​1) Journal articles:

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• Wenyu Zhang, Guy Reeves, and Diethard Tautz. Identification of a genetic network for an ecologically relevant behavioral phenotype in Drosophila melanogaster. Mol Ecol. 2019 Dec 23. doi: 10.1111/mec.15341. [Link]

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• Wenyu Zhang, Yuanxiao Gao, Manyuan Long, and Bairong Shen. Origination and evolution of orphan genes and  de novo  genes in the genome of Caenorhabditis elegans. Sci China Life Sci. 2019 Apr;62(4):579-593. doi: 10.1007/s11427-019-9482-0. [Link]

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• Jian Zu, Yuexi Gu, Yu Li, Chentong Li, Wenyu Zhang, Yong E. Zhang, UnJin Lee, Li Zhang, and Manyuan Long. Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures  in human ancestors. Sci China Life Sci. 2019 Apr;62(4):594-608. doi: 10.1007/s11427-019-9483-6. [Link]

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• Wenyu Zhang, Patrick Landback, Andrea R Gschwend, Bairong Shen, and Manyuan Long. New genes drive the evolution  of gene interaction networks in the human and mouse genomes. Genome Biol. 2015 Oct 1;16:202. doi: 10.1186/s13059-015-0772-4. [Link]

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• Jin Zhu(*), Sugui Wang(*), Wenyu Zhang(*), Junyi Qiu, Yuxi Shan, Dongrong Yang, and Bairong Shen. Screening key  microRNAs for castration-resistant prostate cancer based on miRNA/mRNA functional  synergistic network. Oncotarget.  2015 Dec 22; 6(41):43819-30. doi: 10.18632/oncotarget.6102. [Link]

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• Wenying Yan, Lihua Xu, Zhandong Sun, Yuxin Lin, Wenyu Zhang, Jiajia Chen, Shaoyan Hu, and Bairong Shen. MicroRNA  biomarker identification for pediatric acute myeloid leukemia based on a novel bioinformatics model. Oncotarget. 2015 Sep 22;6(28):26424-36. doi: 10.18632/oncotarget.4459. [Link]

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• Wenyu Zhang(*), Jin Zang(*), Xinhua Jing, Zhandong Sun, Wenying Yan, Dongrong Yang, Feng Guo, and Bairong Shen.  Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. J Transl Med. 2014 Mar 11;12:66. doi: 10.1186/1479-5876-12-66. [Link]

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• Wenying Yan, Maomin Sun, Guang Hu, Jianhong Zhou, Wenyu Zhang, Jiajia Chen, Biao Chen, and Bairong Shen. Amino  acid contact energy networks impact protein structure and evolution. J Theor Biol. 2014 Aug 21;355:95-104. doi: 10.1016/ j.jtbi. 2014.03.032. [Link]

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• Jing Shang, Fei Zhu, Wanwipa Vongsangnak, Yifei Tang, Wenyu Zhang, and Bairong Shen. Evaluation and comparison of multiple aligners for next-generation sequencing data analysis. Biomed Res Int. 2014:309650. doi: 10.1155/2014/309650.  [Link]

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• Jiajia Chen, Daqing Zhang, Wenyu Zhang, Yifei Tang, Wenying Yan, Lingchuan Guo, and Bairong Shen. Clear cell renal  cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis. J Transl Med. 2013 Jul 10;11:169. doi: 10.1186/1479-5876-11-169. [Link]

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• Wenyu Zhang, Jiajia Chen, Yang Yang, Yifei Tang, Jing Shang, and Bairong Shen. A practical comparison of de novo  genome assembly software tools for next-generation sequencing technologies. PLoS One. 2011 Mar 14;6(3):e17915. doi: 10.1371/ journal.pone.0017915. [Link]

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• Li- Ping Gan, Wen-Yu Zhang, Yan-Shan Niu, Li Xu, Jian Xi, Ming-Ming Ji, and Shi-Qing Xu. Construction and application of an electronic spatio-temporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori. J Insect Sci. 2010;10:114. doi: 10.1673/031.010.11401. [Link]

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  (*): co-first authorship

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​2) Book chapters:

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• Wenyu Zhang (2017). Chapter 5: Short reads assembly; Chapter 10: Single cell sequencing data analysis. Bioinformatics for Deep Sequencing Data with Examples. (In Chinese). SCIENCE PRESS. [Link to the book] [Link to the examples]

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• Yuxin Lin, Zhandong Sun, Wenyu Zhang, Wenying Yan, Jiajia Chen, and Bairong Shen. (2015). Chapter 1: Proceedings on  the bioinformatics studies of microRNA biomarkers. Annual Reviews on new biology 2015. (In Chinese). SCIENCE PRESS. [Link]

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• Wenyu Zhang and Bairong Shen (2013). Chapter 8: Identification of Cancer MicroRNA Biomarkers Based on miRNA–mRNA Network. Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases. Translational Bioinformatics Volume 4. Springer, Dordrecht. [Link]

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3) PhD thesis:

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• Wenyu Zhang (2015). The application of biological molecular network analysis on the discovery of cancer diagnostic  biomarkers and the exploration of gene-gene interaction network evolution mechanisms. (In Chinese). [Link]