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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  
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  
Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs 期刊论文
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2018, 卷号: 127, 页码: 723-731
Authors:  Liu, Zuyao;  Chen, Guoling;  Zhu, Tianqi;  Zeng, Zhaochi;  Lyu, Zhitong;  Wang, Jian;  Messenger, Kevin;  Greenberg, Anthony;  Guo, Zixiao;  Yang, Ziheng;  Shi, Suhua;  Wang, Yingyong
Favorite  |  View/Download:17/0  |  Submit date:2019/01/11
Cryptic species  Delimitation  Diversity  Megophrys  Phylogeography  
Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing 期刊论文
SCIENTIFIC REPORTS, 2018, 卷号: 8, 页码: 11
Authors:  Tu, Bin;  Bai, Shiyang;  Lu, Benzhuo;  Fang, Qiaojun
Favorite  |  View/Download:12/0  |  Submit date:2018/07/30
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
Authors:  Chen, Jinyu;  Zhang, Shihua
Favorite  |  View/Download:20/0  |  Submit date:2018/07/30
bioinformatics  multi-dimensional genomics  matrix integrative analysis  data integration  module discovery  non-negative matrix factorization (NMF)  partial least squares (PLS)  
A remark on copy number variation detection methods 期刊论文
PLOS ONE, 2018, 卷号: 13, 期号: 4, 页码: 11
Authors:  Li, Shuo;  Dou, Xialiang;  Gao, Ruiqi;  Ge, Xinzhou;  Qian, Minping;  Wan, Lin
Favorite  |  View/Download:16/0  |  Submit date:2018/07/30
Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing 期刊论文
SCIENTIFIC REPORTS, 2018, 卷号: 8
Authors:  Tu, Bin;  Bai, Shiyang;  Lu, Benzhuo;  Fang, Qiaojun
Favorite  |  View/Download:12/0  |  Submit date:2019/12/31
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
Authors:  Yang, Xiaofei;  Gao, Lin;  Zhang, Shihua
Favorite  |  View/Download:16/0  |  Submit date:2018/07/30
cancer genomics  DNA-methylation  pan-cancer study  bioinformatics  
Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling 期刊论文
BMC BIOINFORMATICS, 2017, 卷号: 18, 页码: 14
Authors:  Zhang, Sheng;  Wang, Bo;  Wan, Lin;  Li, Lei M.
Favorite  |  View/Download:15/0  |  Submit date:2018/07/30
Base-calling  Logistic regression  Quality score  L-1 regularization  AIC  BIC  Empirical discrimination power