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RegScaf: a regression approach to scaffolding 期刊论文
BIOINFORMATICS, 2022, 页码: 8
Authors:  Li, Mengtian;  Li, Lei M.
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Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise 期刊论文
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2021, 卷号: 43, 期号: 4, 页码: 1184-1196
Authors:  Zhang, Chihao;  Zhang, Shihua
Favorite  |  View/Download:159/0  |  Submit date:2021/04/26
Matrix decomposition  Bayes methods  Data integration  Inference algorithms  Data models  Data mining  Gaussian distribution  Bayesian methods  matrix decomposition  data integration  variational Bayesian inference  maximum a posterior  
Group-Sparse SVD Models via L-1- and L-0-norm Penalties and their Applications in Biological Data 期刊论文
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 2021, 卷号: 33, 期号: 2, 页码: 536-550
Authors:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
Favorite  |  View/Download:141/0  |  Submit date:2021/04/26
Sparse SVD  low-rank matrix decomposition  group-sparse penalty  overlapping group-sparse penalty  coordinate descent method  alternating direction method of multipliers (ADMM)  data mining  
An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2021, 卷号: 18, 期号: 1, 页码: 355-364
Authors:  Jing, Fang;  Zhang, Shao-Wu;  Cao, Zhen;  Zhang, Shihua
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Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network 期刊论文
BMC BIOINFORMATICS, 2020, 卷号: 21, 期号: 1, 页码: 16
Authors:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
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Enhancer–  promoter interactions  Cell line  Convolutional neural network  Transfer learning  Gradient reversal layer  
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:151/0  |  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  
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
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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  
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:245/0  |  Submit date:2020/01/10
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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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:150/0  |  Submit date:2020/01/10