaowei Li,Hao Liang,Mengru Liu,Yundong Zou,Yuanwei Zhang,Yuxuan Wang,Xiaolin Sun,Fanlei Hu,Yan Du,Xiaodong Mo,Xu Liu,Yue Yang,Huanjie Yang,Xinyu Wu,Xuewu Zhang,Huijue Jia,Hui Jiang,Yong Hou,Xin Liu,Yin Su,Mingrong Zhang,Huanming Yang,Jian Wang,Liangdan Sun,Liang Liu,Leonid Padyukov,Luhua Lai,Kazuhiko Yamamoto,Xuejun Zhang,Lars Klareskog,Xun Xu,Zhanguo Li.
Ann Rheum Dis, 2019. 78(6): p. 773-780 . [Html]
Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast.
William R. Blevins,Teresa Tavella,Simone G. Moro,Bernat Blasco-Moreno,Adrià Closa-Mosquera,Juana Díez,Lucas B. Carey,M. Mar Albà.
Sci Rep, 2019. 9(1): p. 11005 . [Html]
Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise.
Jörn M. Schmiedel,Lucas B. Carey,Ben Lehner.
Nat Commun, 2019. 10(1): p. 3180 . [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,Jianguo Chen.
Autophagy, 2019. [Html]
Detecting virus integration sites based on multiple related sequencing data by VirTect.
Yuchao Xia,Yun Liu,Minghua Deng,Ruibin Xi.
BMC Med Genomics, 2019. 12(Suppl 1): p. 19 . [Html]
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation.
Dhar, R., et al. .
Elife, 2019. 8. [Html]
Constructing network topologies for multiple signal-encoding functions.
Lili Wu,Hongli Wang,Qi Ouyang.
BMC Syst Biol, 2019. 13(1): p. 6 . [Html]
Novel Allosteric Activators for Ferroptosis Regulator Glutathione Peroxidase 4.
Cong Li,Xiaobing Deng,Weilin Zhang,Xiaowen Xie,Marcus Conrad,Ying Liu,José Pedro Friedmann Angeli,Luhua Lai.
Journal of Medicinal Chemistry, 2019. 62(1): p. 266-275 . [Html]
Bi-functional biochemical networks.
Zhang, M.Y. and C. Tang .
Physical Biology, 2019. 16(1). [Html]
Targeting intrinsically disordered proteins at the edge of chaos.
Hao Ruan,Qi Sun,Weilin Zhang,Ying Liu,LuhuaLai.
Drug Discovery Today, 2019. 24(1): p. 217-227 . [Html]
Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Yuanchen Dong,Shuwen Zhang,Zhaolong Wu,Xuemei Li,Wei Li Wang,Yanan Zhu,Svetla Stoilova-McPhie,Ying Lu,Daniel Finley,Youdong Mao.
Nature, 2019. 565(7737): p. 49-55 . [Html]
Development of a New Calcium Ion Model for Simulating Biomolecules.
Zhang, A.H., et al. .
Biophysical Journal, 2019. 116(3): p. 145a-145a . [Html]
Computational Study on the Regulation of Fam20C by Fam20A.
Yu, H., et al. .
Biophysical Journal, 2019. 116(3): p. 343a-343a . [Html]
Escape band in Escherichia coli chemotaxis in opposing attractant and nutrient gradients.
Xuanqi Zhang,Guangwei Si,Yiming Dong,Kaiyue Chen,Qi Ouyang,Chunxiong Luo,Yuhai Tu.
Proc Natl Acad Sci U S A, 2019. 116(6): p. 2253-2258 . [Html]
Clinical characteristic and fecal microbiota responses to probiotic or antidepressant in patients with diarrhea-predominant irritable bowel syndrome with depression comorbidity: a pilot study.
Zhang Lu,Liu Yi-Xuan,Wang Zhe,Wang Xiao-Qi,Zhang Jing-Jing,Jiang Rong-Huan,Wang Xiang-Qun,Zhu Shi-Wei,Wang Kun,Liu Zuo-Jing,Zhu Huai-Qiu,Duan Li-Ping.
Chin Med J (Engl), 2019. 132(3): p. 346-351 . [Html]
Fabrication and application of nanoporous polymer ion-track membranes.
Liu, F., et al. .
Nanotechnology, 2019. 30(5). [Html]
How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.
Xiaoqing Jiang,Xin Li,Longshu Yang,Chunhong Liu,Qi Wang,Weilai Chi,Huaiqiu Zhu.
Genomics Proteomics Bioinformatics, 2019. 17(1): p. 91-105 . [Html]
A Catalog of GAL4 Drivers for Labeling and Manipulating Circadian Clock Neurons in Drosophila melanogaster.
Manabu Sekiguchi,Kotaro Inoue1,Tian Yang,Dong-Gen Luo,Taishi Yoshii.
J Biol Rhythms, 2019: p. 748730419895154 . [Html]
Why and how the nematode's early embryogenesis can be precise and robust: a mechanical perspective.
Binghui Tian,Guoye Guan,Lei-Han Tang,Chao Tang.
Phys Biol, 2019. [Html]
Pathways connecting two opposed bilayers with a fusion pore: a molecularly-informed phase field approach.
Yucen Han,Zirui Xu,An-Chang Shi,Lei Zhang.
Soft Matter, 2019. [Html]
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells.
Ying Chen,Ke Li,Xiao Chu,Lucas B. Carey,Wenfeng Qian.
Genome Res, 2019. 29(12): p. 1929-1938 . [Html]
Overdosage of Balanced Protein Complexes Reduces Proliferation Rate in Aneuploid Cells.
Ying Chen,Siyu Chen,Ke Li,Yuliang Zhang,Xiahe Huang,Ting Li,Shaohuan Wu,Yingchun Wang,Lucas B. Carey,Wenfeng Qian.
Cell Syst, 2019. 9(2): p. 129-+ . [Html]
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,Jing-Dong J Han..
Bioinformatics, 2019. [Html]
Spatial coordination in a mutually beneficial bacterial community enhances its antibiotic resistance.
Li, L.J., et al. .
Communications Biology, 2019. 2. [Html]
A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids.
Yu, J.F., et al. .
Biopolymers, 2019. 110(8). [Html]
Molecular architecture of lineage allocation and tissue organization in early mouse embryo.
Guangdun Peng,Shengbao Suo,Guizhong Cui,Fang Yu,Ran Wang,Jun Chen,Shirui Chen,Zhiwen Liu,Guoyu Chen,Yun Qian,Patrick P. L. Tam,Jing-Dong J. Han,Naihe Jing.
Nature, 2019. 572(7770): p. 528-532 . [Html]
Characteristic dysbiosis of gut microbiota of Chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome.
Wang, Zhe,Xu Cong-Min,Liu Yi-Xuan,Wang Xiao-Qi,Zhang Lu,Li Mo,Zhu Shi-Wei,Xie Zhong-Jie,Wang Pei-Hong,Duan Li-Ping,Zhu Huai-Qiu.
Chin Med J (Engl), 2019. 132(8): p. 889-904 . [Html]
Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach.
Wei Li Wang,Zhou Yu,Luis R. Castillo-Menendez,Joseph Sodroski,Youdong Mao.
BMC Bioinformatics, 2019. 20(1): p. 169 . [Html]
Mechanism of DNA-Induced Phase Separation for Transcriptional Repressor VRN1.
Huabin Zhou,Zihan Song,Dr. Sheng Zhong,Linyu Zuo,Zhi Qi,Li‐Jia Qu,Luhua Lai.
Angew Chem Int Ed Engl, 2019. 58(15): p. 4858-4862 . [Html]
A coarse-graining framework for spiking neuronal networks: from strongly-coupled conductance-based integrate-and-fire neurons to augmented systems of ODEs.
Jiwei Zhang,Yuxiu Shao,Aaditya V. Rangan,Louis Tao.
J Comput Neurosci, 2019. 46(2): p. 211-232 . [Html]
An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape.
Victoria O. Pokusaeva,Dinara R. Usmanova,Ekaterina V. Putintseva,Lorena Espinar,Karen S. Sarkisyan,Alexander S. Mishin,Natalya S. Bogatyreva,Dmitry N. Ivankov,Arseniy V. Akopyan,Sergey Ya. Avvakumov,Inna S. Povolotskaya,Guillaume J. Filion,Lucas B. Carey,Fyodor A. Kondrashov.
PLoS Genet, 2019. 15(4): p. e1008079 . [Html]
Associating 197Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach.
Shuo Gu,Lu-hua Lai.
Acta pharmacologica Sinica, 2019. [Html]
Correlation Between Allosteric and Orthosteric Sites.
Weilin Zhang,Juan Xie,Luhua Lai.
Adv Exp Med Biol, 2019. 1163: p. 89-105 . [Html]
Computational Calibration and Correction for Gigapixel Imaging System.
Jiazhi Zhang,Jie He,Haiwen Li,Yuanchao Bai,Huizhu Jia,Louis Tao,Heng Mao.
Proceedings of the International Conference on Sensing and Imaging, 2019. 506: p. 293-302 . [Html]
Discovery of novel helix binding sites at protein-protein interfaces.
Wei Yang,Xiangyu Sun,Changsheng Zhang,Luhua Lai.
Comput Struct Biotechnol J, 2019. 17: p. 1396-1403 . [Html]
Deepprune: Learning Efficient and Interpretable Convolutional Networks Through Weight Pruning for Predicting DNA-Protein Binding.
Xiao Luo, Weilai Chi,Minghua Deng.
Front Genet, 2019. 10: p. 1145 . [Html]
