Data Analysis, Bio-Statistics, Bio-Mathematics

[1] Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics

Shenggao Zhou Soochow University R. G. Weiss ETH Zurich Li-Tien Cheng University of California, San Diego Joachim Dzubiella University of Freiburg J. Andrew McCammon University of California, San Diego Bo Li University of California, San Diego

Numerical Analysis and Scientific Computing Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2005.25001

Proceedings of the National Academy of Sciences of the United States of America, 116, (30), 14989–14994, 2019.7
[ Download ] [ 2020-05-22 17:28:54 uploaded by sgzhou ] [ 15 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[2] Markovian approaches to modeling intracellular reaction processes with molecular memory

Jiajun Zhang Sun Yat-sen University Tianshou Zhou Sun Yat-sen University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2004.42003

PNAS, 116, 23542-23550, 2019.11
[ Download ] [ 2020-04-26 14:59:30 uploaded by zhjiajun ] [ 20 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[3] An enriched network motif family regulates multistep cell fate transitions with restricted reversibility

Yujie Ye Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America Xin Kang Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China Jordan Bailey Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America Chunhe Li Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China Tian Hong Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America

Dynamical Systems Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2004.11001

PLOS Computational Biology, 15, (3), e1006855, 2019.3
[ Download ] [ 2020-04-25 02:24:20 uploaded by chan65 ] [ 31 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[4] Fast and accurate genome comparison using genome images: The Extended Natural Vector Method

Shaojun Pei Tsinghua University Wenhui Dong Tsinghua University Xiuqiong Chen Tsinghua Univerisity Rong Lucy He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2004.42002

Molecular Phylogenetics and Evolution, 141, 106633
[ Download ] [ 2020-04-23 21:45:09 uploaded by psj17 ] [ 28 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[5] A novel alignment-free method for HIV-1 subtype classification

Lily He Tsinghua University Rui Dong Tsinghua University Rong Lucy He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2004.42001

Infection, Genetics and Evolution, 77, 104080, 2020.1
[ Download ] [ 2020-04-23 10:51:36 uploaded by RuiDong ] [ 20 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[6] G-sup: a clustering algorithm for cryo-electron microscopy images of asymmetric particles

Ting-Li Chen Institute of Statistical Science, Academia Sinica Dai-Ni Hsieh Institute of Statistical Science, Academia Sinica Hung Hung Institute of Epidemiology and Preventive Medicine I-Ping Tu Institute of Statistical Science, Academia Sinica Pei-Shien Wu Dept. of Biostatistics, Duke University Yi-Ming Wu Institute of Chemistry, Academia Sinica Wei-Hau Chang Institute of Chemistry, Academia Sinica Su-Yun Huang Institute of Statistical Science, Academia Sinica

Statistics Theory and Methods Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:2004.33002

The Annals of Applied Statistics , 8, (1), 259-285, 2014
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[7] A novel approach to clustering genome sequences using inter-nucleotide covariance

Rui Dong Tsinghua University Lily He Tsinghua University Rong Lucy He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1909.42002

Frontiers in Genetics, 10, (234), 234, 2019.4
[ Download ] [ 2019-09-15 13:55:12 uploaded by Stephenyau ] [ 116 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[8] Large-Scale Genome Comparison Based on Cumulative Fourier Power and Phase Spectra: Central Moment and Covariance Vector

Shaojun Pei Department of Mathematical Sciences, Tsinghua University, Beijing, PR China Rui Dong Department of Mathematical Sciences, Tsinghua University, Beijing, PR China Rong Lucy He Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA Stephen S.-T. Yau Department of Mathematical Sciences, Tsinghua University, Beijing, PR China

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1909.42001

Computational and Structural Biotechnology Journal, 17, 982-994, 2019.7
[ Download ] [ 2019-09-04 17:31:31 uploaded by Stephenyau ] [ 111 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[9] Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus

Changchuan Yin University of Illinois at Chicago Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1908.42001

2019.1
[ Download ] [ 2019-08-21 02:42:56 uploaded by cyinbox ] [ 123 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[10] An age-structured continuum model for myxobacteria

Pierre Degond Imperial College London Angelika Manhart New York University Hui Yu Tsinghua University

Fluid Dynamics and Shock Waves Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1906.14001

Mathematical Models and Methods in Applied Sciences, 28, (9), 1737–1770, 2018
[ Download ] [ 2019-06-26 11:22:58 uploaded by HuiYu ] [ 59 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[11] TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Zixuan Cang Michigan State University Guo-Wei Wei Michigan State University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42007

PLOS Computational Biology, 13, (7), e1005690, 2017.7
[ Download ] [ 2019-04-30 00:41:13 uploaded by cangzx ] [ 138 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[12] Randomly distributed embedding making short-term high-dimensional data predictable

Huanfei Man Soochow University Siyang Leng Fudan University Kazuyuki Aihara Tokyo University Wei Lin Fudan University Luonan Chen Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42006

Proceedings of the National Academy of Sciences of the United States of America, 115, (43), E9994-E10002, 2018.10
[ Download ] [ 2019-04-28 19:34:56 uploaded by wlinfudan ] [ 249 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[13] Convex hull analysis of evolutionary and phylogenetic relationships between biological groups

Kun Tian Tsinghua University Xin Zhao Tsinghua University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42005

[ Download ] [ 2019-04-27 22:39:44 uploaded by zhaox15 ] [ 165 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[14] Establishing the phylogeny of Prochlorococcus with a new alignment-free method

Xin Zhao Tsinghua University Kun Tian Tsinghua University Rong L. He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42004

[ Download ] [ 2019-04-27 21:48:02 uploaded by zhaox15 ] [ 110 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[15] Comparing protein structures and inferring functions with a novel three dimensional Yau Hausdorff method

Kun Tian Tsinghua University Xin Zhao Tsinghua University Yuning Zhang Tsinghua University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42003

[ Download ] [ 2019-04-27 21:26:35 uploaded by zhaox15 ] [ 106 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[16] A new efficient method for analyzing fungi species using correlations between nucleotides

Xin Zhao Tsinghua Universityf Kun Tian Tsinghua University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42002

[ Download ] [ 2019-04-27 21:10:40 uploaded by zhaox15 ] [ 136 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[17] Convex hull principle for classification and phylogeny of eukaryotic proteins

Xin Zhao Tsinghua University Kun Tian Tsinghua University Rong L. He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1904.42001

[ Download ] [ 2019-04-27 21:07:09 uploaded by zhaox15 ] [ 97 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[18] A new method to cluster genomes based on cumulative Fourier power spectrum

Rui Dong Tsinghua University Ziyue Zhu Tsinghua University Changchuan Yin University of Illinois at Chicago Rong L. He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42005

Gene, 673, 2018.6
[ Download ] [ 2019-03-18 10:32:15 uploaded by RuiDong ] [ 146 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[19] Virus Database and Online Inquiry System Based on Natural Vectors

Rui Dong Tsinghua University Hui Zheng The University of Illinois at Chicago Kun Tian Tsinghua University Shek-Chung Yau The Hong Kong University of Science and Technology Weiguang Mao Tsinghua University Wenping Yu Nankai University Changchuan Yin The University of Illinois at Chicago Chenglong Yu South Australian Health and Medical Research Institute Rong Lucy He Chicago State University Jie Yang The University of Illinois at Chicago Stephen S.-T Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42004

Evolutionary Bioinformatics, 13, 1-7, 2017.10
[ Download ] [ 2019-03-18 10:27:40 uploaded by RuiDong ] [ 230 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[20] Zika and Flaviviruses Phylogeny Based on the Alignment-Free Natural Vector Method

Yongkun Li Department of Mathematical Sciences, Tsinghua University Lily He Department of Mathematical Sciences, Tsinghua University Rong Lucy He Department of Biological Sciences, Chicago State University Stephen S.-T. Yau(Corresponding Department of Mathematical Sciences, Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42003

Dna & Cell Biology, 36, (2), 1-8, 2017
[ Download ] [ 2019-03-15 15:03:30 uploaded by hell16 ] [ 145 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[21] A novel fast vector method for genetic sequence comparison

Yongkun Li 1Department of Mathematical Sciences, Tsinghua University Lily He 1Department of Mathematical Sciences, Tsinghua University Rong Lucy He 2Department of Biological Sciences, Chicago State University Stephen S.-T. Yau(Corresponding author) 1Department of Mathematical Sciences, Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42002

Scientific Reports, 1, (12226), 2017.9
[ Download ] [ 2019-03-15 14:57:39 uploaded by hell16 ] [ 149 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[22] A novel alignment-free vector method to cluster protein sequences

Lily He Department of Mathematical Sciences, Tsinghua University Yongkun Li Department of Mathematical Sciences, Tsinghua University Rong Lucy He Department of Biological Sciences, Chicago State University Stephen S.-T. Yau(Corresponding author) Department of Mathematical Sciences, Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1903.42001

Journal of Theoretical Biology, 427, 41-52, 2017.6
[ Download ] [ 2019-03-15 14:50:00 uploaded by hell16 ] [ 183 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[23] Nearly Optimal Stochastic Approximation for Online Principal Subspace Estimation

Xin Liang National Chiao Tung University Zhen-Chen Guo National Chiao Tung University Ren-Cang Li University of Texas at Arlington Wen-Wei Lin National Chiao Tung University

Optimization and Control Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1711.27001

2018.8
[ Download ] [ 2017-11-18 01:14:40 uploaded by jinsanliang ] [ 175 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[24] Graph connection laplacian methods can be made robust to noise

Noureddine El Karoui UC Berkeley Hau-tieng Wu University of Toronto

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1704.42002

2016
[ Download ] [ 2017-04-29 11:10:13 uploaded by hauwu ] [ 415 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[25] Wave-Shape Function Analysis: When Cepstrum Meets Time–Frequency Analysis

Chen-Yun Lin University of Toronto Li Su Academia Sinica Hau-Tieng Wu University of Toronto

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1704.42001

Journal of Fourier Analysis and Applications , 2017.2
[ Download ] [ 2017-04-24 23:39:53 uploaded by cylin ] [ 666 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[26] A novel strategy for clustering major depression individuals using whole-genome sequencing variant data

Chenglong Yu South Australian Health and Medical Research Institute Bernhard T. Baune University of Adelaide Julio Licinio South Australian Health and Medical Research Institute Ma-Li Wong South Australian Health and Medical Research Institute

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42005

Scientific Reports, 7, (44389), 2017
[ Download ] [ 2017-03-14 08:37:18 uploaded by yclong8848 ] [ 373 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[27] Mathematical modeling of vertebrate limb development

Yong-Tao Zhang University of Notre Dame Mark S. Alber University of Notre Dame Stuart A. Newman New York Medical College

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42004

Mathematical Biosciences, 243, 1-17, 2013
[ Download ] [ 2017-03-13 22:08:27 uploaded by ytzhangND ] [ 467 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[28] DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Chenglong Yu South Australian Health and Medical Research Institute Mo Deng Lu Zheng Rong Lucy He Jie Yang Stephen S.-T. Yau

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42003

PLoS ONE, 2014
[ Download ] [ 2017-03-13 20:56:51 uploaded by yclong8848 ] [ 299 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[29] Real Time Classification of Viruses in 12 Dimensions

Chenglong Yu South Australian Health and Medical Research Institute Troy Hernandez Hui Zheng Shek-Chung Yau Hsin-Hsiung Huang Rong Lucy He Jie Yang Stephen S.-T. Yau

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42002

PLoS ONE, 2013
[ Download ] [ 2017-03-13 20:54:32 uploaded by yclong8848 ] [ 201 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[30] Protein space: A natural method for realizing the nature of protein universe

Chenglong Yu South Australian Health and Medical Research Institute Mo Deng Shiu-Yuen Cheng Shek-Chung Yau Rong L. He Stephen S.-T. Yau

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1703.42001

Journal of Theoretical Biology, 318, 197-204, 2013
[ Download ] [ 2017-03-13 20:50:42 uploaded by yclong8848 ] [ 264 downloads ] [ 0 comments ] [ Abstract ] [ Full ]
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[31] A new method for studying the evolutionary origin of the SAR11 clade marine bacteria

Xin Zhao Tsinghua University Xiaogeng Wan Tsinghua University Rong L.He Chicago State University Stephen S.-T. Yau Tsinghua University

Data Analysis, Bio-Statistics, Bio-Mathematics mathscidoc:1611.13004

Molecular Phylogenetics and Evolution, 98, 271-279, 2016.5
[ Download ] [ 2016-11-25 19:58:36 uploaded by zhaox15 ] [ 312 downloads ] [ 0 comments ] [ Cited by 1 ] [ Abstract ] [ Full ]
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