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BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2022, 页码: 12
作者:  Chen, Ziwei;  Gong, Fuzhou;  Wan, Lin;  Ma, Liang
收藏  |  浏览/下载：158/0  |  提交时间：2022/06/21
single-cell DNA sequencing  intra-tumor heterogeneity  single nucleotide variation  copy number alteration  Bayesian modeling  cancer evolution  
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：160/0  |  提交时间：2021/04/26
Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
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：180/0  |  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  
Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data 期刊论文
QUANTITATIVE BIOLOGY, 2020, 卷号: 8, 期号: 2, 页码: 143-154
作者:  Wan, Lin;  Kang, Xin;  Ren, Jie;  Sun, Fengzhu
收藏  |  浏览/下载：182/0  |  提交时间：2021/01/14
DNA  FREQUENCIES  PREDICTION  Markov chains  next generation sequencing  transition probabilities  confidence intervals  
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：136/0  |  提交时间：2018/07/30
cancer genomics  DNA-methylation  pan-cancer study  bioinformatics  
Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types 期刊论文
BRIEFINGS IN FUNCTIONAL GENOMICS, 2016, 卷号: 15, 期号: 6, 页码: 399-407
作者:  Yang, Xiaofei;  Shao, Xiaojian;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：158/0  |  提交时间：2018/07/30
DNA methylation patterns  differentially methylation regions  comparative studies  tissue-specific methylation  cancer epigenomics  
Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data 期刊论文
NATIONAL SCIENCE REVIEW, 2016, 卷号: 3, 期号: 2, 页码: 240-251
作者:  Wang, Yong;  Jiang, Rui;  Wong, Wing Hung
收藏  |  浏览/下载：120/0  |  提交时间：2018/07/30
gene regulatory network  open chromatin  DNA accessibility  transcription factor colocalization  statistical model  data integration  
Optimal two-stage design for case-control association analysis incorporating genotyping errors 期刊论文
ANNALS OF HUMAN GENETICS, 2008, 卷号: 72, 页码: 375-387
作者:  Zuo, Y.;  Zou, G.;  Wang, J.;  Zhao, H.;  Liang, H.
收藏  |  浏览/下载：97/0  |  提交时间：2018/07/30
DNA pooling  genotyping errors  individual genotyping  measurement errors  power  two-stage design  
An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors 期刊论文
EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, 2007, 卷号: 182, 期号: 1, 页码: 413-427
作者:  Zhang, Ji-Hong;  Wu, Ling-Yun;  Zhao, Yu-Ying;  Zhang, Xiang-Sun
收藏  |  浏览/下载：107/0  |  提交时间：2018/07/30
positional sequencing by hybridization  reconstruction of DNA fragment  positive errors and negative errors  dynamic programming  branch and bound algorithm  
Family-based association tests for different family structures using pooled DNA 期刊论文
ANNALS OF HUMAN GENETICS, 2005, 卷号: 69, 页码: 429-442
作者:  Zou, GH;  Zhao, HY
收藏  |  浏览/下载：98/0  |  提交时间：2018/07/30
family-based association study  family structure  DNA pooling  measurement error  sample size