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Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2018, 卷号: 15, 期号: 3, 页码: 944-953
Authors:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
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Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection  
The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2018, 卷号: 15, 期号: 3, 页码: 988-998
Authors:  Zhang, Junhua;  Zhang, Shihua
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Bioinformatics  cancer genomics  driver gene  driver pathway  mutual exclusivity  co-occurring mutation  
An Application of Invertibility of Boolean Control Networks to the Control of the Mammalian Cell Cycle 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2017, 卷号: 14, 期号: 1, 页码: 225-229
Authors:  Zhang, Kuize;  Zhang, Lijun;  Mou, Shaoshuai
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Boolean control network  invertibility  mammalian cell cycle  
A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2016, 卷号: 13, 期号: 2, 页码: 281-290
Authors:  Ni, Xumin;  Guo, Wei;  Yuan, Kai;  Yang, Xiong;  Ma, Zhiming;  Xu, Shuhua;  Zhang, Shihua
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Population genetics  identity by descent  probabilistic method  Markov process  
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2015, 卷号: 12, 期号: 5, 页码: 1112-1122
Authors:  Qiu, Yu-Qing;  Tian, Xue;  Zhang, Shihua
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Metagenomics  abundance estimation  taxonomy tree  expectation-maximization algorithm  
Guest Editorial for Special Section on ISB/TBC 2014 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2015, 卷号: 12, 期号: 5, 页码: 1074-1075
Authors:  Zhang, Shihua;  Chen, Luonan
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Colored Noise Induced Bistable Switch in the Genetic Toggle Switch Systems 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2015, 卷号: 12, 期号: 3, 页码: 579-589
Authors:  Wang, Pei;  Lu, Jinhu;  Yu, Xinghuo
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Colored noise  bistable switch  bifurcation  synchronization  quorum sensing  
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2011, 卷号: 8, 期号: 6, 页码: 1458-1467
Authors:  Zhao, Wenqi;  Xu, Guoliang;  Bajaj, Chandrajit
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Polynomial splines  molecular surfaces  prismatic scaffolds  Bernstein-Bezier basis  solvation energetics  error bounds  rate of convergence  
Evaluating Protein Similarity from Coarse Structures 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2009, 卷号: 6, 期号: 4, 页码: 583-593
Authors:  Wang, Yong;  Wu, Ling-Yun;  Zhang, Ji-Hong;  Zhan, Zhong-Wei;  Zhang, Xiang-Sun;  Chen, Luonan
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Protein structure  structure comparison  protein surface