Representative Publications

Table of Contents:

• A. [RNA-Finder] Bioinfo-Driven Precision Medicine
  • A1. (Cell-free) RNA Biomarker
  • A2. ncRNA Method
• B. [RNA-Talk] AI-Driven RNA Modeling & Drug Design
  • B1. RNA Interaction (trans-pair) and Regulation Network
    • RNA-RNA (trans-pair)
    • RNA-Protein (POSTAR/CLIPdb)
  • B2. RNA Structure (cis-pair) Prediction & Enzyme Design
  • B3. Drug Design Targeting RNA
    • Small RNA drug targeting RNA
    • Small molecule drug targeting RNA

Full list of publications

Software

代表性文章中文解读

A. [RNA-Finder] Bioinfo-Driven Precision Medicine

A1. (Cell-free) RNA Biomarker

• Pengfei Bao¹, Taiwei Wang¹, Xiaofan Liu¹, Shaozhen Xing, Hanjin Ruan, Hongli Ma, Yuhuan Tao, Qing Zhan, Efres Belmonte-Reche, Lizheng Qin, Zhengxue Han, Minghui Mao*, Mengtao Li* & Zhi John Lu* (2025) Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential. Genome Biology 26, 119 (¹contributed equally, *co-corresponding authors) Github: https://github.com/lulab/cfPeak
• Hongke Wang¹, Qing Zhan¹, Meng Ning¹, Hongjie Guo¹, Qian Wang, Jiuliang Zhao, Pengfei Bao, Shaozhen Xing, Shanwen Chen, Shuai Zuo, Xuefeng Xia, Mengtao Li*, Pengyuan Wang*, Zhi John Lu* (2024) Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles Clinical and Translational Medicine 14:e1760 (¹contributed equally, *co-corresponding authors)
• Xiaofan Liu¹, Yuhuan Tao¹, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li*, Yunping Zhu*, Zhi John Lu* (2024) Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data Bioinformatics 40(5), btae316 (¹contributed equally, *co-corresponding authors) Github: https://github.com/lulab/Pathformer
• Mingyang Li¹, Tianxiu Zhou¹, Mingfei Han¹, Hongke Wang, Pengfei Bao, Yuhuan Tao, Xiaoqing Chen, Guansheng Wu, Tianyou Liu, Xiaojuan Wang, Qian Lu*, Yunping Zhu*, Zhi John Lu* (2024) cfOmics: a cell-free multi-Omics database for diseases. Nucleic Acids Research 52(D1):D607-D621 (¹contributed equally, *co-corresponding authors) Website: http://cfOmics.ncRNAlab.org
• 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 potential biomarkers in gastrointestinal cancer patients’ blood. Cell Reports Medicine 4(11):101281 (¹contributed equally, *co-corresponding authors)
• 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 14(5):e1791 (¹contributed equally, *co-corresponding authors)
• 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 93:104645 (¹contributed equally, *co-corresponding authors)
• Shanwen Chen¹, Yunfan Jin¹, Siqi Wang¹, Shaozhen Xing¹, …, Zhenjiang Zech Xu*, Zhi John Lu* and Pengyuan Wang* (2022) Cancer Type Classification Using Plasma Cell Free RNAs Derived from Human and Microbes. eLife 11:e75181 (¹contributed equally, *co-corresponding authors) (IF: 8.7)
• 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) (IF: 11.556) (Patent Protected)
• Shuaishuai Teng¹, Yang Eric Li¹, …, 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) (IF: 25.6)
• 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) (IF: 8.3) (Patent Protected)
• Yang Yang¹, Lei Chen¹, Jin Gu¹, Hanshuo Zhang¹, …, 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) (IF: 17.69)

A2. ncRNA Method

• 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) (IF: 12.78)
• [Algorithm V3] Zhiyu Xu1, Long Hu1, Binbin Shi, SiSi Geng, Longchen Xu, Dong Wang* & Zhi John Lu* (2018) Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Research 46 (18), e109-e109 (IF: 19.16) Github: https://github.com/lulab/Ribowave
• Yang Yang1, Lei Chen1, Jin Gu1, Hanshuo Zhang1, …, Hongyang Wang, Michael Q. Zhang and Zhi John Lu* (2017) Recurrently deregulated lncRNAs in hepatocellular carcinoma.Nature Communications 8, 14421 (1contributed equally) (IF: 17.69)
• [Algorithm V2] 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 (IF: 19.16) Github: https://github.com/lulab/COME
• [Algorithm V1] 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. (IF: 19.16) Github: https://github.com/lulab/RNAfeature
• Gerstein MB, Joel Rozowsky, Koon-Kiu Yan, …, Lu Z, …, Robert Waterston (2014) Comparative Analysis of the Transcriptome across Distant Species. Nature 512(7515):445-448.
• ENCODE Project Consortium#. (2012) An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489, 57–74. (#Lu Z was a member of ENCODE Consortium) [Cover Story]
• [AlgorithmV0] Lu ZJ¹, Yip KY¹, Wang G, Shou C, Hillier LW, et al. (2011) Prediction and characterization of noncoding RNA in C. elegans by integrating conservation, secondary structure and high-throughput sequencing and array data. Genome Research 21: 276-2857 (¹contributed equally) (IF: 10.98)
• [Algorithm V0] Gerstein 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 (^†20 co-first authors, *15 co-corresponding authors, ~150 authors in total) [Cover Story]

B. [RNA-Talk] AI-Driven RNA Modeling & Drug Design

B1. RNA Interaction (trans-pair) and Regulation Network

RNA-RNA (trans-pair)

• [Language Model] Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu (2024) OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics 40 (10), btae577. software: OligoFormer
• Tan X, Lu ZJ ², 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. PNAS, 109(3): 869-74 (²Lu Lab, School of Life Sciences, Tsinghua University) (IF: 12.78)
• [Server] Lu ZJ and Mathews DH (2008) OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research 36:W104-W108. (IF: 19.16) website: OligoWalk
• [Algorithm] Lu ZJ and Mathews DH (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research 36:640-647. (IF: 19.16) software: RNAstructure
• [Biophysical Model] Lu ZJ and Mathews DH (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research 36:3738-3745. (IF: 19.16)

RNA-Protein (POSTAR/CLIPdb)

• [Database V3] Weihao Zhao¹, Shang Zhang¹, …, 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 (IF: 19.16) Website: http://POSTAR3.ncRNAlab.org
• Rui Xiao¹, Jia-Yu Chen¹, Zhengyu Liang¹, Daji Luo, Geng Chen, Zhi John Lu, …, 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
• [Database V2] Yumin Zhu1, Gang Xu1, Yucheng T Yang1, Zhiyu Xu, Xinduo Chen, Binbin Shi, Daoxin Xie, Zhi John Lu* and Pengyuan Wang* (2019) POSTAR2: deciphering the post-transcriptional regulatory logics. Nucleic Acids Research (D1):D203-D211 (1contributed equally) (IF: 19.16) Website: http://POSTAR2.ncRNAlab.org
• [Mathematical Model] 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) (IF: 17.91) Github: https://github.com/lulab/RBPgroup
• [Database V1] 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) (IF: 19.16) Website: http://POSTAR.ncRNAlab.org

B2. RNA Structure (cis-pair) Prediction & Enzyme Design

• [Server] 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) (IF: 19.16)
• [Algorithm] 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) (IF: 19.16) Github: https://github.com/lulab/RME
• [Algorithm] Lu ZJ, Gloor JW and Mathews DH (2009) Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 15: 1805-1813. (IF: 4.9) software: RNAstructure
• [Biophysical Model] Lu ZJ, Turner DH and Mathews DH (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research 34:4912-4924. (IF: 19.16)

B3. Drug Design Targeting RNA

Small RNA drug targeting RNA

• [Language Model] Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu (2024) OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics 40 (10), btae577. software: OligoFormer
• Tan X, Lu ZJ ², 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. PNAS, 109(3): 869-74 (²Lu Lab, School of Life Sciences, Tsinghua University) (IF: 12.78)
• [Server] Lu ZJ and Mathews DH (2008) OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research 36:W104-W108. (IF: 19.16) website: OligoWalk
• [Algorithm] Lu ZJ and Mathews DH (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research 36:640-647. (IF: 19.16) software: RNAstructure
• [Biophysical Model] Lu ZJ and Mathews DH (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research 36:3738-3745. (IF: 19.16)

Small molecule drug targeting RNA

• Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu* and Zhi John Lu*. (2025) RNA–ligand interaction scoring via data perturbation and augmentation modeling. Nature Computational Science 10.1038/s43588-025-00820-x (*co-corresponding authors)
• 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) (IF: 11.62)
• Tan X, Hu L², Luquette LJ, 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 (²Lu Lab, School of Life Sciences, Tsinghua University) (IF: 54.36)