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2017 (#共同作者,*通讯作者)

Chuan-Le Xiao#*, Ying Chen#, Shang-qian Xie, Kai-Ning Chen, Yan Wang, Feng Luo*, and Zhi Xie*, MECAT: an ultra-fast mapping, error correction, and de novo assembly tool kit for single-molecule sequencing reads, Nature Methods,2017, doi:10.1038/nmeth.4432.(Impact factor: 25.06)

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Zhiwen Jiang#, Jiaqi Yang#, Aimei Dai#, Yuming Wang, Wei Li, Zhi Xie*, Ribosome Profiling Reveals Translational Regulation of Mammalian Cells in Response to Hypoxic Stress, BMC Genomics, 2017 18:638, DOI 10.1186/s12864-017-3996-8.(Impact factor: 3.73)

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Hongwei Wang#, Yan Wang#, Zhi Xie*,Computational resources for ribosome profiling: from database to web server and software. Briefings in Bioinformatics, 2017, 1–12, doi: 10.1093/bib/bbx093.(Impact factor: 8.39)

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Chensi Cao#, Feng Liu#, Hai Tan#, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou*, Xiaochen Bo*, Zhi Xie*,Deep Learning and its Applications in Biomedicine. Genomics, Proteomics & Bioinformatics (In Press)(Impact factor: 2.11)

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Yizhao Luan,Jingxing Ou,Vincent P. Kunze,Fengyu Qiao,Yan Wang,Lai Wei,Wei Li,Zhi Xie*,Integrated transcriptomic and metabolomic analysis reveals adaptive changes of hibernating retinas. J Cell Physiol. 2017 May 25. doi: 10.1002/jcp.26030(Impact factor: 4.08)

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Alice Cheng, Zhi Xie,Challenges in Orphan Drug Development and Regulatory Policy in China,Orphanet J Rare Dis. 2017 Jan 18;12(1):13. doi: 10.1186/s13023-017-0568-6.(Impact factor: 3.29)

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Yang Z, Hou Y, Hao T, Rho HS, Wan J, Luan Y, Gao X, Yao J, Pan A, Xie Z, Qian J, Liao W, Zhu H, Zhou X*,A human proteome array approach to identifying key host proteins targeted by Toxoplasma kinase ROP18, Mol Cell Proteomics. 2017 Jan 13. pii: mcp.M116.063602. doi: 10.1074/mcp.M116.063602. (Impact factor: 5.912)

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Xing F#, Luan Y#, Cai J, Wu S, Mai J, Gu J, Zhang H, Li K, Lin Y, Xiao X, Liang J, Li Y, Chen W, Tan Y, Sheng L, Lu B, Lu W, Gao M, Qiu P, Su X, Yin W, Hu J, Chen Z, Sai K, Wang J, Chen F, Chen Y, Zhu S, Liu D, Cheng S, Xie Z*, Zhu W*, Yan G*. The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes, Cell Rep. 2017 Jan 10;18(2):468-481. doi: 10.1016/j.celrep.2016.12.037.(Impact factor: 8.28)

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2016

Aimei Dai#, Shuai Cao#, Pragyesh Dhungel#, Yizhao Luan, Yizhi Liu, Zhi Xie*, Zhilong Yang*, Ribosome Profiling Reveals Translational Upregulation of Cellular Oxidative Phosphorylation mRNAs During Vaccinia Virus-induced Host Shutoff, Journal of Virology, J Virol. 2016 Dec 21. pii: JVI.01858-16. doi: 10.1128/JVI.01858-16.(Impact factor: 4.6)

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Wenyan Hu#, Shengguo Li#, Ji Yeon Park, Sridhar Boppana, Ting Ni, Miaoxin Li, Jun Zhu, Bin Tian, Zhi Xie*, and Mengqing Xiang*, Dynamic landscape of alternative polyadenylation during retinal development, Cellular Molecular Life Science, Cell Mol Life Sci. 2016 Dec 18 (Impact factor: 5.69)

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Hongwei Wang#, Yan Wang#, Shangqian Xie and Zhi Xie*, Global and cell-type specific properties of lincRNAs with ribosome occupancy, Nucleic Acids Research,10.1093.gkw909 (Impact factor: 10.161)

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Pohao Ye#, Yizhao Luan#, Chuanle Xiao#, Kaining Chen, Yizhi Liu, Zhi Xie*, MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing, Nucleic Acids Research,10.1093.gkw950 (Impact factor: 10.161)

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Yingfei Wang*, Ran An, George K. Umanah, Hyejin Park, Kalyani Nambiar, Stephen M. Eacker, BongWoo Kim, Lei Bao, Maged M. Harraz, Calvin Chang, Rong Chen, Jennifer E. Wang, Tae-In Kam, Jun Seop Jeong, Zhi Xie, Stewart Neifert, Jiang Qian, Shaida A. Andrabi, Seth Blackshaw, Heng Zhu, Hongjun Song, Guo-li Ming, Valina L. Dawson*, Ted M. Dawson*, A Nuclease that Mediates Cell Death induced by DNA Damage and Poly(ADP-ribose) Polymerase-1, Science, Oct 7;354(6308). (Impact factor: 34.661)

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The MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report, Microbiome, 2016, 4:24.(impact factor: 9.00)

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2015

Woodard C, Liao G, Goodwin CR, Hu J, Xie Z, Dos Reis TF, Newman R, RhoH, Qian J, Zhu H, Hayward SD. A Screen for Extracellular Signal-Regulated Kinase-Primed GlycogenSynthase Kinase 3 Substrates Identifies the p53 Inhibitor iASPP.J Virol. 2015 Sep;89(18):9232-41.(Impact factor:4.439)

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Xie SQ #, Nie P #, Wang Y #, Wang H, Li H, Yang Z, Liu Y *, Ren J *, Xie Z *.RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. Nucleic Acids Res. 2015 Oct 3. (Impact factor:9.112)

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Yang Z, Cao S, Martens CA, Porcella SF, Xie Z, Ma M, Shen B, Moss B.J Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling.J Virol. 2015 Jul;89(13):6874-86. (Impact factor:4.439)

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Zhong J, Xiao C #, Gu W, Du G, Sun X, He QY, Zhang G.Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress.PLoS Genet. 2015 Jun 19;11(6) (Impact factor:7.528)

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2014

Tsang, J.*, Schwartzberg, P.*, Kotliarov, Y.# , Biancotto, A. #, Xie, Z. #, Germain, R. #, Wang, E. #, Olnes, M. #, Narayanan, M., Golding, H., Moir, S., Dickler, H., Perl, S., Cheung, F., The Baylor HIPC Center, The CHI Consortium, Global analyses of human immune variation reveal baseline predictors of post-vaccination responses. Cell. 157,499-513,2014. (Impact factor:31.9)

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Chuan-Le Xiao,Zhi-Biao Mai,Xin-Lei Lian,Jia-Yong Zhong,Jing-jie Jin,Qing-Yu He,Gong Zhang. FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications.(2014) PLoS ONE 9(4): e94250. doi:10.1371/ journal.pone.0094250. (imapct factor:3.73)

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Lee, Y.-I., Giovinazzo, D., Kang, H.C., Lee, Y., Jeong, J.S., Doulias, P.-T., Xie, Z. , Hu, J., Ghasemi, M., Ischiropoulos, H., Qian, J., Zhu, H., Blackshaw, S., Dawson, VL., Dawson, TM. Protein microarray characterization of the S-nitrosoproteome. Mol. Cell. Proteomics 13, 63–72. 2014. (Impact factor:7.4)

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Ito S, Bollard CM, Carlsten M, Melenhorst JJ, Biancotto A, Wang E, Chen J, Kotliarov Y, Cheung F, Xie, Z. , Marincola F, Tanimoto K, Battiwalla M, Olnes MJ, Perl S, Schum P, Hughes TE, Keyvanfar K, Hensel N, Muranski P, Young NS, Barrett AJ., Ultra-low Dose Interleukin-2 Promotes Immune-modulating Function of Regulatory T Cells and Natural Killer Cells in Healthy Volunteers. Mol Ther. 2014 Apr 1. doi: 10.1038/mt.2014.50. (Impact factor:6.8)

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2013

Newman, R.H. #, Hu, J. #, Rho, H.-S. #, Xie, Z.#, Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, H.M., Hu, S., Hwang, W., Jeong, JS., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, KN., Birnbaum, MJ., Cole, PA., Knapp, S., Ryazanov, AG., Zack, DJ., Blackshaw, S., Pawson, T., Gingras, AC., Desiderio, S., Pandey, A., Turk, BE., Zhang, J., Zhu, H., Qian, J. Construction of human activity-based phosphorylation networks. Mol. Syst. Biol. 9. 2013. (Impact factor:11.3)

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Chuan-Le Xiao#, Xiao-Zhou Chen# , Yang-Li Du# , Zhe-Fu Li, Li Wei, Gong Zhang, Qing-Yu He. Dispec: A Novel Peptide Scoring Algorithm Based on Peptide Matching Discriminability for Candidate Peptides, PLoS ONE. doi:10.1371/journal.pone.0062724 (Impact factor:4.3)

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Chuan-Le Xiao#, Xiao-Zhou Chen# , Yang-Li Du# , Xuesong Sun, Gong Zhang, Qing-Yu He. Binomial Probability Distribution Model-Based Protein Identification Algorithm for Tandem Mass Spectrometry Utilizing Peak Intensity Information. J. Proteome Res.2013 (Impact factor:5.7)

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2012

Tarrant, M.K., Rho, H.-S., Xie, Z., Jiang, Y.L., Gross, C., Culhane, J.C., Yan, G., Qian, J., Ichikawa, Y., Matsuoka, T., Zachara, N., Etzkorn, FA., Hart, GW., Jeong, JS., Blackshaw, S., Zhu, H., Cole, PA. Regulation of CK2 by phosphorylation and O-GlcNA cylation revealed by semisynthesis. Nat. Chemical Biol. 8, 262–269. 2012. (Impact factor:12.9)

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Shamay, M., Liu, J., Li, R., Liao, G., Shen, L., Greenway, M., Hu, S., Zhu, J., Xie, Z., Ambinder, R.F., Qian, J., Zhu, H., Hayward, SD. A protein array screen for Kaposi’s sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. J. Virol. 86, 5179–5191. 2012. (Impact factor:5.1)

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Gong Zhang, Ivan Fedyunin, Sebastian Kirchner, Chuan-Le Xiao, Angelo Valleriani, Zoya Ignatova. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.Nucleic Acids Res. 2012 Jun 1;40(11):e83. ( Impact factor:8.0)

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2012以前

Xie, Z., Hu, S., Qian, J., Blackshaw, S., Zhu, H. *, Systematic characterization of protein-DNA interactions. Cell. Mol. Life Sci. 68, 1657–1668. 2011. (Impact factor:5.6)

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Li, R., Zhu, J., Xie, Z.., Liao, G., Liu, J., Chen, M.-R., Hu, S., Woodard, C., Lin, J., Taverna, S.D., Desai, P., Ambinder, RF., Hayward, GS., Qian, J., Zhu, H., Hayward, SD. Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe 10, 390–400. 2011. (Impact factor:12.6)

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Hyland, E.M., Molina, H., Poorey, K., Jie, C., Xie, Z., Dai, J., Qian, J., Bekiranov, S., Auble, D.T., Pandey, A., Boeke, JD. An evolutionarily “young”lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes Dev. 25, 1306–1319. 2011. (Impact factor:12.4)

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Hu, S., Xie, Z., Qian, J., Blackshaw, S., Zhu, H. *, Functional protein microarray technology. Wiley Interdiscip. Rev. Syst. Biol. Med. 3, 255–268. 2011. (Impact factor:3.7)

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Hu, S., Xie, Z., Blackshaw, S., Qian, J., Zhu, H.*. Characterization of Protein–DNA Interactions Using Protein Microarrays. Cold Spring Harb. Protoc. 2011, pdb. prot5614. 2011a. (Impact factor:4.6)

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Xuesong Sun#,Chuan-Le Xiao#,Ruiguang Ge,Xingfeng Yin,Hui Li,Nan Li,Xiaoyan Yang,Ying Zhu,Xiang He,Qing-Yu He. Putative copper- and zinc-binding motifs in Streptococcus pneumoniae identified by immobilized metal affinity chromatography and mass spectrometry. Proteomics. 2011 Aug;11(16):3288-98 ( Impact factor:4.4).

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Xuesong Sun, Xiaoyan Yang, Xin-Feng Yin, Guangchuang Yu, Chuan-Le Xiao, Qiang Hei, Qing-Yu He. Proteomic analysis of membrane proteins from Streptococcus pneumoniae with multiple separation methods plus high accuracy mass spectrometry.OMICS. 2011 Oct;15(10):683-94. ( Impact factor:2.2).

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Ruiguang Ge, Xuesong Sun,Chuan-Le Xiao, Xingfeng Yin, Weiran Shan, Zhuo Chen, Qing-Yu He. Phosphoproteome analysis of the pathogenic bacterium Helicobacter pylori reveals over-representation of tyrosine phosphorylation and multiply phosphorylated proteins. Accepted manuscript online: 16 FEB 2011.( Impact factor:4.4).

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Li-Ping Li,Chun- Hua Lu, Zhi-Peng Chen, Feng Ge, Tong Wang, Wei Wang, Chuan-Le Xiao, Xin-Feng Yin, Langxia Liu, Jian-Xing He, Qing-Yu He. Subcellular proteomics revealed the epithelial–mesenchymal transition phenotype in lung cancer. Proteomics. 2011 Feb;11(3):429-39. (Impact factor:4.4)。

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Guangchuang Yu#, Chuan-Le Xiao#, Xiaochen Bo, Chun-Hua Lu, Yide Qin, Sheng Zhan, Qing-Yu He.A new method for measuring functional similarity of microRNAs. 2011 Feb;1(1):49-54. (#共同第一)

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Guang-Rong Yan#, Xing-Feng Yin#, Chuan-Le Xiao, Zi-Lu Tan,Song-Hui Xu,Qing-Yu He. Identification of novel signaling components in genistein-regulated signaling pathways by quantitative phosphoproteomics.J Proteomics. 2011 Dec 21;75(2):695-707. ( Impact factor:5.0).

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Guang-Rong Yan, Wen Ding, Song-Hui Xu, Zhen Xu, Chuan-Le Xiao, Xing-Feng Yin, Qing-Yu He. Characterization of phosphoproteins in gastric cancer secretome. OMICS. 2011 Jan-Feb;15(1-2):83-90.( Impact factor:3.0)

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Gangchuang Yu#, Chuan-Le Xiao#, Chun-Hua Lu, Hai-Tao Jia, Feng Ge, Wei Wang, Xing-Feng Yin, Qing-Yu He. Phosphoproteome profile of human lung cancer cell line A549. Molecular Biosystem. 2011 Feb 1;7(2):472-9. (Impact factor:4.3)

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Xie, Z., Hu, S., Blackshaw, S., Zhu, H., Qian, J.*, hPDI: a database of experimental human protein–DNA interactions. Bioinformatics 26, 287–289. 2010. (Impact factor:5.3)

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Xie, Z.*, Kulasiri, D., Samarasinghe, S., Qian, J., An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock. Biotechnol. Bioeng. 105, 250–259. 2010. (Impact factor:3.6)

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Xie, Z. *, Kulasiri, D., On exploring effects of molecular noise in a simple viral infection model. Int. J. Biomath. 3, 1–19. 2010. (Impact factor:0.6)

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Lin, J. #, Xie, Z.., Zhu, H., Qian, J. *, Understanding protein phosphorylation on a systems level. Briefings Funct. Genomics 9, 32–42. 2010. (Impact factor:4.2)

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Xuesong Sun,Feng Ge,Chuan-Le Xiao,Xing-Feng Yin,Ruiguang Ge,Liu-Hui Zhang,and Qing-Yu He. Phosphoproteomic Analysis Reveals the Multiple Roles of Phosphorylation in Pathogenic Bacterium Streptococcus pneumoniae.J Proteome Res. 2010 Jan;9(1):275-82. (Impact factor:5.1)

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Ru Li, Jing Gu, Yuan-Yuan Chen, Chuan-Le Xiao#, Li-Wei Wang, Zhi-Ping Zhang, Li-Jun Bi, Hong-Ping Wei, Xu-De Wang, Jiao-Yu Deng , Xian-En Zhang. CobB regulates Escherichia coli chemotaxis by deacetylating the response regulator CheY. Mol Microbiol 76 (5), 1162-74. (Impact factor:5.2)

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Guang-Rong Yan#, Chuan-Le Xiao#, Gui-Wei He, Xing-Feng Yin, Nan-Peng Chen,Ya Cao , Qing-Yu He.Global Phosphoproteomic Effects of Natural Tyrosine Kinase Inhibitor, Genistein, on Signaling Pathways. Proteomics. 2010 Mar;10(5):976-86. (Impact factor:4.4)

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Feng Ge#,Chuan-Le Xiao#,Xing-Feng Yin,Chun-Hua Lu,Hui-Lan Zeng, Qing-Yu He.Phosphoproteomic Analysis of Primary Human Multiple Myeloma Cells. Journal of Proteomics. 2010 May 7;73(7):1381-90. (Impact factor:5.0)

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Feng Ge#, Chuan-Le Xiao#, Zhi-Ping Zhang, Xian-En Zhang, Li-Ping Li, Chun-Hua Lu,Hai-Tao Jia1, Xin-Feng Yin1, Kaio Kitazato3 and Qing-Yu He. Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells. PLoS ONE. 2010 Sep 29;5(9). pii: e13095 (Impact factor:4.6)

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Chun-Hua Lu, Feng Ge, Zhi Liu, Rong Li, Chuan-Le Xiao#, Hui-Lan Zeng, Xin-Peng Lu, Qing-Yu He. Detection of Abundant Proteins in Multiple Myeloma Cells by Proteomics. J Proteomics Bioinform 3: 005-009.

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Tian, Y., Tan, A.-C., Sun, X., Olson, M.T., Xie, Z., Jinawath, N., Chan, D.W., Shih, I.-M., Zhang, Z., Zhang, H.*, Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with paclitaxel resistance. PROTEOMICS–Clinical Appl. 3, 1288–1295. 2009. (Impact factor:2.9)

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Hu, S.#, Xie, Z.#., Onishi, A., Yu, X., Jiang, L., Lin, J., Rho, H., Woodard, C., Blackshaw, S., * Qian, J. *, Zhu, H. * , Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139, 610–622. 2009. (Impact factor:31.9)

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Lin Jin#, Chuan-Le Xiao#,Chun-Hua Lu, Min Xia, Guo-Wen Xing, Sheng Xiong, Qiu-Ying Liu, Hui Liu, Yi-Cheng Li, Feng Ge, Qing-Duan Wang, Qing-Yu He, Yi-Fei Wang .Transcriptomic and proteomic approach to studying SNX-2112-induced K562 cells apoptosis and anti-leukemia activity in K562-NOD/SCID mice.FEBS Letters . 2009 June;583 (12): 1859-1866(Impact factor:3.26)

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Chuan-Le Xiao#, Zhi-Ping Zhang# , Sheng Xiong , Chun-Hua Lu , Hong-Ping Wei , Hui-Lan Zeng , Zhi Liu , Xian-En Zhang , Feng Ge.Comparative proteomic analysis to discover potential therapeutic targets in human multiple myeloma. Proteomics.2009, 3, 1348–1360(Impact factor:4.4)

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Kulasiri, D.*, Nguyen, L.K., Samarasinghe, S., Xie, Z., A review of systems biology perspective on genetic regulatory networks with examples. Curr. Bioinforma. 3, 197–225. 2008. (Impact factor:1.7)

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Kulasiri, D., Xie, Z. *, Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model. Math. Model. Nat. Phenom. 3, 1–26. 2008. (Impact factor:0.6)

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Xie, Z., Kulasiri, D., Samarasinghe, S. & Rajanayaka, C. (2007). The Estimation of Parameters for Stochastic Differential Equations Using Neural Networks. Inverse. Probl. Sci. Eng. 15(6), 629-641. (Impact factor:0.7)

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Xie, Z., Kulasiri, D. *, Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops. J. Theor. Biol. 245, 290–304. 2007. (Impact factor:2.4)

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