Home >> Publications
In this page:
Date: |
Publications:
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
- 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.
Up to Top |