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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
作者:  Jing, Fang;  Zhang, Shao-Wu;  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载：169/0  |  提交时间：2021/04/26
Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration 期刊论文
IEEE TRANSACTIONS ON FUZZY SYSTEMS, 2020, 卷号: 28, 期号: 9, 页码: 1971-1983
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：147/0  |  提交时间：2021/01/14
Sparse matrices  Pattern recognition  Data integration  Prediction algorithms  Data models  Matrix decomposition  Signal processing algorithms  Bioinformatics  data integration  network-regularized constraint  nonnegative matrix factorization (NMF)  pattern recognition  
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
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：163/0  |  提交时间：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
作者:  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载：188/0  |  提交时间：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  
Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns 期刊论文
FRONTIERS IN GENETICS, 2018, 卷号: 9, 页码: 12
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：176/0  |  提交时间：2018/07/30
bioinformatics  multi-dimensional genomics  matrix integrative analysis  data integration  module discovery  non-negative matrix factorization (NMF)  partial least squares (PLS)  
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
作者:  Zhang, Junhua;  Zhang, Shihua
收藏  |  浏览/下载：208/0  |  提交时间：2018/07/30
Bioinformatics  cancer genomics  driver gene  driver pathway  mutual exclusivity  co-occurring mutation  
Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2017, 卷号: 18, 期号: 5, 页码: 761-773
作者:  Yang, Xiaofei;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：139/0  |  提交时间：2018/07/30
cancer genomics  DNA-methylation  pan-cancer study  bioinformatics  
Integrative cancer genomics: models, algorithms and analysis 期刊论文
FRONTIERS OF COMPUTER SCIENCE, 2017, 卷号: 11, 期号: 3, 页码: 392-406
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：134/0  |  提交时间：2018/07/30
cancer genomics  model  algorithm  data integration  bioinformatics  computational biology  
Extended particle swarm optimisation method for folding protein on triangular lattice 期刊论文
IET SYSTEMS BIOLOGY, 2016, 卷号: 10, 期号: 1, 页码: 30-33
作者:  Guo, Yuzhen;  Wu, Zikai;  Wang, Ying;  Wang, Yong
收藏  |  浏览/下载：135/0  |  提交时间：2018/07/30
proteins  molecular biophysics  molecular configurations  particle swarm optimisation  bioinformatics  extended particle swarm optimisation method  triangular lattice  protein structure prediction problem  two-dimensional hydrophobic-polar model  noncompact conformation  amino acid sequence  single point adjustment strategy  protein folding  
A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors 期刊论文
METHODS, 2015, 卷号: 83, 页码: 3-17
作者:  Zou, Meng;  Zhang, Peng-Jun;  Wen, Xin-Yu;  Chen, Luonan;  Tian, Ya-Ping;  Wang, Yong
收藏  |  浏览/下载：140/0  |  提交时间：2018/07/30
Translational bioinformatics  Multi-biomarker  Colorectal cancer  Mixed integer programming