2017 published
Cusps enable line attractors for neural computation.
Zhuocheng Xiao,Jiwei Zhang,Andrew T. Sornborger,Louis Tao.
Physical Review E, 2017. 96(5). [Html]
Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins.
Yuanchen Dong,Shuobing Chen,Shijian Zhang,Joseph Sodroski,Zhongqiang Yang,Dongsheng Liu,Youdong Mao.
Angew Chem Int Ed Engl, 2017. [Html]
Streamline-based purification of bacterial samples from liquefied sputum utilizing microfluidics.
Tian Wu,Changjun Shao,Lingjun Li,Shujing Wang,Qi Ouyang,Yu Kang,Chunxiong Luo.
Lab on a Chip, 2017. 17(21): p. 3601-3608 . [Html]
Single Living yEast PM Toxicity Sensor (SLEPTor) System.
KaiWei,Minghao Qiu,Rongfei Zhang,Liantong Zhou,Ting Zhang,Maosheng Yao,Chunxiong Luo.
Journal of Aerosol Science, 2017. 107: p. 65-73 . [Html]
Relative biological effectiveness for photons: implication of complex DNA double-strand breaks as critical lesions.
Ying Liang,Qibin Fu,Xudong Wang,Feng Liu,Gen Yang,Chunxiong Luo,Qi Ouyang,Yugang Wang.
Physics in Medicine and Biology, 2017. 62(6): p. 2153-2175 . [Html]
Using Microfluidic Devices to Measure Lifespan and Cellular Phenotypes in Single Budding Yeast Cells.
Ke Zou,Diana S. Ren,Qi Ou-yang,Hao Li,Jiashun Zheng.
Jove-Journal of Visualized Experiments, 2017(121). [Html]
Sequence imperfections and base triplet recognition by the Rad51/RecA family of recombinases.
Ja Yil Lee,Justin B. Steinfeld,Zhi Qi,YoungHo Kwon,Patrick Sung,Eric C. Greene.
Journal of Biological Chemistry, 2017. 292(26): p. 11125-11135 . [Html]
gCoda: Conditional Dependence Network Inference for Compositional Data.
Huaying Fang,Chengcheng Huang,Hongyu Zhao,Minghua Deng.
Journal of Computational Biology, 2017. 24(7): p. 699-708 . [Html]
Rational Design of Selective Allosteric Inhibitors of PHGDH and Serine Synthesis with Anti-tumor Activity.
Qian Wang,Maria V. Liberti,Pei Liu,Xiaobing Deng,Ying Liu,Jason W. Locasale,Luhua Lai.
Cell Chemical Biology, 2017. 24(1): p. 55-65 . [Html]
A global characterization of the translational and transcriptional programs induced by methionine restriction through ribosome profiling and RNA-seq.
Ke Zou,Qi Ouyang,Hao Li,Jiashun Zheng.
Bmc Genomics, 2017. 18. [Html]
Mean field study of a propagation-turnover lattice model for the dynamics of histone marking.
Fan Yao,FangTing Li,TieJun Li.
Science China-Physics Mechanics & Astronomy, 2017. 60(2). [Html]
Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier.
Jemma L. Trick,Chen Song,E. Jayne Wallace,Mark S. P. Sansom.
Acs Nano, 2017. 11(2): p. 1840-1847 . [Html]
Finding non-classical critical nuclei and minimum energy path of Cu precipitates in Fe-Cu alloys.
Li, B.Y., et al. .
Modelling and Simulation in Materials Science and Engineering, 2017. 25(8). [Html]
Rational Design of an Ultrasensitive Quorum-Sensing Switch.
Weiqian Zeng,Pei Du,Qiuli Lou,Lili Wu,Haoqian M. Zhang,Chunbo Lou,Hongli Wang,Qi Ouyang.
Acs Synthetic Biology, 2017. 6(8): p. 1445-1452 . [Html]
Computational design of ligand-binding proteins.
Wei Yang,Luhua Lai.
Current Opinion in Structural Biology, 2017. 45: p. 67-73 . [Html]
Analysis and correction of errors in nanoscale particle tracking using the Single-pixel interior filling function (SPIFF) algorithm.
Yuval Yifat,Nishant Sule,Yihan Lin,Norbert F. Scherer.
Sci Rep, 2017. 7(1): p. 16553 . [Html]
Design of Tunable Oscillatory Dynamics in a Synthetic NF-kappaB Signaling Circuit.
Zhi-Bo Zhang,Qiu-Yue Wang,Yu-Xi Ke,Shi-Yu Liu,Jian-Qi Ju,Wendell A. Lim,Chao Tang,Ping Wei.
Cell Syst, 2017. 5(5): p. 460-470 e5 . [Html]
Odor-evoked inhibition of olfactory sensory neurons drives olfactory perception in Drosophila.
Li-Hui Cao,Dong Yang,Wei Wu,Xiankun Zeng,Bi-Yang Jing,Meng-Tong Li,Shanshan Qin,Chao Tang,Yuhai Tu,Dong-Gen Luo.
Nat Commun, 2017. 8(1): p. 1357 . [Html]
The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer.
Dali Wang,Hua Yu,Xiangdong Liu,Jianqiang Liu,Chen Song.
Sci Rep, 2017. 7(1): p. 16985 . [Html]
Innovating Chinese Herbal Medicine: From Traditional Health Practice to Scientific Drug Discovery.
Shuo Gu,Jianfeng Pei.
Front Pharmacol, 2017. 8: p. 381 . [Html]
Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images.
Mengdi Zhao,Jie An,Haiwen Li,Jiazhi Zhang,Shang-Tong Li,Xue-Mei Li,Meng-Qiu Dong,Heng Mao,Louis Tao.
BMC Bioinformatics, 2017. 18(1): p. 412 . [Html]
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm.
Zhengwei Xie,Tianyu Zhang,Qi Ouyang.
Bioinformatics, 2017. [Html]
Tuning SpyTag-SpyCatcher mutant pairs toward orthogonal reactivity encryption.
Yajie Liu,Dong Liu,Wei Yang,Xia-Ling Wu,Luhua Lai,Wen-Bin Zhang.
Chem Sci, 2017. 8(9): p. 6577-6582 . [Html]
Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction.
Youjun Xu,Jianfeng Pei,Luhua Lai.
J Chem Inf Model, 2017. [Html]
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.
Peng Zhai,Longshu Yang,Xiao Guo,Zhe Wang,Jiangtao Guo,Xiaoqi Wang,Huaiqiu Zhu.
BMC Bioinformatics, 2017. 18(1): p. 434 . [Html]
SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms.
Yuchao Xia,Yun Liu,Minghua Deng,Ruibin Xi.
Bioinformatics, 2017. 33(21): p. 3348-3354 . [Html]
Sequence-based prediction of protein protein interaction using a deep-learning algorithm.
Tanlin Sun,Bo Zhou,Luhua Lai,Jianfeng Pei.
BMC Bioinformatics, 2017. 18(1): p. 277 . [Html]
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.
Xia Wang,Yihang Shen,Shiwei Wang,Shiliang Li,Weilin Zhang,Xiaofeng Liu,Luhua Lai,Jianfeng Pei,Honglin Li.
Nucleic Acids Res, 2017. [Html]
Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters.
Sui Huang,Fangting Li,Joseph X. Zhou,Hong Qian.
J R Soc Interface, 2017. 14(130). [Html]
Designed inhibitor for nuclear localization signal of polo-like kinase 1 induces mitotic arrest.
Fangjin Chen,Xiaolong Zhuo,Tan Qin,Xiao Guo,Chuanmao Zhang,Luhua Lai.
Chem Biol Drug Des, 2017. 89(5): p. 732-740 . [Html]
Computational Multitarget Drug Design.
Weilin Zhang,Jianfeng Pei,Luhua Lai.
J Chem Inf Model, 2017. 57(3): p. 403-412 . [Html]
[Signaling network-based functional cell design].
Ju, J. and P. Wei .
Sheng Wu Gong Cheng Xue Bao, 2017. 33(3): p. 386-392 . [Html]
RCN1 suppresses ER stress-induced apoptosis via calcium homeostasis and PERK-CHOP signaling.
S Xu,Y Xu,L Chen,Q Fang,S Song,J Chen,J Teng.
Oncogenesis, 2017. 6(3): p. e304 . [Html]
Engineering Escherichia coli to bind to cyanobacteria.
Zijian Zhang,Liuyi Meng,Congjian Ni,Lanqiu Yao,Fengyu Zhang,Yuji Jin,Xuelang Mu,Shiyu Zhu,Xiaoyu Lu,Shiyu Liu,Congyu Yu1Chenggong Wang,Pu Zheng,Jie Wu,Li Kang,Haoqian M.Zhang,Qi Ouyang.
J Biosci Bioeng, 2017. 123(3): p. 347-352 . [Html]
Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues.
Weilin Zhang,Jianfeng Pei,Luhua Lai.
J Chem Inf Model, 2017. 57(6): p. 1453-1460 . [Html]
Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts.
Yanru An,Guosheng Xue,Yang Shaobo,Deng Mingxi,Xiaowei Zhou,Weichuan Yu,Toyotaka Ishibashi,Lei Zhang,Yan Yan.
Development, 2017. 144(12): p. 2153-2164 . [Html]
NF-kappaB signaling and cell-fate decision induced by a fast-dissociating tumor necrosis factor mutant.
Xiaoling Zhang,Ning Yin,Annan Guo,Qi Zhang,Yalei Zhang,Youjun Xu,Hongbo Liu,Bo Tang,Luhua Lai.
Biochem Biophys Res Commun, 2017. 489(3): p. 287-292 . [Html]
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.
Yanan Zhu,Qi Ouyang,Youdong Mao.
BMC Bioinformatics, 2017. 18(1): p. 348 . [Html]
Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
Ying Lu,Jiayi Wu,Yuanchen Dong,Shuobing Chen,Shuangwu Sun,Yong-Bei Ma,Qi Ouyang,Daniel Finley,Marc W. Kirschner,Youdong Mao.
Mol Cell, 2017. 67(2): p. 322-333.e6 . [Html]
Cryo-EM structure of the DNA-PK holoenzyme.
Humayun Sharif,Yang Li,Yuanchen Dong,Liyi Dong,Wei Li Wang,Youdong Mao,Hao Wu.
Proc Natl Acad Sci U S A, 2017. 114(28): p. 7367-7372 . [Html]
Insulated transcriptional elements enable precise design of genetic circuits.
Yeqing Zong,Haoqian M. Zhang,Cheng Lyu,Xiangyu Ji,Junran Hou,Xian Guo,Qi Ouyang,Chunbo Lou.
Nat Commun, 2017. 8(1): p. 52 . [Html]
Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
Bin Shao,Haiyu Yuan,Rongfei Zhang,Xuan Wang,Shuwen Zhang,Qi Ouyang,Nan Hao,Chunxiong Luo.
PLoS Comput Biol, 2017. 13(7): p. e1005671 . [Html]
Live visualization of genomic loci with BiFC-TALE.
Huan Hu,Hongmin Zhang,Sheng Wang,Miao Ding,Hui An,Yingping Hou,Xiaojing Yang,Wensheng Wei,Yujie Sun,Chao Tang.
Sci Rep, 2017. 7: p. 40192 . [Html]
Novel T7-like expression systems used for Halomonas.
Han Zhao,Haoqian M.Zhang,Xiangbin Chen,Teng Li,Qiong Wua,Qi Ouyang,Guo-Qiang Chen.
Metab Eng, 2017. 39: p. 128-140 . [Html]
Exploring the inhibitory effect of membrane tension on cell polarization.
Weikang Wang,Kuan Tao,Jing Wang,Gen Yang,Qi Ouyang,Yugang Wang,Lei Zhang,Feng Liu.
PLoS Comput Biol, 2017. 13(1): p. e1005354 . [Html]
Adaptation with transcriptional regulation.
Wenjia Shi,Wenzhe Ma,Liyang Xiong,Mingyue Zhang,Chao Tang.
Sci Rep, 2017. 7: p. 42648 . [Html]
Paired Design of dCas9 as a Systematic Platform for the Detection of Featured Nucleic Acid Sequences in Pathogenic Strains.
Yihao Zhang,Long Qian,Weijia Wei,Yu Wang,Beining Wang,Pingping Lin,Wenchao Liu,Luze Xu,Xiang Li,Dongming Liu,Sida Cheng,Jiaofeng Li,Yixuan Ye,Hang Li,Xiaohan Zhang,Yiming Dong,Xuejin Zhao,Cuihua Liu,Haoqian M. Zhang,Qi Ouyang,Chunbo Lou.
ACS Synth Biol, 2017. 6(2): p. 211-216 . [Html]
Spontaneous activation of visual pigments in relation to openness/closedness of chromophore-binding pocket.
Wendy Wing Sze Yue,Rikard Frederiksen,Xiaozhi Ren,Dong-Gen Luo,Takahiro Yamashita,Yoshinori Shichida,M Carter Cornwall,King-Wai Yau.
Elife, 2017. 6. [Html]
High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response.
Rongfei Zhang,Haiyu Yuan,Shujing Wang,Qi Ouyang,Yong Chen,Nan Hao,Chunxiong Luo.
Sci Rep, 2017. 7: p. 42200 . [Html]
Switching of the substrate specificity of protein tyrosine phosphatase N12 by cyclin-dependent kinase 2 phosphorylation orchestrating 2 oncogenic pathways.
Hui Li,Duxiao Yang,Shanglei Ning,Yinghui Xu,Fan Yang,Rusha Yin,Taihu Feng,Shouqing Han,Lu Guo,Pengju Zhang,Wenjie Qu,Renbo Guo,Chen Song,Peng Xiao,Chengjun Zhou,Zhigang Xu,Jin‐Peng Sun,Xiao Yu.
Faseb j, 2017. [Html]
Hierarchical assembly of centriole subdistal appendages via centrosome binding proteins CCDC120 and CCDC68.
Ning Huang,Yuqing Xia,Donghui Zhang,Song Wang,Yitian Bao,Runsheng He,Junlin Teng,Jianguo Chen.
Nat Commun, 2017. 8: p. 15057 . [Html]
Robust network topologies for generating oscillations with temperature-independent periods.
Lili Wu,Qi Ouyang,Hongli Wang.
PLoS One, 2017. 12(2): p. e0171263 . [Html]
Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.
Jiayi Wu,Yong-Bei Ma,Charles Congdon,Bevin Brett,Shuobing Chen,Yaofang Xu,Qi Ouyang,Youdong Mao.
PLoS One, 2017. 12(8): p. e0182130 . [Html]
Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective.
Shuo Gu,Jianfeng Pei.
Evid Based Complement Alternat Med, 2017. 2017: p. 7198645 . [Html]
Visualizing biological reaction intermediates with DNA curtains.
Zhao, Y., et al.
Journal of Physics D-Applied Physics, 2017. 50(15). [Html]
Barrier Crossing in Escherichia coli Chemotaxis.
Zhaojun Li,Qiuxian Cai,Xuanqi Zhang,Guangwei Si,Qi Ouyang,Chunxiong Luo,Yuhai Tu.
Physical Review Letters, 2017. 118(9): p. 098101 (5 pp.)-098101 (5 pp.). [Html]
VCNet: Vector based gene Co-expression Network construction and its application to RNA-seq data.
Zengmiao Wang,Huaying Fang,Nelson Leung-Sang Tang,Minghua Deng.
Bioinformatics (Oxford, England), 2017. [Html]
