Gaoshan

Shan Gao, majoring in bioinformatics, woks as an associate professor in College of Life Sciences, Nankai University. Until March 26th 2017, he published 64 academic papers including 41 SCI and 5 EI indexed papers, which covered the research fields of plant, animal, bacteria, virus, cancer, protein, RNA and genome. His current interest is to use high throughout omics data analysis to answer fundamental questions in biological sciences.

1995/09 -- 2000/07：National University of Defense Technology | Electronic Engineering | Bachelor 2004/09 -- 2007/07：Shanghai University | Bioinformatics | Master 2007/09 -- 2010/06：Nankai University | Bioinformatics | Doctor

2010/07 –2011/08： Kansas University | Bioinformatics | PostDoctor 2011/08 –2014/08： Cornell University | Bioinformatics | PostDoctor 2014/08 –Now： Nankai University | College of Life Sciences |Associate Professor

High throughout omics data analysis based on the 2nd or 3rd sequencing technology, including genomics data, RNA-seq or small RNA-seq data.

Long non-coding RNAs and data analysis in single-Cell transcriptome sequencing

Bioinformatics in cancer, viruses or other related fields.

Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Haishuo Ji, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan, Shan Gao*. NormExpression: an R package to normalize gene expression data using evaluated methods. Frontiers in Genetics 2019, In revision. (2区，IF= 4.151)

Haishuo Ji, Xiaofeng Xu, Xiufeng Jin, Hong Yin, Jianxun Luo, Guangyuan Liu, Qiang Zhao, Ze Chen, Wenjun Bu, Shan Gao*. Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region. RNA biology 2019: https://doi.org/10.1080/15476286.2019.1591035. (2区，IF= 5.216)

Xiaofeng Xu, Haishuo Ji, Zhi Cheng, Xiufeng Jin, Xue Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen and Shan Gao*. Using pan RNA-seq analysis to reveal the ubiquitous existence of 5' and 3' end small RNAs. Frontiers in Genetics 2019: https://doi.org/10.3389/fgene.2019.00105. (2区，IF= 4.151)

Ze. Chen, Xiaofeng Xu, Yufeng Wang, Jinlong Bei, Xiufeng Jin, Weihao Dou, Haishuo Ji, Yujie Duan, Xiaojun Yang and Shan Gao*. DNA segments of African Swine Fever Virus detected for the first time in hard ticks from sheep and bovines. Systematic & Applied Acarology, 2019, 24(1): 180-184. (4区，IF= 1.696)

Chang Liu, Ze Chen, Yue Hu, Haishuo Ji, Deshui Yu, Wenyuan Shen, Siyu Li, Jishou Ruan, Wenjun Bu and Shan Gao*. Complemented Palindromic Small RNAs First Discovered from SARS Coronavirus. Genes 2018, 9(9):442. (3区，IF= 3.191)

Zhi Cheng, Yu Sun, Xiaoran Niu, Yingchun Shang, Jishou Ruan, Ze Chen, Shan Gao* and Tao Zhang. Gene expression profiling reveals U1 snRNA regulates cancer gene expression. Oncotarget 2017, 8(68):112867-112874. (1区，IF= 5.168)

Zhi Cheng, Yingchun Shang, Shan Gao, Tao Zhang. Overexpression of U1 snRNA induces decrease of U1 spliceosome function associated with Alzheimer’s disease. Journal of neurogenetics 2017:1 (4区，IF= 2.291)

Shan Gao^#, Xiaoxuan Tian, Hong Chang, Yu Sun, Zhenfeng Wu, Zhi Cheng, Pengzhi Dong, Qiang Zhao, Jishou Ruan, and Wenjun Bu. Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data. Mitochondrion 2017, 38:41-47. (2区，IF= 3.704)

Xiaoran Niu, Yu Sun, Ze Chen, Rugang Li, Chellappan Padmanabhan, Jishou Ruan, Jan F. Kreuze, Kaishu Ling, Zhangjun Fei and Shan Gao*. Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses. Genes 2017, 8(6):163. (3区，IF= 3.6)

Ze Chen, Yu Sun, Xiaojun Yang, Zhenfeng Wu, Kaifei Guo, Xiaoran Niu, Qingsong Wang, Jishou Ruan, Wenjun Bu, Shan Gao*. Two featured series of rRNA-derived RNA fragments (rRFs) constitute a novel class of small RNAs. PLoS ONE 2017, 12(4):e0176458. (3区，IF= 2.806)

Yi Zheng, Shan Gao^#, Chellappan Padmanabhan, Rugang Li, Marco Galvez, Dina Gutierrez, Segundo Fuentes, Kai-Shu Ling, Jan Kreuze, Zhangjun Fei. VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 2016, 500(2017):130-138. (3区，IF= 3.353)

Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jiankun Xie, Shan Gao*. Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. BMC Plant Biology 2016, 16(1):103. (2区，IF= 3.631)

Shan Gao^#, Yipeng Ren, Yu Sun, Zhenfeng Wu, Jishou Ruan, Bingjun He, Tao Zhang, Xin Yu, Xiaoxuan Tian, Wenjun Bu. PacBio Full-length transcriptome profiling of insect mitochondrial gene expression. RNA biology 2016, 13(9): 820-825. (2区，IF= 4.076)

Yanlong Wang, Bin Hu, Shipeng Du, Shan Gao, Xiwen Chen, Defu Chen. Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli. PLoS ONE 2016, 11(5):e0153640. (3区，IF= 3.057)

Qinghe Cao, Ang Li, Jinyang Chen, Yu Sun, Jun Tang, An Zhang, Zhilin Zhou, Donglan Zhao, Daifu Ma, Shan Gao*. Transcriptome sequencing of the sweet potato progenitor (Ipomoea trifida (H.B.K.) G. Don.) and discovery of drought tolerance genes. Tropical Plant Biology 2016, 9(2):63-72. (4区，IF= 0.562)

Fang Wang, Yu Sun, Jishou Ruan, Rui Chen, Xin Chen, Chengjie Chen, Jan F. Kreuze, ZhangJun Fei, Xiao Zhu, Shan Gao*. Using small RNA deep sequencing data to detect human viruses. BioMed Research International 2016, 2016 (2016):2596782. (4区，IF= 2.134)

Yuanzhi Wang, Zhen Wang, Xin Chen, Hui Zhang, Fei Guo, Ke Zhang, Hanping Feng, Wenyi Gu, Changxin Wu, Lei Ma, Tiansen Li, Chuangfu Chen, Shan Gao*. The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection. Genes 2016, 7(2):7. (4区，IF= 2.165)

Dangwei Zhou, Shan Gao^#, Huan Wang, Tianxiang Lei, Jianwei Shen, Jie Gao, Shilong Chen, Jia Yin, Jianquan Liu. De novo sequencing transcriptome of endemic Gentiana straminea (Gentianaceae) to identify genes involved in the biosynthesis of active ingredients. Gene 2016, 575(1):160-170. (4区，IF= 2.319)

Heather M. Holl, Shan Gao, Zhangjun Fei, Caroline Andrews, Samantha A. Brooks. Generation of a de novo transcriptome from equine lamellar tissue. BMC Genomics 2015, 16(1):739. (2区，IF= 3.867)

Ari Feder, Joseph Burger, Shan Gao, Efraim Lewinsohn, Nurit Katzir, Arthur A.Schaffer, Ayala Meir, Rachel Davidovich-Rikanati, Vitaly Portnoy, Amit Gal-On, Zhangjun Fei, Yehezkel Kashi, Yaakov Tadmor. A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Muskmelon. Plant Physiology 2015, 169(3):1714-1726. (1区，IF= 6.28)

Ning Zhang, Shan Gao^#, Guangyou Duan, Yuanming Feng, Jishou Ruan, Tao Zhang. SRD: A Universal Software Tool for DNA/Protein Sequence Relationship Visualization Based on Undirected Graphs. Current Bioinformatics 2015, 10(5):69-78. (4区，IF= 0.77)

Yunru Chen, Silin Zhong, Zhangjun Fei, Shan Gao, Shiying Zhang, Zhaofei Li, Ping Wang, Gary W. Blissard. Transcriptome Responses of the Host Trichoplusia ni to Infection by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus. Journal of Virology 2014, 88(23):13781-13797. (2区，IF= 4.439)

Xiao Zhu, Shan Gao^#, Hui Luo, Wenguo Fan, Shicheng Guo, Hong Yao, Shuilong Leng, Zhenhua Xu, Tao Tao, Xingyan Liu, Jingfang Zhang, Ming Zhang, Dongpei Li, Qin Xiao. 9q33.3. A Stress-Related Chromosome Region,Contributes to Reducing Lung Squamous Cell Carcinoma Risk. Journal of Thoracic Oncology 2014, 9(7):1041-1047. (1区，IF= 5.282)

Yudong Cai, Tao Huang, Lei Chen, Shan Gao, Ning Zhang. Novel Computational Methods and Tools in Biomedicine and Biopharmacy. Computational and Mathematical Methods in Medicine 2014, 2014:127515. (4区，IF= 0.766)

Yingjie Yang, Chao Ma, Yanjie Xu, Qian Wei, Muhammad Imtiaz, Haibo Lan, Shan Gao, Lina Cheng, Meiyan Wang, Zhangjun Fei, Bo Hong, Junping Gao. A Zinc Finger Protein Regulates Flowering Time and Abiotic Stress Tolerance in Chrysanthemum by Modulating Gibberellins Biosynthesis. Plant Cell 2014, 26(5):2038-2054. (1区，IF= 9.338)

Shunmei Chen, Shan Gao^#, Dongqiang Cheng, Jingfei Huang. The characterization and comparison of amyloidogenic segments and non-amyloidogenic segments shed light on amyloid formation. Biochemical and Biophysical Research Communications 2014, 447(2):255-262. (3区，IF= 2.297)

Zhang Ning, Shan Gao^#, Chen Lei, Ruan Jishou. Using Multitask Learning Methods to Investigate Signal Peptides and Signal Anchors. Current Bioinformatics 2013, 8(5):533-538. (4区，IF= 1.726)

Yaping Fang, Shan Gao^#, David Tai, C Russell Middaugh, Jianwen Fang. Identification of properties important to protein aggregation using feature selection. BMC Bioinformatics 2013, 14(1):314. (3区，IF= 2.672)

Yanjie Xu, Shan Gao^#, Yingjie Yang, Mingyun Huang, Lina Cheng, Qian Wei, Zhangjun Fei, Junping Gao, Bo Hong. Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genomics 2013, 14(1):662. (2区，IF= 4.041)

Shan Gao^#, Shuo Xu, Yaping Fang, Jianwen Fang. Prediction of core cancer genes using multi-task classification framework. Journal of Theoretical Biology 2013, 317:62-70. (3区，IF= 2.303)

Shan Gao, one of the authors. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 2013, 45(1):51-58. (1区，IF= 35.209)

Ning Zhang, Yuanming Feng, Shan Gao, Jishou Ruan, Tao Zhang. New Insights Regarding Protein Folding As Learned From Beta-Sheets. EXCLI Journal 2012, 11:543-555. (4区，IF= 1.923)

Ning Zhang, Biqing Li, Shan Gao, Jishou Ruan, Yudong Cai. Computational prediction and analysis of protein γ-carboxylation sites based on a random forest method. Mol. BioSyst. 2012, 8(11):2946-2955. (2区，IF= 3.35)

Shan Gao^#, Shuo Xu, Yaping Fang, Jianwen Fang. Using multitask classification methods to investigate the kinase-specific phosphorylation sites. Proteome Science 2012, 10(Suppl1):S7. (3区，IF= 2.42)

Shan Gao, one of the authors in The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485(7400):635-641. (1区，IF= 38.597)

Rugang Li, Shan Gao^#, Alvaro G. Hernandez, W. Patrick Wechter, Zhangjun Fei, Kaishu Ling. Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation. PLoS ONE 2012, 7(5):e37127. (2区，IF= 3.73)

Ning Zhang, Guangyou Duan, Shan Gao, Jishou Ruan, Tao Zhang. Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines. Journal of Theoretical Biology 2010, 263(3):360-368. (3区，IF= 2.371)

Ning Zhang, Jishou Ruan, Guangyou Duan, Shan Gao, Tao Zhang. The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of β-strands. Biochemical and Biophysical Research Communications 2009, 386(3):537-543. (3区，IF= 2.548)

Shan Gao^#, Ning Zhang, Guangyou Duan, Zhuoyang, Jishou Ruan, Tao Zhang. Prediction of function changes associated with single-point protein mutations using support vector machines (SVMs). Human Mutation 2009, 30(8):1161-1166. (1区，IF= 6.887)