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 Papers
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Note: # equally
contributed, * corresponding author
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In submission
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Yupeng Li#, Fan Wang#, Jiaqi Yang, Zirong Han, Linfeng Chen, Wenbing Jiang, Hao Zhou, Tong Li, Zehua Tang, Jianxiang Deng, Xin He, Gaofeng Cha, Jiekai Hu, Yong Hu, Linping Wu, Changyou Zhan, Caijun Sun, Yao He*, Zhi Xie*,
Deep Generative Optimization of mRNA Codon Sequences for Enhanced Protein Production and Therapeutic Efficacy. In submission.
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Yuanyuan Yu#, Zhi Xie*,
Spatial Transcriptomic Alignment, Integration, and de novo 3D Reconstruction by STAIR. In submission. https://doi.org/10.21203/rs.3.rs-3939678/v1.
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2024
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Jingjing Zheng#, Tong Li#, Huijing Ye, Zehang Jiang, Wenbing Jiang, Huasheng Yang*, Zhikun Wu*, Zhi Xie*,
Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing. Cancer Letters. 2024, August 28, Volume 598, 217121, DOI:https://doi.org/10.1016/j.canlet.2024.217121. (Q1, IF=9.1).
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Wenbing Jiang#, Dongchang Xiao#, Cheng Wu#, Jiaqi Yang, Xinghua Peng, Linfeng Chen, Jiamin Zhang, Gaofeng Zha, Wei Li, Rong Ju*, Mengqing Xiang*, Zhi Xie*,
Circular RNA-Based Therapy Provides Sustained and Robust Neuroprotection for Retinal Ganglion Cell. Molecular Therapy-Nucleic Acids. 2024,June 17,DOI:https://doi.org/10.1016/j.omtn.2024.102258. (Q1, IF=8.8).
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Hao Zhou#, Wenhan Yang#, Limei Sun#, Li Huang, Songshan Li, Xiaoling Luo, Yili Jin, Wei Sun, Wenjia Yan, Jing Li, Xiaoyan Ding*, Yao He*, Zhi Xie*,
RDLR: A Robust Deep Learning-Based Image Registration Method for Pediatric Retinal Images. Journal of Imaging Informatics in Medicine. 2024,1-15. (Q2, IF=4.4).
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Hao Zhou#, Yao He#, Xiaoxiao Cui*, Zhi Xie*,
AGSAM: Agent-Guided Segment Anything Model for Automatic Segmentation in Few-Shot Scenarios. Bioengineering. 2024,11,447. (Q2, IF=3.8).
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Yuanyuan Yu, Yao He*, Zhi Xie*,
Accurate Identification of Spatial Domain by Incorporating Global Spatial Proximity and Local Expression Proximity. Biomolecules. 2024,14,674. (Q1, IF=4.8).
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Ludong Yang#, Liang Yi#, Jiaqi Yang, Rui Zhang, Zhi Xie*, Hongwei Wang*,
Temporal landscape and translational regulation of A-to-I RNA editing in mouse retina development. BMC Biology. 2024;22:106. (Q1, IF=4.4).
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Zhikun Wu#, Tong Li#, Zehang Jiang, Jingjing Zheng, Yizhou Gu, Yizhi Liu, Yun Liu, Zhi Xie*,
Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles. Nucleic Acids Research. 2024;gkae086. (Q1, IF=14.9).
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Cheng Wu#, Tianxiang Tu#, Mingzhe Xie, Yiting Wang, Biao Yan, Yajun Gong, Jiayi Zhang, Xiaolai Zhou*, Zhi Xie*,
Spatially resolved transcriptome of the aging mouse brain. Aging Cell. 2024;e14109. (Q1, IF=7.8).
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2023
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Jianxia Li#, Cheng Wu#, Huabin Hu#, Ge Qin#, Xueqian Wu, Fan Bai, Jianwei Zhang, Yue Cai, Yan Huang, Chao Wang, Jiaqi Yang, Yizhao Luan, Zehang Jiang, Jiayu Ling, Zehua Wu, Yaoxu Chen, Zhi Xie, Yanhong Deng*,
Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer. Cancer Cell. 2023;S1535-6108(23)00137-X.(Q1, IF=38.585).
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Yizhao Luan#, Zehua Tang#, Yao He, Zhi Xie*,
Intra-Domain Residue Coevolution in Transcription Factors Contributes to DNA Binding Specificity. Microbiol Spectr. 2023;11(2):e0365122.(Q1, IF=9.043).
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Tong Li#, Yupeng Li#, Xiaoyi Zhu#, Yao He, Yanling Wu, Tianlei Ying*, Zhi Xie*,
Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol. 2023;91:50-69.(Q1, IF=17.012).
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Yuanyuan Chen#, Cheng Wu#, Shanzhen Peng, Dianlei Guo, Hong Ouyang, Yanhong Wei, Rong Ju*, Xiaoyan Ding*, Zhi Xie*, Chunqiao Liu*,
Single-Cell Characterization of the Frizzled 5 (Fz5) Mutant Mouse and Human Persistent Fetal Vasculature (PFV). Invest Ophthalmol Vis Sci. 2023 Mar 1;64(3):8.(Q1, IF=4.299).
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Ying Yang#, Hongwei Wang#, Yuanliang Zhang, Lei Chen, Gennong Chen, Zhaoshi Bao, Yang Yang, Zhi Xie, Qian Zhao*,
An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development. Mol Cell Proteomics. 2023; 22(1): 100480.(Q1, IF=7.381).
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Xintong Zheng, Mingwei Wang, Shuting Liu, Haiqiao Chen, Yifei Li, Fa Yuan, Ludong Yang, Suo Qiu, Hongwei Wang, Zhi Xie, Mengqing Xiang*
, A lncRNA-encoded mitochondrial micropeptide exacerbates microglia-mediated neuroinflammation in retinal ischemia/reperfusion injury. Cell Death Dis. 2023;14(2):126.(Q1, IF=8.5)
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2022
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Zixuan Hu#, Jiaying Zhou#, Yupeng Li#, Yizhao Luan, Huan Li, Bo Jia, Zhi Xie*, Bin Cheng*, Tong Wu*,
Peripheral immune signature resembles tumor microenvironment and predicts clinical outcomes in head and neck squamous cell carcinoma. Front Immunol. 2022;13:915207. (Q1, IF=8.787).
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Cheng Wu, Jiaqi Yang, Wei Xiao, Zehang Jiang, Shuxia Chen, Dianlei Guo, Ping Zhang, Chunqiao Liu, Huasheng Yang*, Zhi Xie*,
Single-cell characterization of malignant phenotypes and microenvironment alteration in retinoblastoma. Cell Death and Disease, (2022) (Q1, IF=8.5).
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Yizhao Luan#, Nan Tang#, Jiaqi Yang#,
Shuting Liu, Chichi Cheng, Yan Wang, Yanan Guo, Hongwei Wang, Mengqing Xiang, Rong Ju*, Zhi Xie*
, Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells, Nucleic Acids Research, (2022) (Q1, IF=16.97).
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Breakthrough Article (Top 5% in NAR)
Faculty Opinions (Top 1% in Developmental Biology)
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Mingzhe Xie#, Ludong Yang#, Gennong Chen#,
Yan Wang, Zhi Xie*, Hongwei Wang*
, RiboChat: a chat-style web interface for analysis and annotation of ribosome profiling data. Briefings in Bioinformatics, 2022 Mar 10;23(2):bbab559. (Q1, IF=11.62)
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2021
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Zhikun Wu#, Zehang Jiang#, Tong Li#,
Chuanbo Xie#, Liansheng Zhao#, Jiaqi Yang,
Shuai Ouyang, Yizhi Liu, Tao Li*, Zhi Xie*
, Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptation. Nature Communications 12, 6501 (2021). https://doi.org/10.1038/s41467-021-26856-x (Q1, IF=14.91)
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Nicolas Dierckxsens#, Tong Li, Joris R. Vermeesch,
Zhi Xie*
, A benchmark of structural variation detection by long reads through a realistic simulated model. Genome Biol 22, 342 (2021). (Q1, IF=13.58)
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Kaining Chen#, Congying Chen#, Huihui
Li, Jiaqi Yang,
Mengqing Xiang, Hongwei Wang*, Zhi Xie*
, Widespread translational control regulates retinal development in mouse,
Nucleic Acids Research,
2021;, gkab749, https://doi.org/10.1093/nar/gkab749 (Q1, IF=16.97)
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Hongwei Wang#*, Yan Wang#, Jiaqi
Yang#, Qian Zhao#, Nan Tang, Congying Chen,
Huihui Li, Chichi Cheng, Mingzhe Xie, Yang Yang,
Zhi Xie*
, Tissue- and stage-specific landscape of the mouse
translatome,
Nucleic Acids Research,
2021 Jun 21;49(11):6165-6180. doi: 10.1093/nar/gkab482 (Q1, IF=16.97).
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Huihui Li#, Mingzhe Xie#, Yan Wang#,
Ludong Yang, Zhi Xie*,
Hongwei Wang*
, riboCIRC: a comprehensive database of translatable circRNAs,
Genome Biology,
2021 Mar 8;22(1):79. doi: 10.1186/s13059-021-02300-7. (Q1, IF=13.58).
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Lei Chen, Yuanliang Zhang, Ying Yang, Yang Yang, Huihui Li, Xuan
Dong, Hongwei Wang, Zhi Xie, Qian Zhao*
, An Integrated Approach for Discovering Noncanonical MHC-I Peptides Encoded by Small Open
Reading Frames,
Journal of the American Society for Mass Spectrometry,
2021 32 (9), 2346-2357. doi:10.1021/jasms.1c00076. (IF=3.10).
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2020
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Guocai Yao, Wenliang Zhang, Minglei Yang, Huan Yang, Jianbo Wang,
Haiyue Zhang, Lai Wei,
Zhi Xie, Weizhong Li, MicroPhenoDB Associates Metagenomic Data with Pathogenic
Microbes,
Microbial Core Genes, and Human Disease Phenotypes, Genomics, Proteomics
& Bioinformatics,
2020, November 12; https://doi.org/10.1016/j.gpb.2020.11.001 (IF=7.051).
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Yao He#,
Hao Yuan#, Cheng Wu#,
Zhi Xie*, DISC: a highly scalable and accurate
inference of gene expression and structure for single-cell transcriptomes
using semi-supervised deep learning, Genome Biology,
2020, July, 21(170) (Q1, IF=10.8).
Download
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Surui Pei,
Tao Liu, Xue Ren,Weizhong Li, Chongjian Chen*, Zhi Xie*,
Benchmarking variant callers in next-generation and third-generation sequencing analysis,
Briefings in Bioinformatics,
2020 July 23; https://doi.org/10.1093/bib/bbaa148 (Q1, IF=9.0).
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Xiaorong Lin, Xiaoxiao Dinglin, Siting Cao, Senyou Zheng, Cheng
Wu, Wenying Chen, Qingjian Li, Qian Hu, Fang Zheng, Zhiyong Wu, De-Chen Lin,
Yandan Yao, Xiaoding Xu, Zhi Xie, Qiang Liu, Herui Yao*, and Hai Hu*,
Enhancer-Driven lncRNA BDNF-AS Induces Endocrine Resistance and Malignant Progression of
Breast Cancer through
the RNH1/TRIM21/mTOR Cascade, Cell REPORTS,
2020 June 9;31(10):107753 (Q1, IF=8.1).
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2019
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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, 2019 Jan 8;47(D1):D230-D234 (Q1, IF=11.5).
Download
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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, 2019 Nov 27;20(6):2098-2115. doi: 10.1093/bib/bby071 (Q1,
IF=9.0).
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2018
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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 (Q1, IF=5.1).
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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 (Q1, IF=31.4).
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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. (Q1, IF=10.2).
Download
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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 (Q1, IF=7.1).
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2017
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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. (Q1, IF=28.5).
Download
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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 (Q2, IF=3.7).
Download
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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. (Q1, IF=9.0).
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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 (Q1, IF=5.5).
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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. (Q1, IF=3.6).
Download
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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 (Q1, IF=8.0).
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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 (Q1, IF=5.2).
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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 (Q1, IF=5.2).
Download
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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 (Q1, IF=11.6).
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2016 |
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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 (Q1, IF=4.4).
Download
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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 (Q1, IF=6.7).
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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 (Q1, IF=11.6).
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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) (Q1, IF=37.2).
Download
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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 (Q1, IF=9.1).
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2015 |
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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 (Q1, IF=4.6).
Download
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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 (Q1, IF=10.2).
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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 (Q1, IF=4.6).
Download
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2014
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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 (Q1, IF=32.2).
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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 (Q1, IF=5.9).
Download
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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 (Q1, IF=6.9).
Download
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2013 |
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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 (Q1, IF=10.6).
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2012 |
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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 (Q1, IF=12.9).
Download
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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 (Q1, IF=5.1).
Download
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Before
2012
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Xie, Z.,
Hu, S., Qian, J., Blackshaw, S., Zhu, H.
*, Systematic characterization of
protein-DNA interactions. Cell. Mol. Life Sci. 68,
1657–1668. 2011 (Q1, IF=6.6).
Download
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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 (Q1, IF=13.5).
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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
& Development. 25, 1306–1319.
2011 (Q1, IF=11.7).
Download
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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 (IF=4.2).
Download
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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 (Q1, IF=4.9).
Download
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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 (Q1, IF=3.7).
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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 (Q2, IF=1.7).
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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 (Q1, IF=4.1).
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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 (Q2, IF=1.9).
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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 (Q1, IF=31.2).
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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 (Q2, IF=1.9).
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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 (Q2, IF=0.7).
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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 (Q3, IF=1.3).
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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 (Q1, IF=2.3).
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Laboratory of
Bioinformatics and Genomics, Sun Yat-sen
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