发表论文
生物信息学
Shaohang Xu
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许少行，现任深圳迪谱生物科技有限公司首席技术官，深圳市盐田区“梧桐人才”。毕业于天津大学，曾在华大基因从事蛋白组学生物信息相关工作7年。参与“国际人类染色体蛋白组计划”、国家科技合作专项“中国人类蛋白组学数据的知识发现”等重大项目，发表SCI论文20余篇，申请软件著作权6项，设计、研发科技服务商业流程15套。撰写SapFinder、PGA、PPIP等蛋白基因组软件。
软件类
Rong, M., Zhou, B., Zhou, R., Liao, Q., Zeng, Y., Xu, S.(co-correspondence) and Liu, Z., 2018. PPIP: Automated Software for Identification of Bioactive Endogenous Peptides. Journal of proteome research, 18(2), pp.721-727.
Bo Wen, Shaohang Xu (co-first), Gloria M. Sheynkman, Qiang Feng, Liang Lin, Quanhui Wang, Xun Xu, Jun Wang, Siqi Liu: SapFinder: An R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. Bioinformatics 07/2014; 30(21).
Bo Wen, Shaohang Xu (co-first) et al: PGA: An R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. BMC Bioinformatics 12/2016; 17(1).
Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu: Improvement of peptide identification with considering the abundance of mRNA and peptide. BMC Bioinformatics 12/2017; 18(1)., DOI:10.1186/s12859-017-1491-5
Bo Wen, Chaoqin Du, Guilin Li, Fawaz Ghali, Andrew R Jones, Lukas Käll, Shaohang Xu, Ruo Zhou, Zhe Ren, Qiang Feng, Xun Xu, Jun Wang: IPeak: An open source tool to combine results from multiple MS/MS search engines. Proteomics 05/2015; 15(17).
应用类
Shaohang Xu, Ruo Zhou et al: Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes. Journal of Proteome Research 10/2015; 14(12).
Jiao Guo, Shaohang Xu (co-first) et al: Drug Resistance in Colorectal Cancer Cell Lines is Partially Associated with Aneuploidy Status in Light of Profiling Gene Expression. Journal of Proteome Research 07/2016; 15(11).
Chengpu Zhang, Ning Li, Linhui Zhai, Shaohang Xu (co-first), Xiaohui Liu, Yizhi Cui et al: Systematic Analysis of Missing Proteins Provides Clues to Help Define All of the Protein-Coding Genes on Human Chromosome 1. Journal of Proteome Research 11/2013; 13(1).
Yang Zhang, Guoquan Yan, Linhui Zhai, Shaohang Xu (co-first), Huali Shen, Jun Yao et al: Proteome Atlas of Human Chromosome 8 and Its Multiple 8p Deficiencies in Tumorigenesis of the Stomach, Colon, and Liver. Journal of Proteome Research 12/2012; 12(1).
Nannan Kong, Yang Zhou, Shaohang Xu, Yamei Deng, Yang Fan, Yue Zhang, Zhe Ren, Liang Lin, Yan Ren, Quanhui Wang, Jin Zi, Bo Wen, Siqi Liu: Assessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19. Journal of Proteome Research 10/2015; 14(12).
Yang Fan, Yue Zhang, Shaohang Xu, Nannan Kong, Yang Zhou, Zhe Ren, Yamei Deng, Liang Lin, Yan Ren, Quanhui Wang, Jin Zi, Bo Wen, Siqi Liu: Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected. Journal of Proteome Research 08/2015; 14(9).
Yao Zhang, Qidan Li, Feilin Wu, Ruo Zhou, Yingzi Qi, Na Su, Lingsheng Chen, Shaohang Xu, Tao Jiang et al: The Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins.. Journal of Proteome Research 08/2015; 14(9).
Quanhui Wang, Bo Wen, Tong Wang, Zhongwei Xu, Xuefei Yin, Shaohang Xu, Zhe Ren, Guixue Hou, Ruo Zhou et al: Omics Evidence: Single Nucleotide Variants Transmissions on Chromosome 20 in Liver Cancer Cell Lines. Journal of Proteome Research 11/2013; 13(1).
Quanhui Wang, Bo Wen, Guangrong Yan, Junying Wei, Liqi Xie, Shaohang Xu, Dahai Jiang et al: Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines. Journal of Proteome Research 12/2012; 12(1).
技术类
DIA定量蛋白组学
Jin Zi, Shenyan Zhang, Ruo Zhou, Baojin Zhou, Shaohang Xu, Guixue Hou, Fengji Tan, Bo Wen, Quanhui Wang, Liang Lin, Siqi Liu: Expansion of the Ion Library for Mining SWATH-MS Data through Fractionation Proteomics. Analytical Chemistry 06/2014; 86(15)., DOI:10.1021/ac501828a
Guixue Hou, Xiaomin Lou, Yulin Sun, Shaohang Xu, Jin Zi, Quanhui Wang, Baojin Zhou, Bo Han, Lin Wu, Xiaohang Zhao, Liang Lin, Siqi Liu: Biomarker Discovery and Verification of Esophageal Squamous Cell Carcinoma Using Integration of SWATH/MRM. Journal of Proteome Research 07/2015; 14(9).
MRM定量目标蛋白定量
S. Zhang, B. Wen, B. Zhou, L. Yang, C. Cha, S. Xu, X. Qiu, Q. Wang, H. Sun, X. Lou, J. Zi, Y. Zhang, L. Lin, S. Liu: Quantitative analysis of the human AKR family members in cancer cell lines using the mTRAQ/MRM approach.Journal of Proteome Research (2013) 12:5 (2022-2033)
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周宝津，现任深圳迪谱生物科技有限公司总经理，深圳市盐田区“梧桐人才”，香港中文大学基因组学与生物信息学硕士。曾在华大基因从事质谱相关工作达7年，致力开拓质谱技术在蛋白组、代谢组的应用。在Science，Genome biology，Journal of proteome research等杂志发表文章20余篇，申请软件著作权5份，专利2份。
应用类
iTRAQ定量蛋白组学
Li, Y.H., Sun, W., Zhou, B.J.(co-first), Rosenstein, A., Zhao, J., Wang, J. and Bian, Z.X., 2019. iTRAQ-based pharmacoproteomics reveals potential targets of berberine, a promising therapy for ulcerative colitis. European journal of pharmacology, 850, pp.167-179.
Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., ... Zhou, B., et al. (2017). Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science, 355(6329), eaaf4791.
DIA定量蛋白组学
Zi, J., Zhang, S., Zhou, R., Zhou, B., Xu, S., Hou, G., et al. (2014). Expansion of the ion library for mining SWATH-MS data through fractionation proteomics. Analytical chemistry, 86(15), 7242-7246.
Hou, G., Lou, X., Sun, Y., Xu, S., Zi, J., Wang, Q., Zhou, B., et al. (2015). Biomarker discovery and verification of esophageal squamous cell carcinoma using integration of SWATH/MRM. Journal of proteome research, 14(9), 3793-3803.
MRM目标蛋白定量
Zhang, S., Wen, B., Zhou, B., Yang, L., Cha, C., Xu, S., et al (2013). Quantitative analysis of the human AKR family members in cancer cell lines using the mTRAQ/MRM approach. Journal of proteome research, 12(5), 2022-2033.
Zi, J., Zhang, J., Wang, Q., Zhou, B., et al. (2013). Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One, 8(9), e74229.
非靶向代谢组
Yin, N.W., Wang, S.X., Jia, L.D., Zhu, M.C., Yang, J., Zhou, B.J., Yin, J.M., Lu, K., Wang, R., Li, J.N. and Qu, C.M., 2019. Identification and Characterization of Major Constituents in Different-Colored Rapeseed Petals by UPLC–HESI-MS/MS. Journal of agricultural and food chemistry, 67(40), pp.11053-11065.
Qu C, Yin N, Chen S, Wang S, Chen X, Zhao H, Shen S, Fu F, Zhou B, Xu X, Liu L, Lu K, Li J. Comparative Analysis of the Metabolic Profiles of Yellow- versus Black-Seeded Rapeseed Using UPLC-HESI-MS/MS and Transcriptome Analysis. J Agric Food Chem. 2020 Mar 11;68(10):3033-3049
Ding W, Liu J, Zhou X, Miao Q, Zheng H, Zhou B, Dou G, Tong Y, Long Y, Su L. Clinical Multi-Omics Study on the Gut Microbiota in Critically Ill Patients After Cardiovascular Surgery Combined With Cardiopulmonary Bypass With or Without Sepsis (MUL-GM-CSCPB Study): A Prospective Study Protocol. Front Med (Lausanne). 2020 Jul 8;7:269
脂质组
Liu H, Hong Y, Lu Q, Li H, Gu J, Ren L, Deng L, Zhou B, Chen X, Liang X. Integrated Analysis of Comparative Lipidomics and Proteomics Reveals the Dynamic Changes of Lipid Molecular Species in High-Oleic Acid Peanut Seed. J Agric Food Chem. 2020 Jan 8;68(1):426-438.
靶向代谢定量
Gao, F., Xia, Y., Wang, J., Luo, H., Gao, Z., Han, X., Zhou, B., et al.(2013). Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation. Epigenetics, 8(4), 421-430.
Gao, F., Xia, Y., Wang, J., Lin, Z., Ou, Y., Liu, X., Zhou, B., et al.(2014). Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma. Genome biology, 15(12), 533.
多组学联合分析
蛋白基因组
Rong, M.,Zhou, B.(co-first), Zhou, R., Liao, Q., Zeng, Y., Xu, S. and Liu, Z., 2018. PPIP: Automated Software for Identification of Bioactive Endogenous Peptides. Journal of proteome research, 18(2), pp.721-727.
Li H, Zhou R, Xu S, Chen X, Hong Y, Lu Q, Liu H, Zhou B.(co-respond), Liang X. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow. J Proteome Res. 2020 Jun 5;19(6):2226-2235
蛋白组与转录组联合分析：
Chen, H., Jin, J., Zhang, H., Wang, Y., Li, Q., Zou, Y., Huang, X., Zhou, B., Zhou, R. and Ding, Y., 2019. Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S. International journal of molecular sciences, 20(18), p.4542.
宏基因组与宏蛋白组联合分析
Zhong, H., Ren, H., Lu, Y., Fang, C., Hou, G., Yang, Z., Chen, B., Yang, F., Zhao, Y., Shi, Z. and Zhou, B., et.al,2019. Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics. EBioMedicine, 47, pp.373-383.
Ruo Zhou
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周若，现任深圳迪谱生物科技有限公司总监。深圳市盐田区“梧桐人才”。毕业于北京理工大学，曾在华大基因从事蛋白组学生物信息相关工作7年。参与“国际人类染色体蛋白组计划”、国家科技合作专项“中国人类蛋白组学数据的知识发现”等重大项目，发表SCI论文20余篇。
应用类
蛋白基因组（人类染色体蛋白组项目CHPP）
Wang, Q., Wen, B., Yan, G., Wei, J., Xie, L., Xu, S., Zhou R, ... & Zhang, J. (2012). Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines. Journal of proteome research, 12(1), 151-161.
Quanhui Wang, Bo Wen, Tong Wang, Zhongwei Xu, Xuefei Yin, Shaohang Xu, Zhe Ren, Guixue Hou, Ruo Zhou et al: Omics Evidence: Single Nucleotide Variants Transmissions on Chromosome 20 in Liver Cancer Cell Lines. Journal of Proteome Research 11/2013; 13(1).
Zhang, C., Li, N., Zhai, L., Xu, S., Liu, X., Cui, Y., Zhou R, ... & Fan, F. (2013). Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1. Journal of proteome research, 13(1), 114-125.
Xu S, Zhou R(co-first), Ren Z, et al. Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes[J]. Journal of proteome research, 2015, 14(12): 4976-4984.
Li, S., He, Y., Lin, Z., Xu, S., Zhou, R., Liang, F., ... & Ren, Y. (2017). Digging more missing proteins using an enrichment approach with ProteoMiner. Journal of proteome research, 16(12), 4330-4339.
蛋白基因组（拟南芥）
Zhu, F. Y., Chen, M. X., Ye, N. H., Shi, L., Ma, K. L., Yang, J. F., Zhou,R... & Fan, G. Y. (2017). Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. The Plant Journal.
蛋白基因组（水稻）
Ren, Z., Qi, D., Pugh, N., Li, K., Wen, B., Zhou, R., ... & Jones, A. R. (2018). Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets. Molecular & Cellular Proteomics
Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A. R., Zhou R,... & Wen, B. (2019). Rapid evolution of protein diversity by de novo origination in Oryza. Nature ecology & evolution, 3(4), 679.
软件类
Wen, B., Zhou, R.(co-first), Feng, Q., Wang, Q., Wang, J., & Liu, S. (2014). IQuant: an automated pipeline for quantitative proteomics based upon isobaric tags. Proteomics, 14(20), 2280-2285.
Wen, B., Xu, S., Zhou, R., Zhang, B., Wang, X., Liu, X., ... & Liu, S. (2016). PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. BMC bioinformatics, 17(1), 244.
Wen, B., Du, C., Li, G., Ghali, F., Jones, A. R., Käll, L., Xu, S., Zhou, R., Ren, Z., Feng, Q., Xu, X. and Wang, J. (2015), IPeak: An open source tool to combine results from multiple MS/MS search engines. Proteomics, 15: 2916–2920. doi:10.1002/pmic.201400208
应用类
Su L, Cao L, Zhou R(co-first), Jiang Z, Xiao K, Kong W, et al. (2013) Identification of Novel Biomarkers for Sepsis Prognosis via Urinary Proteomic Analysis Using iTRAQ Labeling and 2D-LC-MS/MS. PLoS ONE 8(1): e54237. doi:10.1371/journal.pone.0054237
Su L, Zhou R(co-first), Liu C, et al. Urinary proteomics analysis for sepsis biomarkers with iTRAQ labeling and two-dimensional liquid chromatography–tandem mass spectrometry[J]. Journal of trauma and acute care surgery, 2013, 74(3): 940-945.
Yao Zhang, Qidan Li, Feilin Wu, Zhou R(co-first), Yingzi Qi, Na Su, Lingsheng Chen, Shaohang Xu, Tao Jiang et al: The Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins.. Journal of Proteome Research 08/2015; 14(9).
Zi J, Zhang S, Zhou R, et al. Expansion of the ion library for mining SWATH-MS data through fractionation proteomics[J]. Analytical chemistry, 2014, 86(15): 7242-7246.
Guo, J., Xu, S., Huang, X., Li, L., Zhang, C., Pan, Q., Zhou, R., ... & Wu, L. (2016). Drug Resistance in colorectal cancer cell lines is partially associated with aneuploidy status in light of profiling gene expression. Journal of proteome research, 15(11), 4047-4059.
Chen, H., Jin, J., Zhang, H., Wang, Y., Li, Q., Zou, Y.,Zhou R,... & Ding, Y. (2019). Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S. International journal of molecular sciences, 20(18), 4542.
Rong M, Zhou B, Zhou R, et al. PPIP: Automated Software for Identification of Bioactive Endogenous Peptides[J]. Journal of proteome research, 2018, 18(2): 721-727.
