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Disease category-specific annotation of variants using an ensemble learning framework 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2022, 卷号: 23, 期号: 1, 页码: 15
Authors:  Cao, Zhen;  Huang, Yanting;  Duan, Ran;  Jin, Peng;  Qin, Zhaohui S.;  Zhang, Shihua
Favorite  |  View/Download:38/0  |  Submit date:2022/06/21
complex disease  disease category  functional annotation  non-coding variant  ensemble learning  
Modes of genetic adaptations underlying functional innovations in the rumen 期刊论文
SCIENCE CHINA-LIFE SCIENCES, 2020, 页码: 21
Authors:  Pan, Xiangyu;  Cai, Yudong;  Li, Zongjun;  Chen, Xianqing;  Heller, Rasmus;  Wang, Nini;  Wang, Yu;  Zhao, Chen;  Wang, Yong;  Xu, Han;  Li, Songhai;  Li, Ming;  Li, Cunyuan;  Hu, Shengwei;  Li, Hui;  Wang, Kun;  Chen, Lei;  Wei, Bin;  Zheng, Zhuqing;  Fu, Weiwei;  Yang, Yue;  Zhang, Tingting;  Hou, Zhuoting;  Yan, Yueyang;  Lv, Xiaoyang;  Sun, Wei;  Li, Xinyu;  Huang, Shisheng;  Liu, Lixiang;  Mao, Shengyong;  Liu, Wenqing;  Hua, Jinlian;  Li, Zhipeng;  Zhang, Guojie;  Chen, Yulin;  Wang, Xihong;  Qiu, Qiang;  Dalrymple, Brian P.;  Wang, Wen;  Jiang, Yu
Favorite  |  View/Download:110/0  |  Submit date:2021/01/14
rumen innovations  comparative transcriptomics  comparative genomics  evo-devo  evolution of organs  
Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model 期刊论文
BMC GENOMICS, 2018, 卷号: 19, 页码: 13
Authors:  Wang, Can;  Zhang, Shihua
Favorite  |  View/Download:156/0  |  Submit date:2019/01/11
Epigenomics  Cell type-specific regulatory elements  Hidden Markov model  Histone modification  
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 卷号: 115, 期号: 30, 页码: 7723-7728
Authors:  Duren, Zhana;  Chen, Xi;  Zamanighomi, Mahdi;  Zeng, Wanwen;  Satpathy, Ansuman T.;  Chang, Howard Y.;  Wang, Yong;  Wong, Wing Hung
Favorite  |  View/Download:116/0  |  Submit date:2019/12/13
coupled clustering  NMF  single-cell genomic data  
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
Authors:  Yang, Xiaofei;  Shao, Xiaojian;  Gao, Lin;  Zhang, Shihua
Favorite  |  View/Download:100/0  |  Submit date:2018/07/30
DNA methylation patterns  differentially methylation regions  comparative studies  tissue-specific methylation  cancer epigenomics  
IIIDB: a database for isoform-isoform interactions and isoform network modules 期刊论文
BMC Genomics, 2015, 卷号: 16, 期号: Suppl 2
Authors:  Tseng,Yu-Ting;  Li,Wenyuan;  Chen,Ching-Hsien;  Zhang,Shihua;  Chen,Jeremy JW;  Zhou,Xianghong Jasmine;  Liu,Chun-Chi
Favorite  |  View/Download:80/0  |  Submit date:2018/07/30
Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data 期刊论文
BMC Systems Biology, 2013, 卷号: 7, 期号: Suppl 2
Authors:  Zhang,Junhua;  Zhang,Shihua;  Wang,Yong;  Zhang,Xiang-Sun
Favorite  |  View/Download:96/0  |  Submit date:2018/07/30
Bridging protein local structures and protein functions 期刊论文
AMINO ACIDS, 2008, 卷号: 35, 期号: 3, 页码: 627-650
Authors:  Liu, Zhi-Ping;  Wu, Ling-Yun;  Wang, Yong;  Zhang, Xiang-Sun;  Chen, Luonan
Favorite  |  View/Download:97/0  |  Submit date:2018/07/30
functional genomics  functional motifs  local structures  protein function prediction  
Analysis of protein surface patterns by pocket similarity network 期刊论文
PROTEIN AND PEPTIDE LETTERS, 2008, 卷号: 15, 期号: 5, 页码: 448-455
Authors:  Liu, Zhi-Ping;  Wu, Ling-Yun;  Wang, Yong;  Zhang, Xiang-Sun;  Chen, Luonan
Favorite  |  View/Download:118/0  |  Submit date:2018/07/30
protein surface pattern  pocket similarity  complex network  functional genomics  systems biology  
Inferring protein interactions from experimental data by association probabilistic method 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 卷号: 62, 期号: 4, 页码: 833-837
Authors:  Chen, LN;  Wu, LY;  Wang, Y;  Zhang, XS
Favorite  |  View/Download:101/0  |  Submit date:2018/07/30
protein interaction  domain interaction  protein network  bioinformatics