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MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2021, 卷号: 22, 期号: 6, 页码: 14
Authors:  Zou, Meng;  Duren, Zhana;  Yuan, Qiuyue;  Li, Henry;  Hutchins, Andrew Paul;  Wong, Wing Hung;  Wang, Yong
Favorite  |  View/Download：74/0  |  Submit date：2022/04/02
cell type-specific marker  TFs  surface markers  dimension reduction  hierarchical topology  
hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context 期刊论文
COMMUNICATIONS BIOLOGY, 2021, 卷号: 4, 期号: 1, 页码: 16
Authors:  Feng, Zhanying;  Duren, Zhana;  Xiong, Ziyi;  Wang, Sijia;  Liu, Fan;  Wong, Wing Hung;  Wang, Yong
Favorite  |  View/Download：106/0  |  Submit date：2021/06/01
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation 期刊论文
NATURE COMMUNICATIONS, 2020, 卷号: 11, 期号: 1, 页码: 20
Authors:  Xin, Jingxue;  Zhang, Hui;  He, Yaoxi;  Duren, Zhana;  Bai, Caijuan;  Chen, Lang;  Luo, Xin;  Yan, Dong-Sheng;  Zhang, Chaoyu;  Zhu, Xiang;  Yuan, Qiuyue;  Feng, Zhanying;  Cui, Chaoying;  Qi, Xuebin;  Ouzhuluobu;  Wong, Wing Hung;  Wang, Yong;  Su, Bing
Favorite  |  View/Download：98/0  |  Submit date：2021/01/14
Time course regulatory analysis based on paired expression and chromatin accessibility data 期刊论文
GENOME RESEARCH, 2020, 卷号: 30, 期号: 4, 页码: 622-634
Authors:  Duren, Zhana;  Chen, Xi;  Xin, Jingxue;  Wang, Yong;  Wong, Wing Hung
Favorite  |  View/Download：128/0  |  Submit date：2020/06/30
DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data 期刊论文
NATURE COMMUNICATIONS, 2019, 卷号: 10, 页码: 11
Authors:  Zeng, Wanwen;  Chen, Xi;  Duren, Zhana;  Wang, Yong;  Jiang, Rui;  Wong, Wing Hung
Favorite  |  View/Download：133/0  |  Submit date：2020/01/10
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：144/0  |  Submit date：2019/12/13
coupled clustering  NMF  single-cell genomic data  
Modeling gene regulation from paired expression and chromatin accessibility data 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 卷号: 114, 期号: 25, 页码: E4914-E4923
Authors:  Duren, Zhana;  Chen, Xi;  Jiang, Rui;  Wang, Yong;  Wong, Wing Hung
Favorite  |  View/Download：117/0  |  Submit date：2018/07/30
gene regulation  transcription factor  regulatory element  chromatin regulator  chromatin activity  
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data 期刊论文
NUCLEIC ACIDS RESEARCH, 2017, 卷号: 45, 期号: 10, 页码: 5666-5677
Authors:  Zamanighomi, Mahdi;  Lin, Zhixiang;  Wang, Yong;  Jiang, Rui;  Wong, Wing Hung
Favorite  |  View/Download：106/0  |  Submit date：2018/07/30
Simultaneous dimension reduction and adjustment for confounding variation 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 卷号: 113, 期号: 51, 页码: 14662-14667
Authors:  Lin, Zhixiang;  Yang, Can;  Zhu, Ying;  Duchi, John;  Fu, Yao;  Wang, Yong;  Jiang, Bai;  Zamanighomi, Mahdi;  Xu, Xuming;  Li, Mingfeng;  Sestan, Nenad;  Zhao, Hongyu;  Wong, Wing Hung
Favorite  |  View/Download：88/0  |  Submit date：2018/07/30
dimension reduction  confounding variation  transcriptome  
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
Authors:  Wang, Yong;  Jiang, Rui;  Wong, Wing Hung
Favorite  |  View/Download：84/0  |  Submit date：2018/07/30
gene regulatory network  open chromatin  DNA accessibility  transcription factor colocalization  statistical model  data integration