Thursday, 22 October 2015 11:34

2013

Cao C, Jiang W, Wang B, Fang J, Lang J, Tian G*, Jiang J*, and Zhu TF*. (2014) Inhalable microorganisms in Beijing's PM2.5 and PM10 pollutants during a severe smog event. Environ Sci Technol, 48(3):1499-1507, .

Samira Kiani, Jacob Beal, Mohammad R Ebrahimkhani, Jin Huh, Richard N. Hall1, Zhen Xie, Yinqing Li and Ron Weiss*. (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nature Methods 11, 723-6.

Jonathan Leo Schmid-Burgk, Zhen Xie, Yaakov Benenson*. (2014) Hierarchical ligation-independent assembly of PCR fragments. Methods Molecular Biology 1116:49-58.

Zhen Xie, Liliana Wroblewska and Ron Weiss*. (2014) RNAi synthetic logic circuits for sensing, information processing and actuation. RNA Regulation, Encyclopedia of Molecular Cell Biology and Molecular Medicine. Edition April 2014, ISBN 978-3-527-33156-7-Wiley-VCH, Weinheim (Book chapter).

Jin Gu*#, Yang Chen*, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Zhang#. (2014) Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystems, 10(12):3249-3254.

Ting Wang, Jin Gu#, Yanda Li. (2014) Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. BMC Bioinformatics, 15:255.

Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding. (2014) OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. Bioinformatics, 30(15):2237-2238.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbanian F, Kasowski M, Zhang MQ, Snyder MP (2014). Genome-wide map of regulatory interactions in the human genome. Genome Res. 24:1905-17.

Sephton CF, Tang AA, Kulkarni A, West J, Brooks M, Stubblefield JJ, Liu Y, Zhang MQ, Green CB, Huber KM, Huang EJ, Herz J, Yu G (2014) Activity-Dependent FUS Dysregulation Disrupts Synaptic Homeostasis. PNAS, 111:E4769-78.

Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy K-W, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H (2014) Exome sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nosyndromic hearing loss in a Chinese family. AHG. In press.

Sheng MM†, Zhong Y†, Chen Y, Du J, Ju X, Zhao C, Zhang G, Zhang L, Liu K, Yang N, Xie P, Li D, Zhang MQ* Jiang C*. (2014) Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci 57:959-972.

Liao W, Ouyang W, Zhang MQ, Li MO (2014) Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data, 2:280-281.

Rajagopal N, Ernst J, Ray R, Wu J, Zhang MQ, Kellis M, Ren B (2014) Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies. G3, 4:2051-55.

Lu Y, Zhou X, Jin Z, Cheng J, Shen W, Ji F, Liu L, Zhang X, Zhang M, Cao Y, Han D, Choy K, Yuan H. (2014) Resolving the Genetic Heterogeneity of Prelingual Hearing Loss within One Family: Performance Comparison and Application of Two Targeted Next Generation Sequencing Approaches. JHG, 59:599-607.

Li Y, Ehrhardt K, Zhang MQ, Bleris L (2014) Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries. Sci. Rep. 4:4857.

Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, Jiang F, Chen C, Yang Y, Gu J, Wu D, Guo L, Cao D, Li H, Cao G, Wu M, Zhang MQ, Chen L, Wang H (2014) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 64:156-67.

He C, Wang X*, Zhang MQ* (2014) Nucleosome eviction and multiple co-factor binding predict estrogen receoptor alpha associated long-range interactions. NAR, 42:6935-44.

Li W, Wu J, Kim S-Y, Zhao M, Zhang MQ, Meistrich ML, Mills AA (2014) Chd5 orchestrates chromatin remodeling during sperm development. Nat. Comm. 5:3812.

Xie P, Liu Y, Li Y, Zhang MQ*, Wang X* (2014) MIROR: a method for cell-type specific microRNA occupancy rate prediction. Mol. BioSyst. 10:1377-84.

Li GP, Li M, Zhang YW, Wang D, Li R, Guimera R, Gao J*, Zhang MQ* (2014) ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks. PLoS ONE, 9:e94608.

16. Weyn-Vanhentenryck S, Sun S, Yan Q, Mele A, Farny N, Silver Z, Zhang MQ, Krainer AR, Darnell RB, Zhang C (2014) HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports, S2211-1247(14)00084-9. PMID:24613350.

Zhixing Feng, Jing Li, Jing-Ren Zhang, Xuegong Zhang*. (2014) qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data, Nucleic Acids Research, 42(22): 13488-13499.

Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang*. (2014) Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation, Quantitative Biology, 2(2): 71-79.

Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang*, Yan Zhu*. (2014) Improvement of Dscam hemophilic binding affinity throughout Drosophila evolution, BMC Evolutionary Biology, 4: 186.

YingXue Li, XueNing Liu, XiaoWo Wang, XueGong Zhang*. (2014) Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58.

Xavier Roge, Xuegong Zhang*. (2014) RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892.

Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu. (2014) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064.

Shufang Zhang, Xueya Zhou, Shengnan Liu, Tingting Bai, Yingai Zhang, Jing Wang, Shunlan Wang, Xuegong Zhang, Binbin, Wang. (2014) MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations, Acta Haematologica, 132: 193-198.

Jing Cheng, Xueya Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong-Wai Choy, Dongyi Han, Pak C. Sham, Michael Q. Zhang, Xuegong Zhang, Huijun Yuan. (2014) Exom sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese Family, Annals of Human Genetics, 78: 410-423.

Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Michael Zhang, Ye Cao, Dongyi Han, KwongWai Choy, Huijun Yuan. (2014) Resolving the genetic heterogeneity of prelingual hearing loss within one family: performance comparison and application of two targeted next generation sequencing approaches, Journal of Human Genetics, 59: 599-607.

Chao Ye, Xuegong Zhang. (2014) A simulation study on gene expression regulation via stochastic model, Proceedings of the 33rd Chinese Control Conference, pp. 6885-6888, July 28-30, Nanjing, China.

Qifeng Xu, Xuegong Zhang. (2014) Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529.

Liang X, Li H, Li S*. (2014) A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-wei-di-huang Pill as a case study. Molecular BioSystems 10(5):1014-1022.

Wang L, Wang Y, Hu Q, Li S*. (2014) Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks. CPT: Pharmacometrics and Systems Pharmacology 3:e146.

Liang X, Li H, Tian G, Li S*. (2014) Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer. Scientific Reports 4,4985.

Li S*, Zhang X. (20145) Tongue-coating microbiome characterized by the next-generation sequencing and traditional tongue diagnosis. Encyclopedia of Metagenomics Springer.

Li S*, Fan T, Jia W, Lu A, Zhang W. (2014) Network pharmacology in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine 138460.

Li H, Zhao L, Zhang B, Jiang Y, Wang X, Guo Y, Liu H, Li S*, Tong X*. (2014) A network pharmacology approach to determine active compounds and action mechanisms of Ge-Gen-Qin-Lian decoction for treatment of Type 2 diabetes. Evidence-based Complementary and Alternative Medicine 2014:495840.

ong Hu, Chao Di, Mingxuan Kai, Yu-Cheng T. Yang, Yang Li, Yunjiang Qiu, Xihao Hu, Kevin Y. Yip, Michael Q. Zhang and Zhi John Lu (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research 43(1): 104-114.

u-Cheng T. Yang*, Chao Di*, Boqin Hu*, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu and Zhi John Lu (2015) CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics In press. (*contributed equally)

hao Di*, Jiapei Yuan*, Yue Wu, Jingrui Li, Huixin Lin, Long Hu, Ting Zhang, Yijun Qi, Mark B. Gerstein, Yan Guo and Zhi John Lu (2014) Characterization of Stress-responsive lncRNAs in Arabidopsis thaliana by Integrating Expression, Epigenetic and Structural Features. The Plant Journal 80:848–861

u ZJ*, Yip KY*, Wang G, Shou C, Hillier LW, et al. (2011) Predicting and characterizing non-coding RNA in C. elegans by integrating conservation, secondary structure and high-throughput sequencing and array data. Genome Research 21: 276-2857 (*contributed equally) [modENCODE special issue – Cover Story]

erstein MB *#, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330(6012): 1775-1787 (*co-first authors, #corresponding authors) [Cover Story]

Gerstein MB, Joel Rozowsky, Koon-Kiu Yan, Lu Z, Thomas Gingeras and Robert Waterston (2014) Comparative Analysis of the Transcriptome across Distant Species. Nature 512(7515):445-448.

Yang YC, Umetsu J, Lu ZJ (2014) Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae. Science China Life Sciences (Tsinghua Special Issue) 57:1, 22-35

Hu X, Wong TKF, Lu ZJ, Chan TF, Lau TCK, Yiu SM and Yip KY. (2014) Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data. Bioinformatics vol. 30, no. 8, pp. 1049-1055.

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