Table of Contents:
2023
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Xing, S.1, Zhu, Y.1, You, Y., Wang, S., Wang, H., Ning, M., Jin, H., Liu, Z., Zhang, X., Yu, C. * & Lu, Z. J.* (2023). Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WIREs RNA, e1791 (1contributed equally, *co-corresponding authors)
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Chun Ning1, Peng Cai1, Xiaofan Liu1, Guangtao Li1, Pengfei Bao, Lu Yan, Meng Ning, Kaichen Tang, Yi Luo, Hua Guo, Lu Chen*, Zhi John Lu *, Jianhua Yin* (2023) A Comprehensive Evaluation of Full-spectrum Cell-free RNAs highlights cell-free RNA fragments for Early-Stage Hepatocellular Carcinoma Detection eBioMedicine in press (1contributed equally, *co-corresponding authors)
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Hongke Wang1, Qing Zhan1, Hongjie Guo1, Jiuliang Zhao, Shaozhen Xing, Shanwen Chen, Shuai Zuo, Mengtao Li*, Pengyuan Wang*, Zhi John Lu* (2023) Depletion-assisted multiplexing cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicle bioRxiv 10.1101/2023.01.31.526408 (1contributed equally, *co-corresponding authors)
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Yuhuan Tao1, Shaozhen Xing1, Shuai Zuo1, Pengfei Bao, Yunfan Jin, Yu Li, Yingchao Wu, Shanwen Chen, Xiaojuan Wang, Yumin Zhu, Ying Feng, Xiaohua Zhang, Xianbo Wang, Qiaoran Xi, Qian Lu*, Pengyuan Wang*, Zhi John Lu* (2023) Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer ptients’ plasma bioRxiv 10.1101/2023.01.31.526431 (1contributed equally, *co-corresponding authors)
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Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Yunping Zhu*, Zhi John Lu* (2023) Pathformer: biological pathway informed Transformer model integrating multi-modal data of cancer bioRxiv 10.1101/2023.05.23.541554 (*co-corresponding authors)
2022
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Shanwen Chen1, Yunfan Jin1, Siqi Wang1, Shaozhen Xing1, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu*, Zhi John Lu*, Pengyuan Wang* (2022) Cancer Type Classification Using Plasma Cell Free RNAs Derived from Human and Microbes. eLife 11:e75181 (1contributed equally, *co-corresponding authors)
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Haipeng Fu, Tingyu Wang, Xiaohui Kong, Kun Yan, Yang Yang, Jingyi Cao, Yafei Yuan, Nan Wang, Kehkooi Kee, Zhi John Lu & Qiaoran Xi (2022) A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nature Communications 13(1):3984
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Liuqing Yang, Kequan Lin, Lin Zhu, Huili Wang, Shuaishuai Teng, Lijun Huang, Shiyi Zhou, Guanbin Zhang, Zhi John Lu & Dong Wang (2022) Long non-coding RNA DARS-AS1 promotes tumor progression by directly suppressing PACT-mediated cellular stress. Communications Biology 5, 822
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Weihao Zhao1, Shang Zhang1, Yumin Zhu, Xiaochen Xi, Pengfei Bao, Ziyuan Ma, Thomas H Kapral, Shuyuan Chen, Bojan Zagrovic, Yucheng T Yang*, Zhi John Lu* (2022) POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Research 50(D1):D287-D294 (1contributed equally, *co-corresponding authors)
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Thomas H Kapral, Fiona Farnhammer, Weihao Zhao, Zhi J Lu and Bojan Zagrovic (2022) Widespread autogenous mRNA–protein interactions detected by CLIP-seq. Nucleic Acids Research, 50(17):9984-9999
2017 - 2021
2021
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Yumin Zhu1, Siqi Wang1, Xiaochen Xi1, Minfeng Zhang1, Xiaofan Liu, Weina Tang, Peng Cai, Shaozhen Xing, Pengfei Bao, Yunfan Jin, Weihao Zhao, Yinghui Chen, Huanan Zhao, Xiaodong Jia, Shanshan Lu, Yinying Lu, Lei Chen*, Jianhua Yin*, Zhi John Lu* (2021) Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 11(1):181-193 (1contributed equally, *co-corresponding authors)
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Jing Gong1, Kui Xu1, Ziyuan Ma, Zhi John Lu & Qiangfeng Cliff Zhang (2021) A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments. Nature Machine Intelligence 3:995–1006
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Jia Li, Lei Sun, Xue-Liang Peng, Xiao-Ming Yu, Shao-Jun Qi, Zhi John Lu, Jing-Dong J Han, Qin Shen (2021) Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons. PLoS Genetics 17(3):e1009355 View Detail
2020
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Shuaishuai Teng1, Yang Eric Li1, Ming Yang, Rui Qi, Yiming Huang, Qianyu Wang, Yanmei Zhang, Shanwen Chen, Shasha Li, Kequan Lin, Yang Cao, Qunsheng Ji, Qingyang Gu, Yujing Cheng, Zai Chang, Wei Guo, Pengyuan Wang, Ivan Garcia-Bassets, Zhi John Lu* and Dong Wang* (2020) Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer. Cell Research 30(1):34-49 (1contributed equally, *co-corresponding authors)
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Yu-Xiang Chen1, Zhi-yu Xu1, Xueliang Ge, Suparna Sanyal, Zhi John Lu* and Babak Javid* (2020) Selective translation by alternative bacterial ribosomes. PNAS 117(32):19487-19496 (1contributed equally, *co-corresponding authors)
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Yu Ma1, Shang Zhang1, Chao Bi1, Chao Mei, Shang-Chuan Jiang, Xiao-Fang Wang, Zhi John Lu* and Da-Peng Zhang* (2020) Arabidopsis exoribonuclease USB1 interacts with the PPR-domain protein SOAR1 to negatively regulate abscisic acid signaling. Journal of Experimental Botany 71(19): 5837-5851 (1contributed equally, *co-corresponding authors)
2019
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Kequan Lin1, Lu Li1, Yifei Dai, Huili Wang, Shuaishuai Teng, Xilinqiqige Bao, Zhi John Lu* and Dong Wang* (2019) A comprehensive evaluation of connectivity methods for L1000 data Briefings in Bioinformatics bbz129 (1contributed equally, *co-corresponding authors)
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Rui Xiao1,*, Jia-Yu Chen1, Zhengyu Liang1, Daji Luo, Geng Chen, Zhi John Lu, Yang Chen, Bing Zhou, Hairi Li, Xian Du, Yang Yang, Mingkui San, Xintao Wei, Wen Liu, Eric Lecuyer, Brenton R. Graveley, Gene W. Yeo, Christopher B. Burge, Michael Q. Zhang, Yu Zhou and Xiang-Dong Fu* (2019) Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription Cell 178, 107–121 (1contributed equally, *co-corresponding authors)
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Maoguo Luo, Jianbo Bai, Bofeng Liu, Peiqiang Yan, Feifei Zuo, Hongyao Sun, Ye Sun, Xuanhao Xu, Zhihong Song, Yang Yang, Joan Massagué, Xun Lan, Zhi Lu, Ye-Guang Chen, Haiteng Deng, Wei Xie, Qiaoran Xi (2019) H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling Stem Cell Reports 13(4):642-656
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Chang Tan1, Jingyi Cao1, Lu Chen1, Xiaochen Xi, Siqi Wang, Yumin Zhu, Liuqing Yang, Longteng Ma, Dong Wang, Jianhua Yin*, Ti Zhang* and Zhi John Lu* (2019) Noncoding RNAs serve as diagnosis and prognosis biomarkers for hepatocellular carcinoma Clinical Chemistry 65(7):905-915 (1contributed equally, *co-corresponding authors)
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Yumin Zhu1, Gang Xu1, Yucheng T Yang1, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu*, Pengyuan Wang* (2019) POSTAR2: deciphering the post-transcriptional regulatory logics Nucleic Acids Research (D1):D203-D211 (1contributed equally, *co-corresponding authors)
2018
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Zhiyu Xu1, Long Hu1, Binbin Shi, SiSi Geng, Longchen Xu, Dong Wang* and Zhi John Lu* (2018) Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Research 46 (18), e109-e109 (1contributed equally, *co-corresponding authors)
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Shasha Li1, Shuaishuai Teng1, Junquan Xu, Guannan Su, Yu Zhang, Jianqing Zhao, Suwei Zhang, Haiyan Wang, Wenyan Qin, Zhi John Lu, Yong Guo, Qianyong Zhu and Dong Wang (2018) Microarray is an efficient tool for circRNA profiling. Briefings in Bioinformatics doi: 10.1093/bib/bby006 (1contributed equally)
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[spotlight]: Binbin Shi and Zhi John Lu* (2018) Decoding Plant RNA Structurome. Molecular Plant 11:3
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J Yuan1, J Li1, Y Yang, C Tan, Y Zhu, L Hu, Y Qi*, ZJ Lu* (2018) Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa. The Plant Journal 93:5, 814-827 (1contributed equally, *co-corresponding authors)
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J Gong, D Shao, K Xu, Z Lu, ZJ Lu, YT Yang, QC Zhang (2018) RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Research 46 (D1), D194-D201
2017
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Yang Eric Li1, Mu Xiao1, Binbin Shi1, Yu-Cheng T. Yang, Dong Wang, Fei Wang, Marco Marcia and Zhi John Lu* (2017) Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. Genome Biology 18:169 (1contributed equally)
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Yang Yang1, Lei Chen1, Jin Gu1, Hanshuo Zhang1, Jiapei Yuan, Qiuyu Lian, Guishuai Lv, Siqi Wang, Yang Wu, Yu-Cheng T. Yang, Dongfang Wang, Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang, Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang*, Michael Q. Zhang* and Zhi John Lu* (2017) Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications 8, 14421 (1contributed equally, *co-corresponding authors)
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Xiaochen Xi1, Tianxiao Li1, Yiming Huang, Jiahui Sun, Yumin Zhu, Yang Yang* and Zhi John Lu* (2017) RNA Biomarkers: Frontier of Precision Medicine for Cancer. Non-Coding RNA3, 9 (1contributed equally, *co-corresponding authors)
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Yang Yang1, Yu-Cheng T. Yang1, Jiapei Yuan, Zhi John Lu* and Jingyi Jessica Li* (2017) Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states. Nucleic Acids Research 45 (4): 1657-1672 (1contributed equally, *co-corresponding authors)
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Zhonglin Tang1,*, Yang Wu1, Yalan Yang, Yu-Cheng T. Yang, Zishuai Wang, Jiapei Yuan, Yang Yang, Chaoju Hua, Xinhao Fan, Guanglin Niu, Yubo Zhang, Zhi John Lu* and Kui Li* (2017) Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa. Scientific Reports 7:43166 (1contributed equally, * co-corresponding authors)
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Dan Gao, Yingjie Han, Yang Yang, James G Herman, Enqiang Linghu, Qimin Zhan, François Fuks, Zhi John Lu, Mingzhou Guo (2017) Methylation of TMEM176A is an independent prognostic marker and is involved in human colorectal cancer development. Epigenetics12(7):575-583
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Long Hu, Zhiyu Xu, Boqin Hu and Zhi John Lu* (2017) *COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. ** *Nucleic Acids Research 45 (1): e2
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Boqin Hu1, Yu-Cheng T. Yang1, Yiming Huang, Yumin Zhu and Zhi John Lu* (2017) POSTAR: a platform of post-transcriptional regulation coordinated by RNA binding proteins. Nucleic Acids Research 45 (D1): D104-D114 (1contributed equally)
2012 - 2016
2016
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Mengrong Liu1, Yu-Cheng T. Yang1, Gang Xu, Chang Tan, and Zhi John Lu* (2016) CCG: an integrative resource of cancer protein-coding and long noncoding RNA genes. Discovery Medicine 22 (123): 351-359 (1contributed equally)
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Yang Wu1, Rihao Qu1, Yiming Huang1, Binbin Shi, Mengrong Liu, Yang Li and Zhi John Lu* (2016) RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure probing data. Nucleic Acids Research 44 (W1): W294-W301 (1contributed equally)
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Jiapei Yuan1, Ye Zhang1, Jinsong Dong, Xinbao Sun, Yuzhe Sun, Boon L. Lim, Dong Liu* and Zhi John Lu* (2016) Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17:655 (1contributed equally, *: co-corresponding authors)
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Baoping Cao1, Nanxi Song1, Meiying Zhang, Runsheng Chen, Youyong Lu, Runshen Chen*, Zhi John Lu* and Mingzhou Guo* (2016) Systematic study of novel lncRNAs in different gastrointestinal cancer cell lines. Discovery Medicine 21(115):159-171 (1contributed equally, *: co-corresponding authors)
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[review]: Xihao Hu1, Yang Wu1, Zhi John Lu and Kevin Y. Yip. (2016) Analysis of Sequencing Data for Probing RNA Secondary Structures and Protein-RNA Binding in Studying Post-Transcriptional Regulations. Briefings in Bioinformatics 17(6): 1032-1043 (1contributed equally)
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Kejia Wen1, Lijuan Yang1, Tuanlin Xiong, Chao Di, Danhui Ma, Menghua Wu, Zhaoyu Xue, Xuedi Zhang, Li Long, Weimin Zhang, Jiaying Zhang, Xiaolin Bi, Junbiao Dai, Qiangfeng Zhang, Zhi John Lu and Guanjun Gao (2016) Critical roles of long noncoding RNAs in Drosophila spermatogenesis. Genome Research 26: 1233-1244 (1contributed equally)
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Sibo Tao1, Ye Zhang1, Xiaoyue Wang, Xiaofeng Fang, Le Xu, Zhi John Lu and Dong Liu (2016) The THO/TREX complex active in mRNA export suppresses root-associated acid phosphatase activity induced by phosphate starvation. Plant Physiology 171(4):2841-53 (1contributed equally)
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Sai Luo, J. Yuyang Lu, Lichao Liu, Yafei Yin, Chunyan Chen, Xue Han, Bohou Wu, Ronggang Xu, Wei Liu, Pixi Yan, Wen Shao, Zhi Lu, Haitao Li, Jie Na, Fuchou Tang, Jianlong Wang, Yong E. Zhang, Xiaohua Shen (2016) Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells. Cell Stem Cell 21(115):159-171
2015
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Yang Wu1, Binbin Shi1, Xinqiang Ding, Tong Liu, Xihao Hu, Kevin Y. Yip, Zheng Rong Yang, David H. Mathews and Zhi John Lu* (2015) Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic Acids Research 43(15): 7247-59 (1contributed equally)
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Long 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
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Yu-Cheng T. Yang1, Chao Di1, Boqin Hu1, 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 16:51 (1contributed equally)
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Yinghan Fu, Zhengjiang Zech Xu, Zhi J. Lu, Shan Zhao, and David H. Mathews(2015) Discovery of Novel ncRNA Squences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PloS one10(6):e0130200
2014
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Chao Di1, Jiapei Yuan1, 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(5), 848-861 (1contributed equally)
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Mark B. Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander,… Chao Di, … Zhi Lu, … Thomas R. Gingeras and Robert Waterston.(2014) Comparative analysis of the transcriptome across distant species. Nature 512:445-448
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YC Yang, J Umetsu, ZJ Lu* (2014) Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae. Science China Life Sciences 57 (1), 22-35 (Tsinghua Special Issue)
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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 30(8), 1049-1055.
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B Ren, H Shen, ZJ Lu, H Liu, Y Xu. (2014) The phzA2-G2 Transcript Exhibits Direct RsmA-Mediated Activation in Pseudomonas aeruginosa M18. PloS one 9 (2), e89653
2013
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Freeberg MA, Han T,Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology 14, R13.
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Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology 14:R5
2012
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Tan X, Hu L2, Luquette JL, Gao G, Liu YF2, Qu HJ, Xi RB, Lu ZJ2, Park PJ & Elledge SJ. (2012) Systematic Identification of Synergistic Drug Pairs Targeting HIV. Nature Biotech 30:1125-1130. (2 Lu Lab, School of Life Sciences, Tsinghua University)
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Tan X, Lu ZJ2, Gao G, Xu QK, Hu L2, Fellmann C, Li MZ, Qu HJ, Lowe SW, Hannon GJ & Elledge SJ. (2012) Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proc. Natl. Acad. Sci. U. S. A., 109(3):869-74. (2Lu Lab, School of Life Sciences, Tsinghua University)
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The ENCODE Project Consortium# (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74 (# ZJL was a member of ENCODE Consortium)
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He C, Li YX, Zhang G, Gu Z, Yang R, Li J, Lu ZJ, Zhou ZH, Zhang C, Wang J. (2012) MiRmat: Mature microRNA Sequence Prediction. PloS one 7 (12), e51673.
2010 - 2011 (Postdoc)
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Lu ZJ1, Yip KY1, Wang G, Shou C, Hillier LW, et al. (2011) Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Research 21: 276-285. (1contributed equally) [modENCODE special issue]
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Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, et al. (2011) Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research 21: 245-254.
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Mu XJ, Lu ZJ, Kong Y, Lam HYK, Gerstein MB. (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research 39 (16):7058-7076.
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Li Y, Du X, Lu ZJ, Wu D, Zhao Y, et al. (2011) Regulatory Feedback Loop of Two phz Gene Clusters through 5’ Untranslated Regions in Pseudomonas sp. M18.PLoS ONE 6(4): e19413
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Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Joel R, Lu ZJ, Niu W, Alves P, Kato M, Gerstein MB. (2011) Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol 7: e1002190
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Gerstein MB1,*, Lu ZJ1, Van Nostrand EL1, Cheng C1, Arshinoff BI1, et al. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project Science 330 (6012): 1775-1787 (120 co-first authors, *15 co-corresponding authors, ~150 authors in total) [Cover Story]
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Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, et al. (2010) Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response. PLoS Genetics 9.532) 6(2): e1000848.
2006 - 2009 (Ph.D.)
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Lu ZJ, Gloor JW, Mathews DH. (2009) Improved RNA secondary structure prediction by maximizing expedted pair accuracy. RNA 15:1805-1813.
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Lu ZJ, Mathews DH. (2008) Efficient siRNA selection using hybridization thermodynamics.Nucleic Acids Research 36:640-647.
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Lu ZJ, Mathews DH. (2008) OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research 36:W104-W108.
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Lu ZJ, Mathews DH. (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research 36:3738-3745.
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Lu ZJ, Turner DH, Mathews DH. (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research34:4912-4924.