Yuxuan Hu, Lin Gao*, et al. Optimal control nodes in disease-perturbed networks as targets for combination therapy. Nature Communications, 2019, 10:2180【IF=12.353,中科院I区】
 Yusen Ye, Lin Gao*, Shihua Zhang*. CIRCLET Circular trajectory reconstruction uncovers cell-cycle progression and regulatory dynamics from single-cell Hi-C maps. Advanced Science, 2019:1900986【IF=15.804 ,中科院I区】
 Yusen Ye, Lin Gao*, Shihua Zhang. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. Nucleic Acids Research, 2019, 47(11):e65【IF=11.561 ,中科院I区】
 Xiaofei Yang, Lin Gao*, et al. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. Briefings in Bioinformatics, 2017,18(5):761-773【IF= 7.065,中科院I区】
 Xiao-Tai Huang, Y. Zhu*, L. LH. Chan, Z. Zhao, H. Yan. Inference of cellular level signaling networks using single-cell gene expression data in C. elegans reveals mechanisms of cell fate specification. Bioinformatics, 2017, 33(10): 1528-1535.【IF= 7.307，中科院I区】
 Fei Song, Chunmei Cui, Lin Gao*, et al. miES: predicting the essentiality of miRNAs with machine learning and sequence features. Bioinformatics, 2019, 35(6):1053-1054 【IF= 7.307，中科院I区】
 Xiao Wen, Lin Gao*, Yuxuan Hu. LAceModule: Identification of Competing Endogenous RNA Modules by Integrating Dynamic Correlation. Frontiers in Genetics, 2020,11:235, 0318.
 Ran Duan, Lin Gao* et al. CEPICS: a comparison and evaluation platform for integration methods in cancer subtyping. Frontiers in Genetics, 2019,10:966, 0814.
 Liang Yu, Shunyu Yao, Lin Gao, YunhongZha. Conserved disease modules extracted from multilayer heterogeneous disease and gene networks for understanding disease mechanisms and predicting disease treatments. Frontiers in Genetics. 2019; 9: 745.
 Yusen Ye, Lin Gao* et al.Integrative analysis of transcription factor combinatorial interactions using a Bayesian tensor factorization approach. Frontiers in Genetics, 2017,8:140.
 Xiao Wen, Lin Gao*, et al. LNCSLDB: a resource for long non coding RNA subcellular localization. Database(Oxford), 018,1-6.
 SongweiJia, Lin Gao*, Yong Gao, et al. Exploring triad-rich substructures by graph-theoretic characterizations in complex networks.PhysicaA ,2017,468:53-69.
 Liang Yu, Lin Gao. Human pathway-based disease network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, 16(4): 1240 - 1249.
 Liang Yu, Ruidan Su, Bingbo Wang, Long Zhang, Yapeng Zou, Jing Zhang, Lin Gao. Prediction of novel drugs for hepatocellular carcinoma based on multi-source random walk. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(4):966-977.
 Feng Li, Lin Gao, Bing bo Wang. Detection of Driver Modules with Rarely Mutated Genes in Cancers. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, 17(2): 390-401.
 X. Yuan, J. Bai, J. Zhang, L. Yang, J. Duan, Y. Li, M. Gao, CONDEL: Detecting Copy Number Variation and Genotyping Deletion Zygosity from Single Tumor Samples using Sequence Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Nov 26, 2018.
 X. Yuan, M. Gao, J. Bai, J. Duan, SVSR: a Program to Simulate Structural Variations and Generate Sequencing Reads for Multiple Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Oct 17, 2018.
 X. Yuan, J. Yu, J. Xi, L. Yang, J. Shang, Z. Li, J. Duan, CNV_IFTV: an isolation forest and total variation-based detection of CNVs from short-read sequencing data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Jun, 2019.
 Yuan X, Ma C, Zhao H, et al., STIC: Predicting Single Nucleotide Variants and Tumor Purity in Cancer Genome. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Feb 19, 2020.
 X. Yuan, J. Li, J. Bai, and J. Xi, "A local outlier factor-based detection of copy number variations from NGS data." IEEE/ACM Transactions on Computational Biology and Bioinformatics, Dec 24, 2019.
 X. Yuan, X. Xu, H. Zhao, and J. Duan, ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Nov 19, 2019.
 X. Yuan, J. Zhang, and L. Yang, IntSIM: An Integrated Simulator of Next-Generation Sequencing Data. IEEE Transactions on Biomedical Engineering, 2017, 64(2): 441-451.
 X. Yuan, J. Zhang, L. Yang, J. Bai, P. Fan, Detection of Significant Copy Number Variations from Multiple Samples in Next-Generation Sequencing Data. IEEE Transactions on NanoBioscience, 2018, 17(1): 12 - 20.
 Yaoyao Li, Junying Zhang*, Xiguo Yuan, Junping Li, dpGMM: a Dirichlet process Gaussian Mixture Model for copy number variation detection in low-coverage whole-geneome sequencing data. IEEE Access, 2020, 8:27973-27985.
 Qiang Yu* Xiao Zhang. A new efficient algorithm for quorum planted motif search on large DNA datasets. IEEE Access, 2019, 7(1): 129617-129626.
 SongweiJia, Lin Gao*, et al. Viewing the Meso-Scale Structures in Protein-Protein Interaction Networks Using 2-Clubs. IEEE Access, 2018, 6: 36780–36797.
 Tuo, Shouheng, Junying Zhang*, Xiguo Yuan, Zongzhen He, Yajun Liu, and Zhaowen Liu. Niche harmony search algorithm for detecting complex disease associated high-order SNP combinations. Scientific Reports, 2017, 7, no. 1: 1-18.
 Qin, Guimin, Saurav Mallik, RamkrishnaMitra, Aimin Li, PeilinJia, Christine M. Eischen, and Zhongming Zhao. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Scientific Reports 10, no. 1 (2020): 1-14.
 He Zongzhen, Zhang Junying*, Yuan Xiguo, Xi Jianing, Liu Zhaowen, Zhang Yuanyuan. Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables. Molecules, 2019, 24(3): 631.
 Junying Zhang*, Liying Yang, Jun Bai, Shan Jiang. SM-RCNV: A Statistical Method to Detect Recurrent Copy Number Variations in Sequenced Samples. Genes & Genomics, 2019, 41(5):529–536.
 Li, Aimin, Guimin Qin, Akiko Suzuki, Mona Gajera, Junichi Iwata, PeilinJia, and Zhongming Zhao. Network-based identification of critical regulators as putative drivers of human cleft lip. BMC medical genomics, 2019, 12, no. 1: 16.
 Qiang Yu, Xiang Zhao, HongweiHuo*. A new algorithm for DNA motif discovery using multiple sample sequence sets. Journal of Bioinformatics and Computational Biology, 2019, 17(4): 1950021.
 Qiang Yu, Dingbang Wei, HongweiHuo*. SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets. BMC Bioinformatics, 2018, 19: 228.
 Yang Liying*, Shen Yunyan, Yuan Xiguo, hangJunying ,WeiJianhua. Analysis of breast cancer subtypes by AP-ISA biclustering. BMC bioinformatics, 2017, 18(1):481.
 Qin, Guimin, Luqiong Yang, Yuying Ma, Jiayan Liu, and QiuyanHuo. The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma. BMC bioinformatics, 2019(20) 22: 1-13.
 Peizhuo Wang, Lin Gao*, Yuxuan Hu, Feng Li. Feature Related Multi-view Nonnegative Matrix Factorization for Identifying Conserved Functional Modules in Multiple Biological Networks. BMC Bioinformatics,2018,19:39
 Guo, Xingli, Lin Gao, Yu Wang, David KY Chiu, Bingbo Wang, Yue Deng, and Xiao Wen. Large-scale investigation of long noncoding RNA secondary structures in human and mouse. Current Bioinformatics, 2018, 13, no. 5: 450-460.