2012

---

• Dijun Chen, Chun-hui Yuan, Jian Zhang, Zhao Zhang, Lin Bai, Yijun Meng, Ling-ling Chen, Ming Chen*
  PlantNATsDB: a comprehensive database of plant natural antisense transcripts
  Nucleic Acids Research, 40(1): D1187-D1193.
• Yijun Meng*, Chaogang Shao, Huizhong Wang, Ming Chen*
  Are all the miRBase-registered microRNAs true?: A structure- and expression-based re-examination in plants
  RNA Biology, 9(4): .
• Chao Feng, Ming Chen, Chang-jie Xu, Lin Bai, Xue-ren Yin, Xian Li, Andrew C. Allan, Ian B. Ferguson and Kun-song Chen
  Genetic, transcriptomic, and metabolic analysis of Chinese bayberry (Myrica rubra) using RNA-Seq
  BMC Genomics, 13: 19.
• 陈铭 主编
  生物信息学
  科学出版社, 2012. ISBN: 978-7-03-033205-9.

  

2011

---

• Donglin Huang, Yiling Huang, Youhuang Bai, Dijun Chen, Ralf Hofestädt, Christian Klukas, Ming Chen*
  MyBioNet: interactively visualize, edit and merge biological networks on the Web
  Bioinformatics, 27(23): 3321-3322 .
• Yijun Meng, Chaogang Shao, Ming Chen*
  Toward microRNA-mediated gene regulatory networks in plants
  Briefings in Bioinformatics, 12(6): 645-659.
• Dijun Chen, Yijun Meng, Chunhui Yuan, Lin Bai, Donglin Huang, Shaolei Lv, Ping Wu, Lingling Chen, Ming Chen*
  Plant siRNAs from introns mediate DNA methylation of host genes
  RNA, 17(6): 1012-1024.
• Yijun Meng*, Chaogang Shao, Huizhong Wang, Ming Chen*
  The regulatory activities of plant microRNAs: a more dynamic perspective
  Plant Physiology, 157(4): 1583-1595.
• Yijun Meng, Chaogang Shao, Lingfeng Gou, Yongfeng Jin, Ming Chen*
  Construction of MicroRNA- and MicroRNA*-mediated regulatory networks in plants
  RNA Biology, 8(6): 1124-1148.
• Yijun Meng, Lingfeng Gou, Dijun Chen, Chuanzao Mao, Yongfeng Jin, Ping Wu, Ming Chen*
  PmiRKB: a plant microRNA knowledge base
  Nucleic Acids Research, 39(Database issue): D181-D187.
• Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng and Ming Chen*
  PRIN, a predicted rice interactome network
  BMC Bioinformatics, 12:161.
• Pengcheng Zhu, Haibin Gu, Yinming Jiao, Donglin Huang, Ming Chen*
  Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network
  Genomics, Proteomics & Bioinformatics, 9(4-5): 128-137.
• Yihui Luo, Yan Liu, Dexter Sun, David M. Ojcius, Jinfang Zhao, Xuai Lin, Dong Wu, Rongguang Zhang, Ming Chen, Lanjuan Li, Jie Yan
  InvA protein: a nudix hydrolase required for infection by pathogenic leptospira in cell lines and animals
  The Journal of Biological Chemistry , 286(42):36852-36863.
• Yijun Meng, Ping Wu, Ming Chen
  MicroRNAs in plant roots: current understanding and future perspectives
  In Non Coding RNAs in Plants (Erdmann & Barciszewski, ed.), ISBN 978-3-642-19453-5, pp. 269-284.

  

• Youhuang Bai, Yijun Meng, Donglin Huang, Yanhua Qi, Ming Chen*
  Origin and Evolutionary Analysis of the Plant-specific TIFY Transcription Factor Family
  Genomics, 98: 128-136. (cover page)
• Lili Liu, Lin Bai, Cong Luo, Donglin Huang, Ming Chen*
  Systematic Annotation and Bioinformatics Analyses of Large-scale Oryza sativa Proteome
  Current Protein & Peptide Science, 12(7): 621-630.
• Yu ZhiMing, Kang Bo, He XiaoWei, Lv ShaoLei, Bai YouHuang, Ding WoNa, Chen Ming, Cho Hyung-Taeg and Wu Ping
  Root hair-specific EXPANSINs modulate root hair elongation in rice
  The Plant Journal, doi: 10.1111/j.1365-313X.2011.04533.x.
• Jian-ying Li, Hui-juan Yang, Tian-yun Lan, Hao Wei, Hua-rong Zhang, Ming Chen, Wei Fan, Ying-ying Ma, Bo-xiong Zhong
  Expression Profiling and Regulation of Genes Related to Silkworm Posterior Silk Gland Development and Fibroin Synthesis
  Journal of Proteome Research, dx.doi.org/10.1021/pr200196x.
• Yong Min, Xiaogang Jin*, Ming Chen*, Zhengzheng Pan, Ying Ge, Jie Chang
  Pathway knockout and redundancy in metabolic networks
  Journal of Theoretical Biology, 270: 63-69.
• Ming Chen, Minjie Hu, Ralf Hofestädt
  A Systematic Petri Net Approach for Multiple Scale Modeling and Simulation of Biochemical Processes
  Applied Biochemistry and Biotechnology, 164(3): 338-352.
• Ming Chen et al. (2011)
  Two articles selected
  In Biological Petri Nets (Edgar Wingender ed.) , ISBN 978-1-60750-703-1

  

• 曹俊杰, 郑利斌, 陈铭*
  蛋白质互作网络的分形分析
  浙江大学学报(理学版), 38(4): 445-449.

2010

---

• Yijun Meng, Lingfeng Gou, Dijun Chen, Ping Wu, Ming Chen*
  High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism
  Journal of Experimental Botany, 61(14): 3833-3837.
• Dijun Chen, Yijun Meng, Xiaoxia Ma, Chuanzao Mao, Youhuang Bai, Junjie Cao, Haibin Gu, Ping Wu, Ming Chen*
  Small RNAs in angiosperms: sequence characteristics, distribution, and generation
  Bioinformatics, 26(11): 1391-1394.
• Donglin Huang, Yiling Huang, Christian Klukas, Ralf Hofestaedt, Ming Chen*
  PBSK Browser: navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats
  2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops.  pp: 13-17.
• Ming Chen, Yijun Meng, Haibin Gu, Dijun Chen
  Functional characterization of plant small RNAs based on next-generation sequencing data
  Computational Biology and Chemistry, 34: 308–312.
• Chaogang Shao, Yijun Meng, Shaolei Lv, Wei Zhong, Zheyu Wang, Ming Chen*
  CloneAssistant 1.0: a stand-alone software for automated cloning primer design
  Journal of Biotechnology, 150: 294-298.
• Yijun Meng, Dijun Chen, YongFeng Jin, Chuanzao Mao, Ping Wu, Ming Chen*
  RNA editing of nuclear transcripts in Arabidopsis thaliana
  BMC Genomics, 10(S4): S12.
• ChenJia Shen, YouHuang Bai, SuiKang Wang, SaiNa Zhang, YunRong Wu, Ming Chen, Tom J Guilfoyle, Ping Wu, YanHua Qi
  Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.)
  Journal of Experimental Botany, 61(14): 3971-3981.
• ChenJia Shen, YouHuang Bai, SuiKang Wang, SaiNa Zhang, YunRong Wu, Ming Chen, DeAn Jiang, YanHua Qi
  Auxin transporters PIN, AUX/LAX and PGP in Sorghum Bicolor
  FEBS Journal, 277(14): 2954-2969.
• SuiKang Wang, YouHuang Bai, ChenJia Shen, YunRong Wu, SaiNa Zhang, DeAn Jiang, Tom J Guilfoyle, Ming Chen*, YanHua Qi*
  Auxin-related gene families in abiotic stress response in Sorghum bicolor
  Functional & Integrative Genomics, 10: 533-546.
• Ming Chen, Shaolei Lv, Yijun Meng
  The Epigenetic Performers in Plants
  Development, Growth and Differentiation, 52(6): 555-566.
• Yijun Meng, Xiaoxia Ma, Dijun Chen, Ping Wu, Ming Chen*
  MicroRNA-mediated signaling involved in plant root development
  Biochemical and Biophysical Research Communications, 393: 345-349.
• Ming Chen, Yijun Meng, Chuanzao Mao, Dijun Chen, Ping Wu
  Methodological framework for functional characterization of plant microRNAs
  Journal of Experimental Botany, 61(9): 2271-2280.
• Jianying Li, S. Hossein Hosseini Moghaddam, Xiang Chen, Ming Chen, Boxiong Zhong
  Shotgun strategy-based proteome profiling analysis on the head of silkworm Bombyx mori
  Amino Acids, 39(3): 751-761.
• Jian-ying Li, S. Hossein Hosseini Moghaddam, Jin-e Chen, Ming Chen, Bo-xiong Zhong
  Shotgun proteomic analysis on the embryos of silkworm Bombyx mori at the end of organogenesis
  Insect Biochemistry and Molecular Biology, 40: 293-302.
• Qingyun Shi, Yijun Meng, Dijun Chen, Fei He, Haibin Gu, Ping Wu, Ming Chen*
  OsCAS: a comprehensive web-based annotation platform for rice microarray data
  BioChip Journal, 4(1): 9-15.
• CHEN DiJun, ZHANG Fan, YUAN ChunHui, LU Jing, LI Xia, CHEN Ming*
  A web-based platform for rice microarray annotation and data analysis
  Science in China Series C: Life Sciences, 53(12): 1459-1466.
• Yijun Meng, Dijun Chen, Xiaoxia Ma, Chuanzao Mao, Junjie Cao, Ping Wu, Ming Chen*
  Mechanisms of microRNA-mediated auxin signaling inferred from the rice mutant osaxr
  Plant Signaling & Behavior, 5(3): 252-254.
• Sebastian Janowski, Benjamin Kormeier, Thoralf Töpel, Klaus Hippe, Ralf Hofestädt, Nils Willassen, Rafael Friesen, Sebastian Rubert, Daniela Borck, Peik Haugen and Ming Chen
  Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing
  In Silico Biology, 10, 0003.

2009

---

• Xiang Chen, Cong Luo, Xiaoxia Ma, Ming Chen*
  VIRS: a visual tool for identifying restriction sites in multiple DNA sequences
  Biotechnology Progress, 25(5): 1525-1527.
• Yijun Meng, Fangliang Huang, Qingyun Shi, Junjie Cao, Dijun Chen, Jinwei Zhang, Jun Ni, Ping Wu, Ming Chen*
  Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant
  Planta, 230: 883-898.
• Huijuan Yang, Zhonghua Zhou, Huarong Zhang, Ming Chen, Jianying Li, Yingying Ma, Boxiong Zhong
  Shotgun proteomic analysis of the fat body during metamorphosis of domesticated silkworm (Bombyx mori)
  Amino Acids, 38(5): 1333-1342.
• Jian-ying Li, Xiang Chen, Wei Fan, S. Hossein Hosseini Moghaddam, Ming Chen, Zhong-hua Zhou, Hui-juan Yang, Jin-e Chen, Bo-xiong Zhong
  Proteomic and Bioinformatic Analysis on Endocrine Organs of Domesticated Silkworm, Bombyx mori L. for a Comprehensive Understanding of Their Roles and Relations
  Journal of Proteome Research, 8(6): 2620-2632.
• J.-Y. Li, X. Chen, S. H. Hosseini Moghaddam, M. Chen, H. Wei and B.-X. Zhong
  Shotgun proteomics approach to characterize the embryonic proteome of silkworm, Bombyx mori at labrum appearance stage
  Insect Molecular Biology, 18(5): 649-60.
• Shuangyan Chen, Xiu-Qing Li, Aiguo Zhao, Lijuan Wang, Xiaofeng Li, Qingyun Shi, Ming Chen, Juan Guo, Jichong Zhang, Dongmei Qi, Gongshe Liu
  Genes and Pathways Induced in Early Response to Simulated-Grazing Defoliation in Rice Seedlings
  Current Issues in Molecular Biology, 11(2): 81-100.
• Zhaoyuan Fang, Chuan Shao, Yijun Meng, Ping Wu, Ming Chen*
  Phosphate Signaling in Arabidopsis and Oryza sativa (update)
  Plant Science, 176(2): 170-180.
• Ming Chen, Sridhar Hariharaputran, Ralf Hofestädt, Benjamin Kormeier, Sarah Spangardt
  Petri Net Models for the Semi-automatic Construction of Large Scale Biological Networks
  Natural Computing, DOI: 10.1007/s11047-009-9151-y.
• 罗依惠，陈铭，李立伟，钱景，严杰
  问号钩端螺旋体毒力相关蛋白InvA转录和表达特征的研究
  中华微生物学和免疫学杂志，29(1): 24-28.
• 陈迪俊，张帆，吴超，李霞，陈铭*
  基于Web的水稻芯片数据注释和分析平台
  中国科学C辑 生命科学, 39(3): 323-332.

2008

---

• Ming Chen, Andrew Harrison
  In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops
  Genomics, Proteomics & Bioinformatics, 9(3-4): 190-198.
• Zhong-hua Zhou, Hui-juan Yang, Ming Chen, Cheng-fu Lou, Yao-zhou Zhang, Ke-ping Chen, Yong Wang, Mei-lan Yu, Fang Yu, Jian-ying Li and Bo-xiong Zhong
  Comparative Proteomic Analysis between the Domesticated Silkworm (Bombyx mori) Reared on Fresh Mulberry Leaves and on Artificial Diet
  Journal of Proteome Research, 7(12): 5103-5111.
• Hao Tian, Weiren Cui, Tao Wan, Ming Chen*
  A Computational Approach for Recognition of Electronic Microscope Plant Pollen Images
  2008 Congress on Image and Signal Processing, pp. 259-263.
• 陈铭，王祎萍，罗聪
  生物信息学双语词汇通解
  浙江大学出版社, 2008. ISBN: 978-7-308-05924-4.

  

2007

---

• Liming Du, Fangchan Jiao, Jun Chu, Gulei Jin, Ming Chen*, Ping Wu*
  The Two-component Signal System in Rice (Oryza sativa L.): A Genome-Wide Study of Cytokinin Signal Perception and Transduction
  Genomics, 89: 697-707.
• 何飞，施清芸，陈铭*，吴平*
  RiceDB：基于Web界面的水稻基因芯片注释整合数据库
  中国水稻科学, 21(3): 235-241.
• He Fei, Shi Qing-yun, Chen Ming, Wu Ping
  RiceDB: A Web-Based Integrated Database for Annotating Rice Microarray
  Rice Science, 14(4): 256-264.
• Jiaofang Shao, Qichao Tu, Ming Chen*
  Comprehensive Computational Analysis Approach for Alzheimer's Disease
  The 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE 2007. IEEE Xplore. pp: 1076-1079.
• Peng Zhou, Ji Wen, Aharon Oren, Ming Chen, Min Wu
  Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)
  Genomics, 90: 103-109.
• 陈铭
  系统生物学（Systems Biology）的几大重要问题
  生物信息学, 5(3): 129-136.

2006

---

• Xiaohui Chen, Ming Chen*, Kaida Ning
  BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network
  Bioinformatics, 22: 2952-2954.
• 陈晓辉，宁开达，陈铭*
  基于大规模DNA 微阵列数据的调控亚网络的重建
  生物信息学中的智能计算理论与研究方法（黄德双等主编），pp.65-69.

  

• Ming Chen, Fei He, Qingyun Shi, Ping Wu
  A novel and integrative approach for rice gene expression an annotation and functional analysis
  2nd International Rice Congress, Oct. 9-13, New Delhi, India.
• 陈铭
  整合生物信息学
  计算机教育, 9: 7-10.
• Ming Chen, Ralf Hofestaedt
  Prediction and Alignment of Metabolic Pathways
  In Bioinformatics of Genome Regulation and Structure II (Nikolay Kolchanov ed.), pp.355-365.

  

• Ming Chen, Ralf Hofestaedt
  A Medical Bioinformatics Approach for Metabolic Disorders: Biomedical Data Prediction, Modeling and Systematic Analysis
  Journal of Biomedical Informatics, 39(2): 147-159.

2005

---

• Ming Chen, Andreas Freier, Ralf Hofestaedt
  Bioinformatics Approaches for Metabolic Pathways
  In Handbook of Genome Research (Christoph W. Sensen ed.), pp.461-490.

  

• Zheng Ye, Huan Xu, Qichao Tu, Shu Hong, Tiansheng Xie, Di Xia, Ming Chen*
  A Web-based Platform for Drug Metabolism Research
  2005 Hangzhou International Conference on Drug Metabolism, Oct. 18th-20th, Hangzhou, China.
• Sridhar Hariharaputran, Ming Chen and Ralf Hofestät
  Alignment and Classification of Signaling Pathways
  German Conference on Bioinformatics, Oct. 5th-7th, Hamburg, Germany.
• Ming Chen, Ralf Hofestädt
  Integrative Analysis of Metabolic Disorders by Means of Medical Bioinformatics
  27th Annual International Conference of the IEEE Engineering In Medicine and Biology Society (EMBS), 2005, Sep.1-4, Shanghai, China. pp. 228-231.
• Ming Chen
  Systems Biology Brings Life Sciences Closer
  Genomics, Proteomics & Bioinformatics, 3(3): 194-196.
• 罗辽复，陈铭，张文广
  生物信息学培训班讲义
  内蒙古农业大学.
• 张文广，陈铭
  绒山羊分子生物学数据库的设计与构建
  中国生物工程杂志, 25(B04): 199-203.
• Ming Chen
  Structural Analysis of Generalized and Specific Biological Networks
  Metabolic Pathway Analysis, MPA'05, 2005, March 3-4, Jena, Germany.
• Ming Chen, Ralf Hofestaedt
  An algorithm for linear metabolic pathway alignment
  In Silico Biology, 5: 111-128.

2004

---

• Ming Chen, Ralf Hofestaedt
  PathAligner: Metabolic Pathway Retrieval and Alignment
  Applied Bioinformatics, 3(4), 241-252.
• Ralf Hofestaedt, Ming Chen
  Metabolic Pathway Prediction/Alignment
  Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), July 25-30, 2004, Novosibirsk, Russia, Vol. 2, 68-72.
• Ming Chen, Ralf Hofestaedt
  Web-based Information Retrieval System for the Prediction of Metabolic Pathways
  IEEE Transactions on Nanobioscience, 3(3), 192-199.
• Ming Chen
  In Silico Systems Analysis of Biopathways
  PhD Thesis (Dr. rer. nat), Faculty of Technology, Bielefeld University, Bielefeld, Germany.
• Ming Chen
  A Systems Analysis of Urea Cycle Disorders
  3rd BREW: Bioinformatics Research & Education Workshop, 2004, April 26-28, Helsinki, Finland.
• 陈铭
  后基因组时代的生物信息学
  生物信息学, 2(2): 29-34.
• Ming Chen, Susana Lin and Ralf Hofestaedt
  STCDB: Signal Transduction Classification Database
  Nucleic Acids Research, 32(1), D456-D458.

2003

---

• Ming Chen and Ralf Hofestaedt
  Quantitative Petri net model of gene regulated metabolic networks in the cell
  In Silico Biology, 3(3), 347-365.
• Ming Chen, Susana Lin and Ralf Hofestaedt
  Recommendations for Classification and Nomenclature of Signal Transduction
  In: Signal Transduction: Receptors, Mediators and Genes - abstract proceedings of 7th Meeting of the Signal Transduction Society, 2003, Nov. 6-8, Weimar, Germany, Vol.3-4/2003: 134.
• Susana Lin, Ming Chen and Ralf Hofestaedt
  Signaling Network triggerable by Trypanosoma cruzi through Calcium
  In: Signal Transduction: Receptors, Mediators and Genes - abstract proceedings of 7th Meeting of the Signal Transduction Society, 2003, Nov. 6-8, Weimar, Germany, Vol.3-4/2003: 174.
• Ming Chen
  Reconstruction of Metabolic Pathways via a Web-Based Biological Information Retrieval System
  2nd BREW: Bioinformatics Research & Education Workshop, 2003, April 28-40, ZIF-Uni, Bielefeld, Germany.

2002

---

• Ming Chen, Andreas Freier, Jacob Koehler, Alexander Rueegg
  The Biology Petri Net Markup Language
  In: Juerg Desel, Mathias Weske (Hrsg.), Lecture Notes in Informatics - proceedings of Promise'2002, Oct. 9-11, 2002, Potsdam, Germany, Vol. 21, 150-161.
• Ming Chen
  Modelling and Simulation of Metabolic Networks: Petri Nets Approach and Perspective
  Proceedings of the 16th European Simulation Multiconference (ESM'2002), June 3-5, 2002, Darmstadt, Germany, pp: 441-444.
• Ming Chen
  Systems Biology Modeling and Simulating Metabolic Networks with Petri Nets
  In Poster Abstracts' Book of the ICSB'02 - International Conference on Systems Biology, 2002, Dec. 13-15, Stockholm, Sweden, p85.
• Ming Chen
  Matabolic Pathway Alignment and Alternative Pathways Indentification
  In Poster Abstracts' Book of the ECCB'02 (in conjunction with the GCB'02) - European Conference on Computational Biology, 2002, Oct. 6-9, Saarbrücken, Germany, p22: 40-41.
• Ming Chen
  Pairwise Metabolic Pathway Alignment
  In abstract of the WABI'02 - 2nd Workshop on Algorithms in Bioinformatics, 2002, Sep. 16-21, Rome, Italy.
• Ming Chen, Andreas Freier and Ralf Hofestaedt
  Graph Theory Based Metabolic Network Initial Analysis and Metabolic Pathway Alignment
  the abstract proceeding of "ICM 2002, The 3rd International Conference on Mathematical Biology", 2002, Aug. 15-18, Guilin, China.
• Ming Chen and Andreas Freier
  Petri Net Based Modelling and Simulation of Metabolic Networks in the Cell
  1st BREW: Bioinformatics Research & Education Workshop, 2002, April 17-19, EMBL-EBI, Cambridge, England.

2000-2001

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• Ming Chen, Ralf Hofestaedt and Andreas Freier
  A Workable Approach for Modeling and Simulation of Biochemical Processes with a Hybrid Petri nets System
  1st International MTBio Workshop on Function and Regulation of Cellular Systems: Experiments and Models, 2001, June 24-30, Dresden, Germany, p20.
• Ming Chen
  Modelling the glycolysis metabolism using hybrid petri nets
  DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und genomischer Datenmengen, 2000, Mai 19-20, Magdeburg, Germany.
• Andreas Freier, Ming Chen und Ralf Hofestaedt
  MetabSim - Regelbasierte Simulation Metabolischer Prozesse
  DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und genomischer Datenmengen, 2000, Mai 19-20, Magdeburg, Germany.