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Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps 期刊论文
ADVANCED SCIENCE, 2019, 页码: 13
Authors:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
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cell cycle  chromosomal architectures  circular trajectory  dynamic structures  single-cell Hi-C maps  
Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 13, 页码: 6606-6617
Authors:  Zhang, Lihua;  Zhang, Shihua
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AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility 期刊论文
ANALYTICAL CHEMISTRY, 2019, 卷号: 91, 期号: 13, 页码: 8705-8711
Authors:  Gao, Zhiqiang;  Chang, Cheng;  Yang, Jinghan;  Zhu, Yunping;  Fu, Yan
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MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 11, 页码: 11
Authors:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
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Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction 期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 11, 页码: 1837-1843
Authors:  Cao, Zhen;  Zhang, Shihua
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The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 页码: 11
Authors:  Feng, Yance;  Zhang, Sheng;  Li, Liang;  Li, Lei M.
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BASE  Statistical inference  Transcriptional regulation  PUFA  DHA  EPA  Binding strength  
PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome 期刊论文
MOLECULAR & CELLULAR PROTEOMICS, 2019, 卷号: 18, 期号: 2, 页码: 391-405
Authors:  An, Zhiwu;  Zhai, Linhui;  Ying, Wantao;  Qian, Xiaohong;  Gong, Fuzhou;  Tan, Minjia;  Fu, Yan
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LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors 期刊论文
ANALYTICAL CHEMISTRY, 2019, 卷号: 91, 期号: 2, 页码: 1335-1343
Authors:  Chang, Cheng;  Gao, Zhiqiang;  Ying, Wantao;  Fu, Yan;  Zhao, Yan;  Wu, Songfeng;  Li, Mengjie;  Wang, Guibin;  Qian, Xiaohong;  Zhu, Yunping;  He, Fuchu
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Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model 期刊论文
BMC GENOMICS, 2018, 卷号: 19, 页码: 13
Authors:  Wang, Can;  Zhang, Shihua
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Epigenomics  Cell type-specific regulatory elements  Hidden Markov model  Histone modification  
Edge-group sparse PCA for network-guided high dimensional data analysis 期刊论文
BIOINFORMATICS, 2018, 卷号: 34, 期号: 20, 页码: 3479-3487
Authors:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
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