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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：173/0  |  提交时间：2021/04/26
Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
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：164/0  |  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  
ELF: Extract Landmark Features By Optimizing Topology Maintenance, Redundancy, and Specificity 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 411-421
作者:  Feng, Zhan-Ying;  Wang, Yong
收藏  |  浏览/下载：186/0  |  提交时间：2020/05/24
Feature extraction  Topology  Ground penetrating radar  Geophysical measurement techniques  Redundancy  Maintenance engineering  Manganese  Feature selection  topology maintenance  optimization  single cell  
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：190/0  |  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  
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