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Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 657-667
Authors:  Cao, Zhen;  Zhang, Shihua
Favorite  |  View/Download:6/0  |  Submit date:2020/05/24
DNA  Bioinformatics  Kernel  Feature extraction  Support vector machines  Genomics  Task analysis  Bioinformatics  machine learning  gapped k-mer  deep neural network  transcription factor binding site prediction  
Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 376-389
Authors:  Zhang, Lihua;  Zhang, Shihua
Favorite  |  View/Download:6/0  |  Submit date:2020/05/24
Gene expression  Sequential analysis  Bioinformatics  RNA  Matrix converters  Computational biology  Bayes methods  Single-cell RNA-sequencing technique  dropout event  imputation  algorithm  bioinformatics  
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
Favorite  |  View/Download:23/0  |  Submit date:2020/01/10
cell cycle  chromosomal architectures  circular trajectory  dynamic structures  single-cell Hi-C maps  
A cluster-adjusted rank-based test for a clinical trial concerning multiple endpoints with application to dietary intervention assessment 期刊论文
BIOMETRICS, 2019, 卷号: 75, 期号: 3, 页码: 821-830
Authors:  Zhang, Wei;  Liu, Aiyi;  Tang, Larry L.;  Li, Qizhai
Favorite  |  View/Download:14/0  |  Submit date:2020/01/10
generalized Behrens-Fisher hypothesis  multivariate distributions  nonparametrics  rank statistics  type I errors  power of test  
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
Favorite  |  View/Download:17/0  |  Submit date:2020/01/10
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
Favorite  |  View/Download:15/0  |  Submit date:2020/01/10
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
Favorite  |  View/Download:15/0  |  Submit date:2020/01/10
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.
Favorite  |  View/Download:9/0  |  Submit date:2019/10/28
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
Favorite  |  View/Download:24/0  |  Submit date:2019/03/11
Improved matrix pooling 期刊论文
STATISTICAL METHODS IN MEDICAL RESEARCH, 2019, 卷号: 28, 期号: 1, 页码: 211-222
Authors:  Xiong, Wenjun;  Ding, Juan;  He, Yuanzhen;  Li, Qizhai
Favorite  |  View/Download:16/0  |  Submit date:2019/03/05
Matrix pooling  efficiency  group testing  sensitivity  specificity