Optimization and Computational Systems Biology Lab
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PUBLICATIONS (Google Scholar, PubMed)
- The cell-surface 50-nucleotidase CD73 defines a functional T memory cell subset that declines with age. Fengqin Fang, Wenqiang Cao, Weikang Zhu, Nora Lam, Lingjie Li, Sadhana Gaddam, Yong Wang, Chulwoo Kim, Simon Lambert, Huimin Zhang, Bin Hu, Donna L. Farber, Cornelia M. Weyand, Jorg J. Goronzy. Cell Reports. 37, 109981, (2021).
- Reusability report: Compressing regulatory networks to vectors for interpreting gene expression and genetic variants. Wanwen Zeng, Jingxue Xin, Rui Jiang, Yong Wang. Nature Machine Intelligence. 1-5 (2021).
- hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. Zhanying Feng, Zhana Duren, Ziyi Xiong, Sijia Wang, Fan Liu, Wing Hung Wong, Yong Wang. Communications Biology. vol. 4: 1-6 (2021).
- MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. Meng Zou, Zhana Duren, Qiuyue Yuan, Henry Li, Andrew Paul Hutchins, Wing Hung Wong, Yong Wang. bbab235. (2021).
- OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang. Nucleic Acids Research. Volume 49, Issue W1, Pages W483¨CW490, (2021).
- Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation. Jingxue Xin, Hui Zhang, Yaoxi He, Zhana Duren, Caijuan Bai, Lang Chen, Xin Luo, Dong-Sheng Yan, Chaoyu Zhang, Xiang Zhu, Qiuyue Yuan, Zhanying Feng, Chaoying Cui, Xuebin Qi, Wing Hung Wong, Yong Wang, Bing Su. Nature Communications. vol. 11: 1-20 (2020).
- Time course regulatory analysis based on paired expression and chromatin accessibility data. Zhana Duren, Xi Chen, Jingxue Xin, Yong Wang, Wing Wong. Genome Research. vol. 30: 622-634 (2020).
- 3Scover: Identifying safeguard TF from cell type-TF specificity network by an extended minimum set cover model. Qiuyue Yuan, Yong Wang. iScience. vol. 23(6): 101227. (2020).
- ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming. Fei Li, Qiuyue Yuan, Wei Di, Xinyi Xia, Zhang Liu, Ninghui Mao, Lin Li, Chunfeng Li, Juan He, Yunguang Li, Wangxin Guo, Xiaoyu Zhang, Yiqin Zhu, Rebiguli Aji, Shangqian Wang, Ping Chi, Brett Carver, Yong Wang, Yu Chen, Dong Gao. The Journal of Clinical Investigation. vol. 130(11): 5924-5941 (2020).
- Integrating distal and proximal information to predict gene expression via a densely con-nected convolutional neural network.Wanwen Zeng, Yong Wang, Rui Jiang. Bioinformatics. vol. 36, Issue 2, P496-503 (2020).
- Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.Yongcui Wang, Shilong Chen, Wenran Li, Rui Jiang, Yong Wang. NAR Genomics and Bioinformatics. vol. 2 (2), (2020).
- ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor.Wanwen Zeng, Yong Wang, Rui Jiang. Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi, Yong Wang. P1-8 (2020).
- Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. Y Wang, S Chen, L Chen, Y Wang. PLoS Computational Biology. vol. 15 (12), e1007540 (2019).
- Lipid-gene regulatory network reveals coregulations of triacylglycerol with phosphatidylinositol/lysophosphatidylinositol and with hexosyl-ceramide. Wei Wang, Jingxue Xin, Xiao Yang, Sin Man Lam, Guanghou Shui, Yong Wang, Xun Huang. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. vol. 1864, Issue 2, Pages 168-180 (2019).
- scTIM: Seeking Cell-Type-Indicative Marker from single cell RNA-seq data by consensus optimization. Zhanying Feng, Xianwen Ren, Yuan Fang, Yining Yin, Chutian Huang, Yimin Zhao, Yong Wang. Bioinformatics. vol. 36, Issue 8, P2474¨C2485, (2019).
- DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang, Wing Hung Wong. Nature Communications. vol. 10 (1), 1-11 (2019).
- Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana. Zhana Duren, Yaling Wang, Jiguang Wang, Xing-Ming Zhao, Le Lv, Xiaobo Li, Jingdong Liu, Xin-Guang Zhu, Luonan Chen, Yong Wang. npj Systems Biology and Applications. vol. 5(1), 1-11 (2019).
- TFAP2C- and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment.Lingjie Li, Yong Wang, Jessica L Torkelson, Gautam Shankar, Jillian M Pattison, Hanson H Zhen, Fengqin Fang, Zhana Duren, Jingxue Xin, Sadhana Gaddam, Sandra P Melo, Samantha N Piekos, Jiang Li, Eric J Liaw, Lang Chen, Rui Li, Marius Wernig, Wing H Wong, Howard Y Chang, Anthony E Oro. Cell Stem Cell. Vol. 24, Issue 2, P271-284.E8, (2019).
- Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.Zhana Duren, Xi Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman Satpathy, Howard Chang, Yong Wang, Wing Hung Wong. Proceedings of the National Academy of Sciences. 115 (30) 7723-7728 (2018).
- Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data.Lirong Zhang, Gaogao Xue, Junjie Liu, Qianzhong Li, Yong Wang. BMC Genomics. 19 (10), 914 (2018).
- ELF: Extract Landmark Features by optimizing topology maintenance, redundancy, and specificity.Zhanying Feng, Yong Wang. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume: 17, Issue: 2, 411-421 (2018).
- Development of Serum Biomarker Panels for The Early Detection of Breast Cancer.Pengjun Zhang, Meng Zou, Xinyu Wen, Huijuan Wang, Feng Gu, Juan Li, Linzhong Zhu, Xinxin Deng, Guanghong Guo, Jing Gao, Xiaolong Li, Xingwang Jia, Zhennan Dong, Luonan Chen, Yong Wang, Yaping Tian. American Journal of Biomedical Sciences. 10 (1) (2018).
- A Semisupervised Classification Approach for Multidomain Networks With Domain Selection.Michale Ng Chuan Chen, Jingxue Xin, Yong Wang, Luonan Chen. IEEE Transactions on Neural Networks and Learning Systems. Volume: 30, Issue: 1, 269-283 (2018).
- Modeling gene regulation from paired expression and chromatin accessibility data. Duren, Zhana; Chen, Xi; Jiang, Rui; Wang, Yong; Wong, Wing Hung. Proceedings of the National Academy of Sciences, vol. 114 no. 25 E4914-E4923 (2017) .
- A Novel Dual Eigen-Analysis of Mouse Multi-Tissues's Expression Profiles Unveils New Perspectives into Type 2 Diabetes. Li, Lei M; Liu, Xiuxiu; Wang, Lin; Wang, Yong; Liu, Xiuqin; Tian, Xue; Gong, Fuzhou; Shen, Li; Peng, Xiao-ding. Scientific Reports 7 (2017).
- Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data. Zamanighomi, Mahdi; Lin, Zhixiang; Wang, Yong; Jiang, Rui; Wong, Wing Hung. Nucleic Acids Research 45,10,5666-5677 (2017).
- Models of global gene expression define major domains of cell type and tissue identity. Hutchins, Andrew P; Yang, Zhongzhou; Li, Yuhao; He, Fangfang; Fu, Xiuling; Wang, Xiaoshan; Li, Dongwei; Liu, Kairong; He, Jiangping; Wang, Yong; Chen, Jiekai; Esteban, A Miguel; Pei, Duanqing. Nucleic Acids Research 45,5,2354-2367 (2017).
- Drosophila TRF2 and TAF9 regulate lipid droplet size and phospholipid fatty acid composition. Fan, Wei; Lam, Sin Man; Xin, Jingxue; Yang, Xiao; Liu, Zhonghua; Liu, Yuan; Wang, Yong; Shui, Guanghou; Huang, Xun. PLoS Genetics 13,3,e1006664 (2017).
- A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation. Duren, Zhana; Wang, Yong Scientific Report 6, 22656 (2016).
- Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data. Wang, Yong; Jiang, Rui; Wong, Wing Hung. National Science Review 3,2,240-251 (2016).
- Identifying joint biomarker panel from multiple level dataset by an optimization model. Zou, Meng; Zhang, Peng-Jun; Chen, Luonan; Tian, Ya-Ping; Wang, Yong. Biomarkers in medicine 10,6,567-575 (2016).
- Simultaneous dimension reduction and adjustment for confounding variation. Lin, Zhixiang; Yang, Can; Zhu, Ying; Duchi, John; Fu, Yao; Wang, Yong; Jiang, Bai; Zamanighomi, Mahdi; Xu, Xuming; Li, Mingfeng; Nenad Sestan; Hongyu Zhao; Wing Hung Wong Proceedings of the National Academy of Sciences. 113,51,14662-14667 (2016).
- Extended particle swarm optimisation method for folding protein on triangular lattice. Y Guo, Z Wu, Y Wang, Y Wang. IET systems biology 10 (1), 30-33 (2016).
- Revealing Potential Biomarkers of Functional Dyspepsia by Combining 1H NMR Metabonomics Techniques and an Integrative Multi-objective Optimization Method. Wu, Qiaofeng; Zou, Meng; Yang, Mingxiao; Zhou, Siyuan; Yan, Xianzhong; Sun, Bo; Wang, Yong; Chang, Shyang; Tang, Yong; Liang, Fanrong. Scientific Report 6, (2016).
- Prospective stratification of patients at risk for emergency department revisit: resource utilization and population management strategy implications. Jin, Bo; Zhao, Yifan; Hao, Shiying; Shin, Andrew Young; Wang, Yue; Zhu, Chunqing; Hu, Zhongkai; Fu, Changlin; Ji, Jun; Wang, Yong et al. BMC Emergency Medicine 16,10, (2016).
- NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data. Zou, Meng; Liu, Zhaoqi; Zhang, Xiang-Sun; Wang, Yong. Bioinformatics 31 (20), 3330-3338 (2015).
- Computational probing protein-protein interactions targeting small molecules. Wang, Yong-Cui; Chen, Shi-Long; Deng, Nai-Yang; Wang, Yong. Bioinformatics. 32 (2), 226-234 (2015).
- A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors. Zou, Meng; Zhang, Peng-Jun; Wen, Xin-Yu; Chen, Luonan; Tian, Ya-Ping; Wang, Yong. Methods. 83: 3-17 (2015).
- Identifying network biomarkers based on protein-protein interactions and expression data. Xin, Jingxue; Ren, Xianwen; Chen, Luonan; Wang, Yong. BMC Medical Genomics. 8,S11 (2015).
- Real-time web-based assessment of total population risk of future emergency department utilization: statewide prospective active case finding study. Hu, Zhongkai; Jin, Bo; Shin, Andrew Y; Zhu, Chunqing; Zhao, Yifan; Hao, Shiying; Zheng, Le; Fu, Changlin; Wen, Qiaojun; Ji, Jun; Li, Zhen; Wang, Yong. et al. Interactive journal of medical research. 4,1 (2015).
- Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. Y Wang, S Chen, N Deng, Y Wang. PLoS One 8 (11), e78518 (2013).
- Network predicting drug's anatomical therapeutic chemical code. Y Wang, S Chen, N Deng, Y Wang. Bioinformatics 29 (10), 1317-1324 (2013).
- ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. X Ren, Y Wang, L Chen, XS Zhang, Q Jin. Nucleic Acids Research 41 (4), e53-e53 (2012).
- Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection. Y Wang, QF Wu, C Chen, LY Wu, XZ Yan, SG Yu, XS Zhang, FR Liang. BMC Systems Biology. 6 (1), S15 (2012)
- A combinatorial model and algorithm for globally searching community structure in complex networks. XS Zhang, Z Li, RS Wang, Y Wang. Journal of Combinatorial Optimization. 23 (4), 425-442 (2012).
- A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Y Wang, RS Wang, T Joshi, D Xu, XS Zhang, L Chen, Y Xia. Handbook of Research on Computational Methodologies in Gene Regulatory Networks 450-475 (2010).
- Protein evolution in yeast transcription factor subnetworks. Y Wang, EA Franzosa, XS Zhang, Y Xia. Nucleic Acids Res. 38: 5959-5969 (2010).
- Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Y Wang, XS Zhang, Y Xia. Nucleic Acids Res. 37: 5943-5958 (2009).
- Evaluating protein similarity from coarse structures. Y Wang, W Ling-Yun, JH Zhang, ZW Zhan, Z Xiang-Sun, C Luonan. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6 (4), 583-593 (2009).
- A network biology study on circadian rhythm by integrating various omics data. Y Wang, XS Zhang, L Chen. OMICS A Journal of Integrative Biology. 13 (4), 313-324 (2009).
- Condition specific subnetwork identification using an optimization model. Y Wang, Y Xia. Lecture Notes in Operations Research. 9, 333-340 (2008).
- Analysis on multi-domain cooperation for predicting protein-protein interactions. RS Wang, Y Wang, LY Wu, XS Zhang, L Chen. BMC bioinformatics. 8 (1), 391 (2008).
- Inferring gene regulatory networks from multiple microarray datasets. Y Wang, T Joshi, XS Zhang, D Xu, L Chen. Bioinformatics. 22 (19), 2413-2420 (2006).
- Exploring protein's optimal HP configurations by self-organizing mapping. XS Zhang, Y Wang, ZW Zhan, LY Wu, L Chen. Journal of bioinformatics and computational biology. 3 (02), 385-400 (2005).
- A new trust region method for nonlinear equations. J Zhang, Y Wang. Mathematical Methods of Operations Research. 58 (2), 283-298 (2003).
Yong Wang Lab | Academy of Mathematics and Systems Science | Chinese Academy of Sciences