Publications

2021

1. Kang Xu#, Yangyang Cai#, Mengying Zhang#, Haozhe Zou, Zhenghong Chang, Donghao Li, Jing Bai*, Juan Xu*, Yongsheng Li*. Pan-cancer characterization of expression and clinical relevance of m6A-related tissue-elevated long non-coding RNAs. Molecular Cancer 2021. https://doi.org/10.1186/s12943-021-01324-8

2. Jun Xiao#, Xiaoyan Jin#, Chunlong Zhang#, Haozhe Zou#, Zhenghong Chang, Nan Han, Xia Li*, Yunpeng Zhang*, Yongsheng Li*. Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma. Theranostics 2021; 11(7):3060-3073.

3. Ya Zhang#, Sicong Xu#, Gang Xu, Yueying Gao, Si Li, Ke Zhang, Zhanyu Tian, Jing Guo, Xia Li*, Juan Xu*, Yongsheng Li*. Front. Cell Dev. Biol. | doi: 10.3389/fcell.2020.629030

4. Junyi Li#, Tao Pan#, Liuxin Chen#, Qi Wang, Zhenghong Chang, Weiwei Zhou, Xinhui Li, Gang Xu, Xia Li*, Yongsheng Li*, Yunpeng Zhang*. Alternative splicing perturbation landscape identifies RNA binding proteins as potential therapeutic targets in cancer. Molecular Therapy: Nucleic Acids, 2021.

2020

1. Yu Fu#, Yongsheng Li#, Ensong Guo#, Liang He#, Jia Liu, Bin Yang, Fuxia Li, Zizhuo Wang, Yuan Li, Rourou Xiao, Chen Liu, Yuhan Huang, Xue Wu, Funian Lu, Lixin You, Tianyu Qin, Chaolong Wang, Kezhen Li, Peng Wu, Ding Ma*, Chaoyang Sun*, Gang Chen*. Dynamics and Correlation Among Viral Positivity, Seroconversion, and Disease Severity in COVID-19: A Retrospective Study. Annals of Internal Medicine, 2020.

2. Yongsheng Li#, Brandon Burgman#, Ishaani S Khatri, Sairahul R Pentaparthi, Zhe Su, Daniel J McGrail, Yang Li, Erxi Wu, S Gail Eckhardt, Nidhi Sahni*, S Stephen Yi*. e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks. Nucleic Acids Research, 2020.

3. Jun Xiao#, Xiaoyan Jin#, Chunlong Zhang#, Haozhe Zou#, Zhenghong Chang, Nan Han, Xia Li*, Yunpeng Zhang*, Yongsheng Li*. Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma. Theranostics, 2020.

4. Mengying Zhang#, Kang Xu#, Limei Fu#, Qi Wang, Zhenghong Chang, Haozhe Zou, Yan Zhang*, Yongsheng Li*. Revealing epigenetic factors of circRNA expression by machine learning in various cellular contexts. iScience, 2020.

5. Yongsheng Li#*, Tiantongfei Jiang#, Weiwei Zhou#, Junyi Li, Xinhui Li, Qi Wang, Xiaoyan Jin, Jiaqi Yin, Liuxin Chen, Yunpeng Zhang, Juan Xu*, Xia Li*. Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers. Nature Communications, 2020.

6. Yongsheng Li, Brandon Burgman, Daniel J McGrail, Ming Sun, Dan Qi, Sachet A Shukla, Erxi Wu, Anna Capasso, Shiaw-Yih Lin, Catherine J Wu, S Gail Eckhardt, Gordon B Mills, Bo Li, Nidhi Sahni*, S Stephen Yi*. Integrated Genomic Characterization of the Human Immunome in Cancer. Cancer Research, 2020.

7. Chunlong Zhang#, Ning Zhao#, Xue Zhang#, Jun Xiao, Junyi Li, Dezhong Lv, Weiwei Zhou, Yongsheng Li*, Juan Xu*, Xia Li*. SurvivalMeth: A Web Server to Investigate the Effect of DNA Methylation-related Functional Elements on Prognosis. Briefings in Bioinformatics, 2020

8. Mengying Zhang#, Xiyun Jin#, Junyi Li, Yi Tian, Qi Wang, Xinhui Li, Juan Xu*, Yongsheng Li*, Xia Li*. CeRNASeek: an R package for identification and analysis of ceRNA regulation. Briefings in Bioinformatics, 2020

9. Juan Xu#*, Tingting Shao#, Mingxu Song#, Yunjin Xie, Jialiang Zhou, Jiaqi Yin, Na Ding, Haozhe Zou, Yongsheng Li*, Jiwei Zhang*. MIR22HG acts as a tumor suppressor via TGFβ/SMAD signaling and facilitates immunotherapy in colorectal cancer. Molecular Cancer, 2020.

10. Jiwei Zhang#*, Shengli Li#, Lin Zhang, Juan Xu, Mingxu Song, Tingting Shao, Zhaohui Huang*, Yongsheng Li*. RBP EIF2S2 Promotes Tumorigenesis and Progression by Regulating MYC-Mediated Inhibition via FHIT-Related Enhancers. Molecular Therapy, 2020.

11. Dezhong Lv#, Kang Xu#, Xiyun Jin#, Junyi Li, Yuchen Shi, Mengying Zhang, Xiaoyan Jin, Yongsheng Li, Juan Xu*, Xia Li*. LncSpA: LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Cancer Research, 2020.

12. Zishan Wang#, Jiaqi Yin#, Weiwei Zhou#, Jing Bai#, Yunjin Xie, Kang Xu, Xiangyi Zheng, Jun Xiao, Li Zhou, Xiaolin Qi, Yongsheng Li*, Xia Li*, Juan Xu*. Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types, Nucleic Acids Research, 2020.

13. Daniel J. McGrail#*, Jeannine Garnett#, JunYin, Hui Dai, David J.H.Shih, Truong Nguyen Anh Lam, Yang Li, Chaoyang Sun, Yongsheng Li, Rosemarie Schmandt, Ji Yuan Wu, Limei Hu, Yulong Liang, Guang Peng, Eric Jonasch, David Menter, Melinda S.Yates, Scott Kopetz, Karen H.Lu, Russell Broaddus, Gordon B.Mills, Nidhi Sahni*, Shiaw-Yih Lin*. Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. Cancer cell, 2020.

2019

1. Yongsheng Li#*, Jun Xiao#, Jing Bai, Yi Tian, Yinwei Qu, Xiang Chen, Qi Wang, Xinhui Li, Yunpeng Zhang*, Juan Xu*. Molecular characterization and clinical relevance of m6A regulators across 33 cancer types, Molecular Cancer, 2019.

2. Hong Chen#, Jun Xiao#, Tingting Shao#, Li Wang# , Jing Bai , Xiaoyu Lin , Na Ding , Yinwei Qu , Yi Tian , Xiang Chen , Hui Liu*, Hongyu Liu*, Juan Xu* and Xia Li*. Landscape of enhancer-enhancer cooperative regulation during human cardiac commitment. Molecular Therapy — Nucleic Acids, 2019.

3. Yong Fang*, Daniel J. McGrail, Chaoyang Sun*, Marilyne Labrie, Xiaohua Chen, Dong Zhang, Zhenlin Ju, Christopher P. Vellano, Yiling Lu, Yongsheng Li, Kang Jin Jeong, Zhiyong Ding, Jiyong Liang, Steven W. Wang, Hui Dai, Sanghoon Lee, Nidhi Sahni, Imelda Mercado-Uribe, Tae-beom Kim, Ken Chen, Shiaw-Yih Lin, Guang Peng, Shannon N. Westin, Jinsong Liu, Mark J. O'Connor, Timothy A. Yap, Gordon B. Mills. Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy. Cancer cell, 2019.

4. Yongsheng Li#, Yunpeng Zhang#, Xia Li*, Song Yi*, Juan Xu*. Gain-of-function mutations: an emerging advantage for cancer biology. Trends in Biochemical Science, 2019 (Cover figure).

5. Hui Liu#, Tiantongfei Jiang#, Shuyuan Wang#, Xiang Chen, Xiaoyan Jin, Qi Wang, Xinhui Li, Jiaqi Yin, Tingting Shao, Yongsheng Li*, Juan Xu*, Qiong Wu*. A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome. Frontiers in Bioengineering and Biotechnology, 2019.

2018

1. Xiaoyu Lin, Tiantongfei Jiang, Jing Bai, Junyi Li, Tianshi Wang, Jun Xiao, Yi Tian, Xiyun Jin, Tingting Shao, Juan Xu, Lingchao Chen, Lihua Wang, Yongsheng Li: Characterization of transcriptome transition associates long noncoding RNAs with glioma progression. Molecular Therapy — Nucleic Acids, 2018 . PMID: 30472640

2. Patrick Kwok-Shing Ng#, Jun Li#, Kang Jin Jeong#, Shan Shao, Hu Chen, Yiu Huen Tsang, Sohini Sengupta, Zixing Wang, Venkata Hemanjani Bhavana, Richard Tran, Stephanie Soewito, Darlan Conterno Minussi, Daniela Moreno, Kathleen Kong, Turgut Dogruluk, Hengyu Lu, Jianjiong Gao, Collin Tokheim, Daniel Cui Zhou, Amber M Johnson, Jia Zeng, Carman Ka Man Ip, Zhenlin Ju, Matthew Wester, Shuangxing Yu, Yongsheng Li, Christopher P Vellano, Nikolaus Schultz, Rachel Karchin, Li Ding, Yiling Lu, Lydia Wai Ting Cheung, Ken Chen, Kenna R Shaw, Funda Meric-Bernstam, Kenneth L Scott, Song Yi*, Nidhi Sahni*, Han Liang*, Gordon B. Mils. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell, 2018. PMID: 29533785

3. Yongsheng Li, Daniel J. McGrail, Juan Xu, Junyi Li, Ning-Ning Liu, Ming Sun, Richard Lin, Rita Pancsa, Jiwei Zhang, Ju-Seog Lee, Hui Wang, Gordon B. Mills, Xia Li, Song Yi, Nidhi Sahni. MERIT: Systematic analysis and characterization of Mutational Effect on RNA Interactome Topology. Hepatology, 2018. PMID: 30153342.

4. Yongsheng Li, Daniel J. McGrail, Gordon B. Mills, Song Yi, and Nidhi Sahni. Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation. Trends in Biochemical Sciences, 2018 Aug;43(8):576-592. PMID: 29941230.

5. Yongsheng Li, Daniel J. McGrail, Natasha Latysheva, Song Yi, M. Madan Babu, Nidhi Sahni. Pathway perturbations in signaling networks: Linking genotype to phenotype. Seminars in Cell and Developmental Biology, 2018 May 10. pii: S1084-9521(17)30528-1. PMID: 29738884.

6. Chunjie Jiang, Na Ding, Junyi Li, Xiyun Jin, Lili Li, Tao Pan, Caiqin huo, Yongsheng Li, Juan Xu, Xia Li. Landscape of the long non-coding RNA transcriptome in human heart. Brief Bioinform. 2018 Jun 22. PMID: 29939204. (co-Corresponding author)

7. Tingting Shao, Guangjuan Wang, Hong Chen, Yunjin Xie, Xiyun Jin, Jing Bai, Juan Xu, Xia Li, Jian Huang, Yan Jin, Yongsheng Li. Survey of miRNA-miRNA cooperative regulation principles across cancer types. Brief Bioinform. 2018 May 25. PMID: 29800060. (Corresponding author)

8. Jianping Lu, Juan Xu, Junyi Li, Tao Pan, Jing Bai, Liqiang Wang, Xiyun Jin, Xiaoyu Lin, Yunpeng Zhang, Yongsheng Li, Nidhi Sahni, Xia Li. FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators. Nucleic Acids Research, 2018. PMID: 30102398. (co-Corresponding author)

9. Daniel J. McGrail, Lorenzo Federico, Yongsheng Li, Hui Dai, Yiling Lu, Gordon B. Mills, Song Yi, Shiaw-Yih Lin, & Nidhi Sahni. Multiomics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. Nature communications, 2018 Apr 3;9(1):1317. PMID: 29615613.

10. Yongsheng Li, Lili Li, Zishan Wang, Tao Pan, Nidhi Sahni, Xiyun Jin, Guangjuan Wang, Junyi Li, Xiangyi Zheng, Yunpeng Zhang, Juan Xu, Song Yi, Xia Li. LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Research. 2018 Feb 16;46(3):1113-1123. PMID:29325141.

11. Juan Xu, ZiShan Wang, Shengli Li, Juan Chen, Jinwen Zhang, Chunjie Jiang, Zheng Zhao, Jing Li, Yongsheng Li, Xia Li. Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes. Brief Bioinform. 2018 Jan 1;19(1):52-64. PMID: 27742663 (co-corresponding author)

2017

1. Song Yi, Shengda Lin, Yongsheng Li, Wei Zhao, Gordon B. Mills, Nidhi Sahni: Functional variomics and network perturbation: connecting genotype to phenotype in cancer. Nat Rev Genet. 2017 Jul;18(7):395-410. PMID: 28344341 (co-first author).

2. Yongsheng Li, Nidhi Sahni, Rita Pancsa, Daniel J. McGrai, Juan Xu, Xu Hua, Jasmin Coulombe-Huntington, Michael Ryan, Boranai Tychhon, Dhanistha Sudhaka, Limei Hu, Michael Tyers, Xiaoqian Jiang, Shiaw-Yih Lin, M. Madan Babu, Song Yi: Revealing the determinants of widespread alternative splicing perturbation in cancer. Cell Rep. 2017 Oct 17;21(3):798-812. PMID:29045845

3. Yongsheng Li, Xiyun Jin, Zishan Wang, Lili Li, Hong Chen, Xiaoyu Lin, Song Yi, Yunpeng Zhang, Juan Xu: Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk. Brief Bioinform. 2017 Oct 25. PMID:29077860

4. Yongsheng Li, Jinwen Zhang, Caiqin Huo, Na Ding, Junyi Li, Jun Xiao, Xiaoyu Lin, Benzhi Cai, Yunpeng Zhang, Juan Xu: Dynamic Organization of lncRNA and Circular RNA Regulators Collectively Controlled Cardiac Differentiation in Humans. EBioMedicine. 2017 Oct;24:137-146. PMID:29037607

5. Yongsheng Li, Caiqin Huo, Tao Pan, Lili Li, Xiyun Jin, Xiaoyu Lin, Juan Chen, Jinwen Zhang, Zheng Guo, Juan Xu, Xia Li: Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases. Brief Bioinform. 2017 Aug 16. PMID:28968629

6. Juan Xu, Tingting Shao, Na Ding, Yongsheng Li, Xia Li: miRNA–miRNA crosstalk: from genomics to phenomics. Brief Bioinform. 2017 Nov 1;18(6):1002-1011. PMID:27551063 (co-corresponding author)

7. Juan Chen, Juan Xu, Yongsheng Li, Jinwen Zhang, Hong Chen, Jianping Lu, Zishan Wang, Xueying Zhao, Kang Xu, Yixue Li, Xia Li, Yan Zhang: Competing endogenous RNA network analysis identifies critical genes among the different breast cancer subtypes. Oncotarget. 2017 Feb 7;8(6):10171-10184. PMID: 28052038 (co-first author)

2016

1. Yongsheng Li, Nidhi Sahni, Song Yi: Comparative analysis of protein interactome networks prioritizes candidate genes with cancer signatures. Oncotarget, 2016 Nov 29;7(48):78841-78849. PMID: 27791983

2. Juan Xu, Lin Feng, Zujing Han, Yongsheng Li, Aiwei Wu, Tingting Shao, Na Ding, Lili Li, Wei Deng, Xuebing Di, Jian Wang, Lianfeng Zhang, Xia Li, Kaitai Zhang, Shujun Cheng: Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues. Nucleic Acids Res. 2016 Nov 2;44(19):9438-9451. PMID: 27365046 (co-first author)

3. Yongsheng Li, Zishan Wang, Yuan Wang, Zheng Zhao, Jinwen Zhang, Jianping Lu, Juan Xu, Xia Li: Identification and characterization of lncRNA mediated transcriptional dysregulation dictates lncRNA roles in glioblastoma. Oncotarget, 2016 Jul 19;7(29):45027-45041. PMID: 26943771

4. Chunjie Jiang, Yongsheng Li, Zheng Zhao, Jianping Lu, Hong Chen, Na Ding, Guangjuan Wang, Juan Xu, Xia Li: Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs. Oncotarget 2016. PMID: 26760768 (co-first author)

2015

1. Juan Xu, Yongsheng Li, Jianping Lu, Tao Pan, Na Ding, Zishan Wang, Tingting Shao, Jinwen Zhang, Lihua Wang, Xia Li: The mRNA related ceRNA–ceRNA landscape and significance across 20 major cancer types. Nucleic Acids Res. 2015 Sep 30;43(17):8169-82. PMID: 26304537 (co-first author)

2. Yongsheng Li, Hong Chen, Tao Pan, Chunjie Jiang, Zheng Zhao, Zishan Wang, Jinwen Zhang, Juan Xu, Xia Li: LncRNA Ontology: inferring lncRNA functions based on chromatin states and expression patterns. Oncotarget. 2015 Nov 24;6(37):39793-805. PMID: 26485761

3. Yongsheng Li, Juan Chen, Jinwen Zhang, Zishan Wang, Tingting Shao, Chunjie Jiang, Juan Xu, Xia Li: Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer. Oncotarget. 2015 Sep 22;6(28):25003-16. PMID: 26305674

4. Yongsheng Li, Tingting Shao, Chunjie Jiang, Jing Bai, Zishan Wang, Jinwen Zhang, Lili Zhang, Zheng Zhao, Juan Xu, Xia Li: Construction and analysis of dynamic transcription factor regulatory networks in the progression of glioma. Sci Rep. 2015 Nov 3;5:15953. PMID: 26526635

5. Yongsheng Li, Yunpeng Zhang, Shengli Li, Jianping Lu, Juan Chen, Yuan Wang, Yixue Li, Juan Xu, Xia Li: Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer. Sci Rep. 2015 Mar 5;5:8790. PMID: 25739977

6. Yongsheng Li, Cynthia Camarillo, Juan Xu, Tania BedardArana, Yun Xiao, Zheng Zhao, Hong Chen, Michael A Escamilla, Alfonso Ontiveros, Humberto Nicolini, Alvaro Jerez, Lewis P. Rubin, Xia Li, Chun Xu: Genome-Wide Methylome Analyses Reveal Novel Epigenetic Regulation Patterns in Schizophrenia and Bipolar Disorder. Biomed Res Int. 2015;2015:201587. PMID: 25734057

7. Zheng Zhao, Jing Bai, Aiwei Wu, Yuan Wang, Jinwen Zhang, Zishan Wang, Yongsheng Li, Juan Xu, Xia Li: Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. Database (Oxford). 2015 Sep 10;2015. PMID: 26363020 (co-corresponding author)

8. Tingting Shao, Aiwei Wu, Juan Chen, Hong Chen, Jianping Lu, Jing Bai, Yongsheng Li, Juan Xu, Xia Li: Identification of module biomarkers from the dysregulated ceRNA-ceRNA interaction network in lung adenocarcinoma. Mol Biosyst. 2015 Nov;11(11):3048-58. PMID: 26325208 (corresponding author)

9. Zhaoyu Liu, Lei Han, Yucui Dong, Yanli Tan, Yongsheng Li, Manli Zhao, Hui Xie, Huanyu Ju, He Wang, Yu Zhao, Qifan Zheng, Qixue Wang, Jun Su, Chuan Fang, Songbin Fu, Tao Jiang, Jiaren Liu, Xia Li, Chunsheng Kang, Huan Ren: EGFRvIII/integrin β3 interaction in hypoxic and vitronectinenriching microenvironment promote GBM progression and metastasis. Oncotarget. 2016 Jan 26;7(4):4680-94. PMID: 26717039

10. Tingting Shao, Zheng Zhao, Aiwei Wu, Jing Bai, Yongsheng Li, Hong Chen, Chunjie Jiang, Yuan Wang, Shengli Li, Letian Wang, Fengmin Zhang, Juan Xu, Xia Li: Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database. Mol Biosyst. 2015 May;11(5):1319-28. PMID: 25787233

Before 2014

1. Yongsheng Li, Shengli Li, Juan Chen, Tingting Shao, Chunjie Jiang, Yuan Wang, Hong Chen, Juan Xu, Xia Li: Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes. Hum Mol Genet. 2014 Oct 15;23(20):5378-93. PMID: 24871326

2. Jing Bai, Yongsheng Li, Tingting Shao, Zheng Zhao, Yuan Wang, Aiwei Wu, Hong Chen, Shengli Li, Chunjie Jiang, Juan Xu, Xia Li: Integrating analysis reveals microRNA-mediated pathway crosstalk among Crohn's disease, ulcerative colitis and colorectal cancer. Mol Biosyst. 2014 Jul 29;10(9):2317-28. PMID: 24949825 (co-first author)

3. Zheng Zhao, Yongsheng Li, Hong Chen, Jianping Lu, Peter M Thompson, Juan Chen, Zishan Wang, Juan Xu, Chun Xu, Xia Li: PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders. BMC Med Genomics. 2014 Dec 31;7:71. PMID: 25551368

4. Yongsheng Li, Juan Xu, Hong Chen, Jing Bai, Shengli Li, Zheng Zhao, Tingting Shao, Tao Jiang, Huan Ren, Chunsheng Kang, Xia Li: Comprehensive analysis of the functional microRNA–mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. Nucleic Acids Res. 2013 Dec;41(22):e203. PMID: 24194606

5. Yongsheng Li, Juan Xu, Huanyu Ju, Yun Xiao, Hong Chen, Junying Lv, Tingting Shao, Jing Bai, Yunpeng Zhang, Li Wang, Xishan Wang, Huan Ren, Xia Li: A network-based, integrative approach to identify genes with aberrant co-methylation in colorectal cancer. Mol Biosyst. 2014 Feb;10(2):180-90. PMID: 24317156

6. Yongsheng Li, Juan Xu, Hong Chen, Zheng Zhao, Shengli Li, Jing Bai, Aiwei Wu, Chunjie Jiang, Yuan Wang, Bin Su, Xia Li: Characterizing Genes with Distinct Methylation Patterns in the Context of Protein-Protein Interaction Network: Application to Human Brain Tissues. PLoS One. 2013 Jun 12;8(6):e65871. PMID: 23776563

7. Juan Xu, Yongsheng Li, Xiang Li, Chuanxing Li, Tingting Shao, Jing Bai, Hong Chen, Xia Li: Dissection of the potential characteristic of miRNA–miRNA functional synergistic regulations. Mol Biosyst. 2013 Feb 2;9(2):217-24. PMID: 23154827 (co-first author)

8. Chuanxing Li, Yongsheng Li, Juan Xu, Junying Lv, Ye Ma, Tingting Shao, Binsheng Gong, Renjie Tan, Yun Xiao, Xia Li: Disease-driven detection of differential inherited SNP modules from SNP network. Gene. 2011 Dec 10;489(2):119-29. PMID: 21920414 (co-first author)

9. Juan Xu, Chuan-Xing Li, Jun-Ying Lv, Yong-Sheng Li, Yun Xiao, Ting-Ting Shao, Xiao Huo, Xiang Li, Yan Zou, Qing-Lian Han, Xia Li, Li-Hua Wang, Huan Ren: Prioritizing Candidate Disease miRNAs by Topological Features in the miRNA Target-Dysregulated Network: Case Study of Prostate Cancer. Mol Cancer Ther. 2011 Oct;10(10):1857-66. PMID: 21768329

10. Juan Xu, Chuan-Xing Li, Yong-Sheng Li, Jun-Ying Lv, Ye Ma, Ting-Ting Shao, Liang-De Xu, Ying-Ying Wang, Lei Du, Yun-Peng Zhang, Wei Jiang, Chun-Quan Li, Yun Xiao, Xia Li: MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res. 2011 Feb;39(3):825-36. PMID: 20929877