Papers


Note: # equally contributed, * corresponding author


2018

Hongwei Wang#*, Ludong Yang#, Yan Wang#, Leshi Chen#, Huihui Li, and Zhi Xie*, RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling, Nucleic Acids Research, 2018 Oct 18. doi: 10.1093/nar/gky978.
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Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li*, Computational resources associating diseases with genotypes, phenotypes and exposures, Briefings in Bioinformatics, 2018, Aug
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Qian Yu#, Bingying Lin#, Shangqian Xie, Song Gao, Wei Li, Yizhi Liu, Hongwei Wang, Danping Huang*, Zhi Xie*, A homozygous mutation p.Arg2167Trp in FREM2 causes isolated cryptophthalmos, Human Molecular Genetics, 2018, Jul 1;27(13):2357-2366,
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Jingxing Ou, John M. Ball#, Yizhao Luan#, Tantai Zhao#, Kiyoharu J. Miyagishima#, Yufeng Xu#, Huizhi Zhou, Jinguo Chen, Dana K. Merriman, Zhi Xie, Barbara S. Mallon, Wei Li*, iPSCs from a Hibernator Provide a Platform for Studying Cold Adaptation and Its Potential Medical Applications, Cell, 2018, May


Yongquan Lin#, Yan Wang#, Hui Li, Yuhang Chen, Wentao Qiao, Zhi Xie*, Juan Tan*, Zhilong Yang*, Simultaneous and systematic analysis of cellular and viral gene expression during Enterovirus 71-induced host shutoff, Protein & Cell, 2018, https://doi.org/10.1007/s13238-018-0535-6.

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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, 2018, Volume 16, Issue 1, Pages 17-32
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2017


Chuan-Le Xiao#*, Ying Chen#, Shang-qian Xie, Kai-Ning Chen, Yan Wang, Feng Luo*, and Zhi Xie*, MECAT: Fast mapping, error correction, and de novo assembly for single-molecule sequencing reads, Nature Methods, 2017, doi:10.1038/nmeth.4432.
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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.
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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.


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
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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.

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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.
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Wu FL, Liu Y, Jiang HW, Luan YZ, Zhang HN, ..., Xie Z, ..., Zhang XE, Tao SC., The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis, Mol Cell Proteomics. 2017, Aug;16(8): 1491-1506.
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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. doi: 10.1074/mcp.M116.063602.
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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, 2017 10.1093.gkw909





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
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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
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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



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).
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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.
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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.
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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.


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.
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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.



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.
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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.
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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.


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.
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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.
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Before 2012

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



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 & Development. 25, 1306–1319. 2011.
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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.
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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.
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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.
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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.
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Cover image


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



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.
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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.
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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.
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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.




Laboratory of Bioinformatics and Genomics, Sun Yat-sen University