生物网络的可计算建模

91430217
2014
C0504.物理生物学
汤超
重大研究计划
教授
北京大学
350万元
生物网络;数学模型;算法优化;细胞命运;设计原理
2015-01-01到2018-12-31
  • 中英文摘要
  • 结题摘要
  • 结题报告
  • 项目成果
  • 项目参与人
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序号 标题 类型 作者
1 Low Cell-Matrix Adhesion Reveals Two Subtypes of Human Pluripotent Stem Cells 期刊论文 Yu Leqian;Li Junjun;Hong Jiayin;Takashima Yasuhiro;Fujimoto Nanae;Nakajima Minako;Yamamoto Akihisa;Dong Xiaofeng;Dang Yujiao;Hou Yu;Yang Wei;Minami Itsunari;Okita Keisuke;Tanaka Motomu;Luo Chunxiong;Tang Fuchou;Chen Yong;Tang Chao;Kotera Hidetoshi;Liu Li
2 Uncovering the underlying mechanism of cancer tumorigenesis and development under an immune microenvironment from global quantification of the landscape 期刊论文 Li Wenbo;Jin Wang
3 Early-warning signals of critical transition: Effect of extrinsic noise 期刊论文 Qin Shanshan;Tang Chao
4 Enzymatic Activity and Thermodynamic Stability of Biliverdin IX beta Reductase Are Maintained by an Active Site Serine 期刊论文 Chu Wen-Ting;Nesbitt Natasha M.;Gnatenko Dmitri V.;Li Zongdong;Zhang Beibei;Seeliger Markus A.;Browne Seamus;Mantle Timothy J.;Bahou Wadie F.;Wang Jin
5 Solvent effect on FRET spectroscopic ruler 期刊论文 Qu Songyuan;Liu Chuanbo;Liu Qiong;Wu Wei;Du Baoji;Wang Jin
6 In silico and crystallographic studies identify key structural features of biliverdin IX beta reductase inhibitors having nanomolar potency 期刊论文 Nesbitt Natasha M.;Li Zongdong;Yen Wan-Yi;Malone Lisa E.;Bahou Wadie F.;Wang Jin;Zheng Xiliang;Manso Jose A.;Ripoll-Rozada Jorge;Barbosa Pereira Pedro Jose;Manso Jose A.;Ripoll-Rozada Jorge;Barbosa Pereira Pedro Jose;Mantle Timothy J.;Nesbitt NM;Wang J
7 Feedback from Lateral Organs Controls Shoot Apical Meristem Growth by Modulating Auxin Transport 期刊论文 Shi Bihai;Guo Xiaolu;Wang Ying;Xiong Yuanyuan;Wang Jin;Hayashi Ken-ichiro;Lei Jinzhi;Zhang Lei;Jiao Yuling
8 Recent developments in computational Modeling of Nucleation in Phase Transformations 期刊论文 Lei Zhang;Weiqing Ren;Amit Samanta;Qiang Du
9 A Cake-Style CoS2@MoS2/RGO Hybrid Catalyst for Efficient Hydrogen Evolution 期刊论文 Guo Yaxiao;Gan Linfeng;Shang Changshuai;Wang Erkang;Wang Jin
10 The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A 期刊论文 Zhao Lingci;Suarez Irina P.;Gauto Diego F.;Rasia Rodolfo M.;Wang Jin
11 Designing metal-contained enzyme mimics for prodrug activation 期刊论文 Du Baoji;Li Dan;Wang Jin;Wang Erkang
12 Non-Markovian Nonequilibrium Information Dynamics 期刊论文 Qian Zeng;Jin Wang
13 Landscape and flux for quantifying global stability and dynamics of game theory 期刊论文 Li Xu;Jin Wang
14 Design of Tunable Oscillatory Dynamics in a Synthetic NF-kappa B Signaling Circuit 期刊论文 Zhang Zhi-Bo;Wang Qiu-Yue;Ke Yu-Xi;Liu Shi-Yu;Ju Jian-Qi;Lim Wendell A.;Tang Chao;Wei Ping
15 Water-Based Synthesis of Palladium Trigonal Bipyramidal/Tetrahedral Nanocrystals with Enhanced Electrocatalytic Oxidation Activity 期刊论文 Shang Changshuai;Hong Wei;Guo Yaxiao;Wang Jin;Wang Erkang
16 Universal statistical fluctuations in thermodynamics and kinetics of single molecular recognition 期刊论文 Zheng Xiliang;Wang Jin
17 Facile fabrication of PdRuPt nanowire networks with tunable compositions as efficient methanol electrooxidation catalysts 期刊论文 Shang Changshuai;Guo Yaxiao;Wang Erkang
18 SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity 期刊论文 Yan Zhiqiang;Wang Jin
19 Landscape and flux theory of non-equilibrium open economy 期刊论文 Zhang Kun;Wang Jin
20 Adaptation through proportion 期刊论文 Xiong Liyang;Shi Wenjia;Tang Chao
21 Uncovering the Underlying Physical Mechanism for Cancer‐immunity of MHC Class I Diversity 期刊论文 Wenbo Li;Jin Wang
22 Network Motifs Capable of Decoding Transcription Factor Dynamics 期刊论文 Gao Zongmao;Chen Siheng;Qin Shanshan;Tang Chao
23 Synthesis of adenosine analogues with indole moiety as human adenosine A(3) receptor ligands 期刊论文 Xia Yan;Zheng Xiliang;Wang Erkang;Li Dongfeng;Hou Ruibin;Wang Jin
24 Quantifying the potential and flux landscapes of multi-locus evolution 期刊论文 Xu Li;Wang Jin
25 Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks 期刊论文 Yan Zhiqiang;Wang Jin
26 Spiclomazine displays a preferential anti-tumor activity in mutant KRas-driven pancreatic cancer 期刊论文 Xiaoyu Guo;Wenjing Zhao;Zuojia Liu;Jin Wang
27 Odor-evoked inhibition of olfactory sensory neurons drives olfactory perception in Drosophila 期刊论文 Cao Li-Hui;Yang Dong;Wu Wei;Zeng Xiankun;Jing Bi-Yang;Li Meng-Tong;Qin Shanshan;Tang Chao;Tu Yuhai;Luo Dong-Gen
28 Spectroscopic Identification of the Au-C Bond Formation upon Electroreduction of an Aryl Diazonium Salt on Gold 期刊论文 Guo Limin;Ma Lipo;Zhang Yelong;Cheng Xun;Xu Ye;Wang Jin;Wang Erkang;Peng Zhangquan
29 Physical mechanism of mind changes and tradeoffs among speed, accuracy, and energy cost in brain decision making: Landscape, flux, and path perspectives 期刊论文 Yan Han;Zhang Kun;Wang Jin
30 Exploring the inhibitory effect of membrane tension on cell polarization 期刊论文 Wang Weikang;Tao Kuan;Wang Jing;Yang Gen;Ouyang Qi;Wang Yugang;Zhang Lei;Liu Feng
31 Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways 期刊论文 Chu Wen-Ting;Chu Xiakun;Wang Jin
32 A Physical Mechanism and Global Quantification of Breast Cancer 期刊论文 Yu Chong;Wang Jin
33 Positively charged graphene/Fe3O4/polyethylenimine with enhanced drug loading and cellular uptake for magnetic resonance imaging and magnet-responsive cancer therapy 期刊论文 Du Baoji;Liu Jianhua;Ding Guanyu;Han Xu;Li Dan;Wang Erkang;Wang Jin
34 One-Step Synthesis of Platinum Nanochain Networks toward Methanol Electrooxidation 期刊论文 Shang Changshuai;Hong Wei;Guo Yaxiao;Wang Jin;Wang Erkang
35 Electrostatic forces govern the binding mechanism of intrinsically disordered histone chaperones 期刊论文 Liu Chuanbo;Wang Tianshu;Bai Yawen;Wang Jin
36 Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling 期刊论文 Gadkari Varun V.;Harvey Sophie R.;Raper Austin T.;Chu Wen-Ting;Wang Jin;Wysocki Vicki H.;Suo Zucai
37 Molecular mechanism of multispecific recognition of Calmodulin through conformational changes 期刊论文 Liu Fei;Chu Xiakun;Lu H. Peter;Wang Jin
38 Optimization-based shrinking dimer method for finding transition states 期刊论文 Zhang Lei;Du Qiang;Zheng Zhenzhen
39 Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes 期刊论文 Chu Wen-Ting;Wang Jin
40 Adaptation with transcriptional regulation 期刊论文 Shi Wenjia;Ma Wenzhe;Xiong Liyang;Zhang Mingyue;Tang Chao
41 Quantification of motor network dynamics in Parkinson's disease by means of landscape and flux theory 期刊论文 Yan Han;Wang Jin
42 Exploring the Underlying Mechanisms of the Xenopus laevis Embryonic Cell Cycle 期刊论文 Zhang Kun;Wang Jin
43 Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1 期刊论文 Chu Wen-Ting;Clarke Jane;Shammas Sarah L.;Wang Jin
44 Uncovering the mechanisms of Caenorhabditis elegans ageing from global quantification of the underlying landscape 期刊论文 Zhao Lei;Wang Jin
45 An Atlas of Network Topologies Reveals Design Principles for Caenorhabditis elegans Vulval Precursor Cell Fate Patterning 期刊论文 Ping Xianfeng;Tang Chao
46 From molecules to cellular networks: past and future outlook 期刊论文 Fang Xiaona;Wang Jin
47 Nanog induced intermediate state in regulating stem cell differentiation and reprogramming 期刊论文 Yu Peijia;Nie Qing;Tang Chao;Zhang Lei
48 Tuning the Composition of PdCuNi Hollow Nanospheres for Low Cost and Efficient Catalyst Towards Glycol Electrooxidation 期刊论文 Hong Wei;Shang Changshuai;Wang Jin;Wang Erkang
49 Cooperative Strategies for Enhancing Performance of Photothermal Therapy (PTT) Agent: Optimizing Its Photothermal Conversion and Cell Internalization Ability 期刊论文 Du Baoji;Ma Chongbo;Ding Guanyu;Han Xu;Li Dan;Wang Erkang;Wang Jin
50 Effects of flexibility and electrostatic interactions on the coupled binding-folding mechanisms of Chz.core and H2A.z-H2B 期刊论文 Shang Xu;Chu Wenting;Chu Xiakun;Liu Chuanbo;Xu Liufang;Wang Jin
51 L-tyrosine methyl ester-stabilized carbon dots as fluorescent probes for the assays of biothiols 期刊论文 Zhu Haishuang;Wang Erkang;Li Jing;Wang Jin
52 Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch 期刊论文 Fang Xiaona;Liu Qiong;Bohrer Christopher;Hensel Zach;Han Wei;Wang Jin;Xiao Jie
53 Quantifying the Kinetic Residence Time as a Potential Complement to Affinity for the Aptamer Selection 期刊论文 Zhiqiang Yan;Jin Wang
54 Potential landscape and flux field theory for turbulence and nonequilibrium fluid systems 期刊论文 Wu Wei;Zhang Feng;Wang Jin
55 Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition 期刊论文 Chu Wen-Ting;Wang Jin
56 Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer 期刊论文 Zhao Lingci;Lu H. Peter;Wang Jin
57 Quantifying risks with exact analytical solutions of derivative pricing distribution 期刊论文 Zhang Kun;Liu Jing;Wang Erkang;Wang Jin
58 Theoretical designing and experimental fabricating unique quadruple multimetallic phosphides with remarkable hydrogen evolution performance 期刊论文 Gu Wenling;Gan Linfeng;Zhang Xiaoyan;Wang Erkang;Wang Jin
59 Bi-functional biochemical networks 期刊论文 Mingyue Zhang;Chao Tang
60 Landscape reveals critical network structures for sharpening gene expression boundaries 期刊论文 Li Chunhe;Zhang Lei;Nie Qing
61 Uncovering the molecular and physiological processes of anticancer leads binding human serum albumin: A physical insight into drug efficacy 期刊论文 Liu Chuanbo;Liu Zuojia;Wang Jin
62 Lighting Up the Thioflavin T by Parallel-Stranded TG(GA)n DNA Homoduplexes 期刊论文 Zhu Jinbo;Yan Zhiqiang;Zhou Weijun;Liu Chuanbo;Wang Jin;Wang Erkang
63 Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect 期刊论文 Yan Zhiqiang;Wang Jin
64 Exploration of nucleoprotein alpha-MoRE and XD interactions of Nipah and Hendra viruses 期刊论文 Shang Xu;Chu Wenting;Chu Xiakun;Xu Liufang;Longhi Sonia;Wang Jin
65 Apical constriction is driven by a pulsatile apical myosin network in delaminating Drosophila neuroblasts 期刊论文 An Yanru;Xue Guosheng;Yang Shaobo;Deng Mingxi;Zhou Xiaowei;Yu Weichuan;Ishibashi Toyotaka;Zhang Lei;Yan Yan
66 Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux. 期刊论文 Li Xu;Xiakun Chu;Zhiqiang Yan;Xiliang Zheng;Kun Zhang;Feng Zhang;Han Yan;Wei Wu;Jin Wang
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