Home >> Publications
In this page:
Date:
|
Publications:
 2024
- Liya Liu#, Enyan Liu, Yueming Hu, Sida Li, Shilong Zhang, Haoyu Chao, Yanshi Hu, Yanyan Zhu, Yifan Chen, Luyao Xie, Yi Shen, Liangwei Wu, Ming Chen* (2024)
ncPlantDB: A plant ncRNA database with potential ncPEP information and cell type-specific interaction
Nucleic Acids Research, gkae1017.   (SCI=4.4; 5.4)
- Haoyu Chao, Zhuojin Li, Dijun Chen*, Ming Chen* (2024)
iSeq: An integrated tool to fetch public sequencing data
Bioinformatics, btae641. (SCI=5.8; 8.3)
- Mengwei Cheng, Yinhuan Zhu, Han Yu, Linlin Shao, Yiming Zhang, Lanxing Li, Haohong Tu, Luyao Xie, Haoyu Chao, Peijing Zhang, Saige Xin, Cong Feng*, Vladimir Ivanisenko, Yuriy Orlov, Dijun Chen, Aloysius Wong, Yixin Eric Yang, Ming Chen* (2024)
Non-coding RNA notations, regulations and interactive resources
Briefings in Functional Genomics, 24: 217. (SCI=4.4; 5.4)
- Yi Shen, Liya Liu, Enyan Liu, Sida Li, Vladimir Ivanisenko, Yuriy Orlov, Ming Chen* (2024)
AthRiboNC: An Arabidopsis Database for ncRNAs with Coding Potential Revealed from Ribosome Profiling
Database, baae123. (SCI=4.4; 5.4)
- Cong Feng#, Ruxiu Tie#, Saige Xin#, Yuhao Chen, Sida Li, Yifan Chen, Xiaotian Hu, Yincong Zhou, Yongjing Liu, Yueming Hu, Yanshi Hu, Hang Pan, Zexu Wu, Haoyu Chao, Shilong Zhang, Qingyang Ni, Jinyan Huang, Wenda Luo, He Huang*, Ming Chen* (2024)
Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition
BMC Biology, 22(1): 143. (SCI=4.4; 5.4)
- Cong Feng#, Haoyan Fan#, Ruxiu Tie, Saige Xin, Ming Chen* (2024)
Deciphering the evolving niche interactome of human hematopoietic stem cells from ontogeny to aging
Frontiers in Molecular Biosciences, 11. (SCI=3.9)
- Yueming Hu#, Yejun Wang#, Xiaotian Hu, Haoyu Chao, Sida Li, Qingyang Ni, Yanyan Zhu, Yixue Hu, Ziyi Zhao, Ming Chen* (2024)
T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors
Computational and Structural Biotechnology, 23: 801-812. (SCI=6.0; 6.3)
- Ningyuan You, Chang Liu, Yuxin Gu, Rong Wang, Hanying Jia, Tianyun Zhang, Song Jiang, Jinsong Shi, Ming Chen, Min-Xin Guan, Siqi Sun, Shanshan Pei, Zhihong Liu*, Ning Shen* (2024)
SpliceTransformer predicts tissue-specific splicing linked to human diseases
Nature Communications, 15: 9129. (SCI=10.3; 11.6)
- Tianqi Lyu, Kerong Wu, Yincong Zhou, Tong Kong, Lin Li, Kaizhe Wang, Pan Fu, Pengyao Wei, Ming Chen, Jianping Zheng* (2024)
Single-cell RNA sequencing reveals the tumor heterogeneity and immunosuppressive microenvironment in urothelial carcinoma
Cancer Science, accpeted. (SCI=10.3; 11.6)
- Shilong Zhang, Tongyao Yu, Ge Zhang, Ming Chen, Dachuan Yin*, Chenyan Zhang* (2024)
Systematic simulation of tumor cell invasion and migration in response to time‑varying rotating magnetic field
Biomechanics and Modeling in Mechanobiology, 23:1617–1630. (SCI=3.0; 3.1)
- Chuanqiang Wu#, Huan Yu#, Fuxiang Liang#, Xiancong Huang#, Bin Jiang, Zhiling Lou, Yafei Liu, Zixiang Wu, Qi Wang, Hong Shen, Ming Chen, Pin Wu*, Ming Wu* (2024)
Hypoxia inhibits the iMo/cDC2/CD8+TRMs immune axis in the tumor microenvironment of human esophageal cancer
Journal for ImmunoTherapy of Cancer, 12(7): e008889. (SCI=10.3; 11.6)
- Shuyang Cai#, Honghu Li#, Ruxiu Tie#, Wei Shan#, Qian Luo#, Shufen Wang#, Cong Feng, Huiqiao Chen, Meng Zhang, Yulin Xu, Xia Li, Ming Chen, Jiahui Lu*, Pengxu Qian*, He Huang* (2024)
TNlrc3 signaling is indispensable for hematopoietic stem cell emergence via Notch signaling in vertebrates
Nature Communications, 15: 226. (SCI=14.7; 16.1)
- Hua Yu*, Jing Zhao, Yuxuan Shen, Lu Qiao, Yuheng Liu, Guanglei Xie, Shuhui Chang, Tingying Ge, Nan Li, Ming Chen, Hu Li, Jin Zhang*, Xi Wang* (2024)
The dynamic landscape of enhancer-derived RNA during mouse early embryo development
Cell Reports, 43(4): 114077. (SCI=7.5; 8.5)
- Ziyu Liu, Yi Shen, Yunliang Jiang*, Hancan Zhu, Hailong Hu*, Yanlei Kang*, Ming Chen, Zhong Li* (2024)
Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization
Frontiers in Microbiology, 15. (SCI=4.0)
- Shilong Zhang, Liangwei Wu, Zhimeng Zhao, Ming Chen* (2024)
Artificial Intelligence in Gerontology: Data-Driven Health Management and Precision Medicine
Advances in Gerontology, accepted. (SCI=7.5; 8.5)
- Zhaohui He#, Yangming Lan#, Xinkai Zhou#, Bianjiong Yu#, Zhu Tao, Fa Yang, Liang-Yu Fu, Haoyu Chao, Jiahao Wang, Rong-Xu Feng, Shimin Zuo, Wenzhi Lan, Chunli Chen, Ming Chen*, Xue Zhao*, Keming Hu*, Dijun Chen* (2024)
Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis
Plant Communications, 5(2): 100717. (SCI=10.5; 10.5)
- Jie Li#, Qingyang Ni#, Guangqi He, Jiale Huang, Haoyu Chao, Sida Li, Ming Chen*, Guoyu Hu*, James Whelan, Huixia Shou* (2024)
SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research
Genomics, Proteomics & Bioinformatics, qzae080. (SCI=11.5; 10.3)
- Mei, Fengyuan; Yang, Tianrui; Chao, Haoyu; Ma, Xiaohui; Wu, Jingjing; Yang, Qi; Ren, Guangpen; Song, Li; Wang, Qian; Qi, Liwang; Fu, Xinxing; Gentu, Ge; Gao, Cuiping; Wang, Ruigang; Chen, Ming; Fang, Xiang-Wen; Liu, Jianquan; Li, Guojing; Wu, Shengdan* (2024)
Genomic insights into drought adaptation of the forage shrub Caragana korshinskii (Fabaceae) widely planted in drylands
The Plant Journal, accepted. (SCI=11.5; 10.3)
- Ningning Yan, Shuqing Yang, Haoyu Chao, Wenbing Zhang, Jian Zhang, Ming Chen*, Jun Zhao* (2024)
Genome-wide characterization of the sunflower kinome: classification, evolutionary analysis and expression patterns under different stresses
Frontiers in Plant Science, 15: 1450936. (SCI=11.5; 10.3)
- Lili Hao*, Ming Chen, Dayong Li, Diego Lijavetzky (2024)
Plant RNA processing: discovery, mechanism and function
Frontiers in Plant Science, 15: 2024 (Editorial). (SCI=4.1; 5.3)
- 陈铭(2024)
人工智能时代生物信息学学科发展和人才培养模式研究
人民论坛·学术前沿, 16: 1 (约稿).
2023
- Hongjun Chen, Yekai Zhou, Yongjing Liu, Peijing Zhang, Ming Chen* (2023)
Network integration and protein structural binding analysis of neurodegeneration-related interactome
Briefings in Bioinformatics, 2023: bbad237. (SCI=9.5; 10.6)
- Zexu Wu#, Cong Feng#, Yanshi Hu, Yincong Zhou, Sida Li, Shilong Zhang, Yueming Hu, Yuhao Chen, Haoyu Chao, Qingyang Ni, Ming Chen* (2023)
HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses
Scientific Data, 10: 853. (SCI=9.8; 10.8)
- Jintian Xu, Can Zhu, Mingzeng Su, Sida Li, Haoyu Chao*, Ming Chen* (2023)
CropGF: A Comprehensive Visual Platform for Crop Gene Family Mining and Analysis
Database, 2023: baad051. (SCI=5.8; 4.6)
- Yanyu Xiao, Jingjing Wang*, Jiaqi Li, Peijing Zhang, Jingyu Li, Yincong Zhou, Qing Zhou, Ming Chen, Xin Sheng, Zhihong Liu, Xiaoping Han*, Guoji Guo* (2023)
An analytical framework for decoding cell type-specific genetic variation of gene regulation
Nature Communications, 14(1): 3884. (SCI=16.6; 17)
- Renying Wang#, Peijing Zhang#,*, Jingjing Wang#, Lifeng Ma#, Weigao E#, Shengbao Suo#, Mengmeng Jiang#, Jiaqi Li#, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang NG*, Guang-Hui Liu*, Guo-Cheng Yuan*, Guoji Guo*, Xiaoping Han* (2023)
Construction of a cross-species cell landscape at single-cell level
Nucleic Acids Research, 51(2): 501-516. (SCI=14.9; 16.4)
- Zhenxiang He#, Haoyu Chao#; Xinkai Zhou#, Qingyang Ni, Yueming Hu, Ranran Yu, Minghuai Wang, Changzhu Li, Jingzhen Chen, Yunzhu Chen, Yong Chen, Chunyi Cui, Liangbo Zhang*, Ming Chen*, Dijun Chen* (2023)
A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis and floral bud development
Horticulture Research, 10(11): uhad196. (SCI=8.7; 9.0)
- Yujie Chen, Yuriy Orlov, Ming Chen* (2023)
Deciphering the Molecular Mechanism of the Intermediate Secondary Growth and Internode Elongation of the Castor Bean (Ricinus communis L.) by the Combined Analysis of the Transcriptome and Metabolome
International Journal of Molecular Sciences, 25(2), 1053. (SCI=5.6; 6.2)
- Haseeb Rehman Khan, Zeeshan Gillani, M. Hasan Jamal, Atifa Athar, Muhammad Tayyab Chaudhry, Haoyu Chao, Yong He, Ming Chen* (2023)
Early Identification of Crop Type for Smallholder Farming Systems Using Deep learning on Time-Series Sentinel-2 Imagery
sensors, 23(4): 1779. (SCI=3.9; 4.1)
- Haoyu Chao, Shilong Zhang, Yueming Hu, Qingyang Ni, Saige Xin, Liang Zhao, Vladimir Ivanisenko, Yuriy Orlov, Ming Chen* (2023)
Integrating Omics Databases for Enhanced Crop Plant Breeding
Journal of Integrative Bioinformatics, 20: 20230012. (SCI=1.9; 2.5)
- A R Volyanskaya, E A Antropova, U S Zubairova, P S Demenkov, A S Venzel, Y L Orlov, A A Makarova, T V Ivanisenko, T A Gorshkova, A R Aglyamova, N A Kolchanov, M Chen, V A Ivanisenko* (2023)
Reconstruction and analysis of the gene regulatory network for cell wall function in Arabidopsis thaliana L. leaves in response to water deficit
Vavilov Journal of Genetics and Breeding, 27(8): 1031-1041. (SCI=1.9; 2.5)
- Tianyi Ling#, Chengyi Wu#, Huan Yu, Tian Cai, Da Wang, Yincong Zhou, Ming Chen*, Kefeng Ding* (2023)
Probabilistic Modeling Ensemble Vision Transformer Improves Complex Polyp Segmentation
In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2023 (Greenspan, H. et al, ed. Lecture Notes in Computer Science), vol. 14226, pp. 572–581.
- Anastasia A Anashkina, Nina G Orlova, Alexander N Ignatov, Ming Chen, Yuriy L Orlov* (2023)
Bioinformatics of Genome Regulation and Systems Biology, Volume III
Frontiers in Genetics, 14: 1215987 (Editorial). (SCI=3.7; 4.3)
- Yuriy L Orlov*, Anastasia A. Anashkina, Vadim V Kumeiko, Ming Chen, Nikolay A Kolchanov (2023)
Research Topic of the Bioinformatics of Gene Regulation
International Journal of Molecular Sciences, 24(10): 8774 (Editorial). (SCI=5.6; 6.2)
- Yuriy L Orlov*, Ming Chen (2023)
Special Issue on "Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0"
International Journal of Molecular Sciences, 24(24): 17588 (Editorial). (SCI=5.6; 6.2)
- Yuriy L Orlov*, Ming Chen, Nikolay A Kolchanov, Ralf Hofestädt (2023)
BGRS: bioinformatics of genome regulation and data integration
Journal of Integrative Bioinformatics, 20: 20230032 (Editorial). (SCI=5.6; 6.2)
2022
- Xiaotian Hu, Cong Feng, Yincong Zhou, Andrew Harrison, Ming Chen* (2022)
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks
Bioinformatics, 38(3): 694-702. (SCI=6.931; 8.778)
- Yuhao Chen, Yanshi Hu, Xiaotian Hu, Cong Feng, Ming Chen* (2022)
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure
Bioinformatics, 38(18): 4380-4386. (SCI=6.931; 8.778)
- Liang-Yu Fu#, Tao Zhu#, Xinkai Zhou#, Ranran Yu#, Zhaohui He, Peijing Zhang, Zhigui Wu, Ming Chen, Kerstin Kaufmann*, Dijun Chen* (2022)
ChIP-Hub provides an integrative platform for exploring plant regulome
Nature Communications, 13: 3413. (SCI=17.694; 17.763)
- Xiaotian Hu, Cong Feng, Tianyi Ling, Ming Chen* (2022)
Deep learning frameworks for protein-protein interaction prediction
Computational and Structural Biotechnology Journal, 20: 3223-3233. (SCI=6.155; 6.836)
- Hongjun Chen, Xiaotian Hu, Yanshi Hu, Jiawen Zhou, Ming Chen* (2022)
CoVM2: molecular biological data integration of SARS-CoV-2 proteins in a Macro-to-Micro method
biomolecules, 12(8): 1067. (SCI=6.064; 6.191)
- Jiao Qu#, Fa Yang#, Tao Zhu#, Yingshuo Wang#, Wen Fang, Yan Ding, Xue Zhao, Xianjia Qi, Qiangmin Xie, Qiang Xu, Ming Chen, Yicheng Xie*, Yang Sun*, Dijun Chen* (2022)
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys
Nature Communications, 13: 4069. (SCI=17.694; 17.763)
- Fang Ye#, Guodong Zhang#, Weigao E#, Haide Chen#, Chengxuan Yu#, Lei Yang#, Yuting Fu, Jiaqi Li, Sulei Fu, Zhongyi Sun, Lijiang Fei, Qile Guo, Jingjing Wang, Yanyu Xiao, Xinru Wang, Peijing Zhang, Li Feng Ma, Dapeng Ge, Suhong Xu, Juan Caballero-Pérez, Alfredo Cruz-Ramírez, Yincong Zhou, Ming Chen, Ji-Feng Fei*, Xiaoping Han*, Guoji Guo* (2022)
Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single cell resolution
Nature Communications, 13: 4228. (SCI=17.694; 17.763)
- Yuan Liao#, Lifeng Ma#, Qile Guo#, Weigao E#, Xing Fang#, Lei Yang#, Fanwei Ruan, Jingjing Wang, Peijing Zhang, Zhongyi Sun, Haide Chen, Zhongliang Lin, Xueyi Wang, Xinru Wang, Huiyu Sun, Xiunan Fang, Yincong Zhou, Ming Chen, Wanhua Shen*, Guoji Guo*, Xiaoping Han* (2022)
Cell landscape of larval and adult Xenopus laevis at single-cell resolution
Nature Communications, 13: 4306. (SCI=17.694; 17.763)
- Fu Guo#, Peijing Zhang#, Yan Wu#, Guiwei Lian, Zhengfei Yang, Wu Liu, B. Buerte, Chun Zhou, Dandan Li, Ning Han, Zaikang Tong, Muyuan Zhu, Lin Xu*, Ming Chen*, Hongwu Bian* (2022)
Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development
Frontiers in Plant Science, 13: 887980. (SCI=6.627; 7.255)
- Obaid Ur Rehman, Muhammad Uzair, Haoyu Chao, Muhammad Ramzan Khan, Ming Chen* (2022)
Decoding RNA Editing Sites through Transcriptome Analysis in Rice under Alkaline Stress
Frontiers in Plant Science, 13: 892729. (SCI=6.627; 7.255)
- Shuaibin Wang, Junping Gao, Haoyu Chao, Zhaowu Li, Wenxuan Pu, Yaofu Wang, Ming Chen* (2022)
Comparative chloroplast genomes of Nicotiana species (Solanaceae): Insights into the genetic variation, phylogenetic relationship and polyploid speciation
Frontiers in Plant Science, 13: 899252. (SCI=6.627; 7.255)
- Bilal Saleem†, Umer Farooq†, Obaid Ur Rehman†, Muhammad Aqeel, Muhammad Shahbaz Farooq, Muhammad Kashif Naeem, Safeena Inam, Wajya Ajmal, Amna Abdul Rahim, Ming Chen, Rabia Kalsoom, Muhammad Uzair*, Sajid Fiaz, Kotb Attia, Hayat Ali Alafari, Muhammad Ramzan Khan*, Guoping Yu* (2022)
Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress
Frontiers in Genetics, 13: 1039548. (SCI=6.627; 7.255)
- Haoyu Chao, Yueming Hu, Liang Zhao, Saige Xin, Qingyang Ni, Peijing Zhang*, Ming Chen* (2022)
Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants
International Journal of Molecular Sciences, 23(7): 3695. (SCI=6.208; 6.628)
- Obaid Ur Rehman, Muhammad Uzair, Haoyu Chao, Sajid Fiaz, Muhammad Ramzan Khan, Ming Chen* (2022)
Role of the type-B authentic response regulator gene family in fragrant rice under alkaline salt stress
Physiologia Plantarum, 174(3): e13696. (SCI=5.081; 5.12)
- Chun Li+, Cong Feng+, Guangyuan Ma+, Shaoyin Fu, Ming Chen*, Wenguang Zhang*, Jinquan Li* (2022)
Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus
BMC Genomics, 23: 140. (SCI=4.547; 4.931)
- Siew Woh Choo, Ju Lian Chong, Philippe Gaubert, Alice Catherine Hughes, Stephen O’Brien, Anne-Lise Chaber, Agostinho Antunes, Sara Platto, Nick Ching-Min Sun, Li Yu, Klaus-Peter Koepfli, Tulshi Laxmi Suwal, Mukesh Thakur, Stephan Ntie, Elisa Panjang, Jayaraj Vijaya Kumaran, Tariq Mahmood, Sean P. Heighton, Dago Dorji, Bi Sery Gonedelé, Bryan Raveen Nelson, Chabi A.M.S. Djagoun, Ing Hoe Loh, Prativa Kaspal, Siim Pauklin, Toby Michelena, Hongxiang Zhu, Leonard Lipovich, Xuechen Tian, Siwei Deng, Christopher E. Mason, Jingyang Hu, Robert White, Nicholas S. Jakubovics, Wei Yee Wee, Tze King Tan, Kum Thong Wong, Steve Paterson, Ming Chen, Yixin Zhang, Rofina Yasmin Othman, Larry C. Brown, Bairong Shen, Guanghou Shui, Mia Yang Ang, Tar Zhao, Yongming Li, Bo Zhang, Cheng Tung Chong, Yu Meng, Aloysius Wong, Jianzhong Su, Hasmahzaiti Omar, Hua Shen, Choo Hock Tan, Hongyu Xu, Ian C Paterson, Minyan Wang, Chee-Kai Chan, Siyuan Zhang, Avirup Dutta, Tay Sun Tee, Noël P.D. Juvigny-Khenafou, Naresh V R Mutha, Muhamad Afiq Aziz (2022)
A collective statement in support of saving pangolins
Science of the Total Environment, 824: 153666. (SCI=10.753; 10.237)
- Hao-ran Wu, Cheng Peng, Ming Chen* (2022)
Rethinking the complexity and uncertainty of spatial networks applied to forest ecology
Scientific Reports, 12: 15917. (SCI=4.996; 5.516)
- Bin Tan, Yongjing Liu, Cong Feng, Yincong Zhou, Xiaotian Shao, Ming Chen* (2022)
LBD: a manually curated database of experimentally validated lymphoma biomarkers
Database, 2022: baac051. (SCI=4.462; 4.776)
- Yongjing Liu, Cong Feng, Yincong Zhou, Xiaotian Shao, Ming Chen* (2022)
Simulating the Dynamic Intra-Tumor Heterogeneity and Therapeutic Responses
cancers, 14(7): 1645. (SCI=6.575; 6.886)
- Xinjian Yu+, Yongjing Liu+, Ming Chen* (2022)
Reassessment of reliability and reproducibility for triple-negative breast cancer subtyping
cancers, 14(11): 2571. (SCI=6.575; 6.886)
- Qing Yang+, Sunan Gao+, Junfen Lin, Ke Lyu, Zexu Wu, Yuhao Chen, Yinwei Qiu, Yanrong Zhao, Wei Wang, Tianxiang Lin, Huiyun Pan, Ming Chen* (2022)
A machine learning-based data mining in medical examination data: a biological features-based biological age prediction model
BMC Bioinformatics, 23: 411. (SCI=3.307; 4.341)
- Yuriy L. Orlov*, Vladimir A. Ivanisenko, Oxana B. Dobrovolskaya, Ming Chen (2022)
Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics
International Journal of Molecular Sciences, 23(12): 6759 (Editorial). (SCI=6.208; 6.628)
- Ming Chen, Ralf Hofestädt, Eds. (2022)
Integrative Bioinformatics: History and Future
Springer, 2022. ISBN: 9811667942, 9789811667947.
- 陈铭 主编 (2022)
生物信息学(第四版)
科学出版社, 2022年3月. ISBN: 978-7-03-071906-5.字数：68.2万
- 陈铭 原春晖主编 (2022)
生物信息学实验
科学出版社, 2022年3月. ISBN: 978-7-03-071689-7.字数：17.2万
- 陈铭(2022)
大数据时代的整合生物信息学
生物信息学, 20(2): 75-83 (约稿).
2021
- Md. Asif Ahsan, Yongjing Liu, Cong Feng, Yincong Zhou, Guangyuan Ma, Youhuang Bai*, Ming Chen* (2021)
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2
Briefings in Bioinformatics, 22(2):714-725. (SCI=11.62; 10.288)
- Jingjing Wang#, Huiyu Sun#, Mengmeng Jiang, Jiaqi Li, Peijing Zhang, Haide Chen, Yuqing Mei, Lijiang Fei, Shujing Lai, Xiaoping Han, Xinhui Song, Suhong Xu, Ming Chen, Hongwei Ouyang, Dan Zhang*, Guo-Cheng Yuan*, Guoji Guo* (2021)
Tracing cell-type evolution by cross-species comparison of cell atlases
Cell Reports, 34: 108803. (SCI=9.432; 10.394)
- Jingjing Wang#，Yuriy L. Orlov#, Xue Li, Yincong Zhou, Yongjing Liu, Chunhui Yuan*, Ming Chen* (2021)
In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana
PeerJ, 9: e10426. (SCI=2.984; 3.369)
- Nann Miky Moh Moh, Peijing Zhang, Yujie Chen, Ming Chen* (2021)
Computational Identification of miRNAs and Temperature Responsive lncRNAs from Mango (Mangifera indica, L.)
Frontiers in Genetics, 12: 607248. (SCI=4.599; 4.888)
- Cong Feng, Min Dai, Yongjing Liu, Ming Chen* (2021)
Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage
Briefings in Bioinformatics, 22(3): bbaa086. (SCI=11.62; 10.288)
- Yekai Zhou, Hongjun Chen and Ming Chen* (2021)
mPPI: A PPI Database Extension for Visualizing Structural Interactome in One-to-Many Manner
Database, baab036. (SCI=3.451; 4.159)
- Wei Shan#, Qin Yu#, Yan Long, Qian Luo, Honghu Li, Yingli Han, Yulin Xu, Shan Fu, Xiangjun Zeng, Cong Wei, Yang Gao, Xiaoqing Li, Xia Li, Lifei Zhang, Lizhen Liu, Ming Chen, Pengxu Qian*, He Huang* (2021)
Enhanced HSC-like cell generation from mouse pluripotent stem cells in a 3D induction system cocultured with stromal cells
Stem Cell Research & Therapy, 12(1): 353. (SCI=6.832; 7.153)
- Hua Yu, Zhen Sun, tianyu Tan, Hongru Pan, Jing Zhao, Ling Zhang, Jiayu Chen, Anhua Lei, Yuqing Zhu, Lang Chen, Yuyan Xu, Yaxin Liu, Ming Chen, Jinghao Sheng, Zhengping Xu, Pengxu Qian, Cheng Li, Shaorong Gao, George Daley, Jin Zhang* (2021)
rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin
Nature Communications, 12: 6365. (SCI=14.919; 15.805)
- Zhen Sun#, Hua Yu#, Jing Zhao#, Tianyu Tan, Hongru Pan, Yuqing Zhu, Lang Chen, Cheng Zhang, Li Zhang, Anhua Lei, Yuyan Xu, Xianju Bi, Xin Huang, Bo Gao, Longfei Wang, Cristina Correia, Ming Chen, Qiming Sun, Yu Feng, Li Shen, Hao Wu, Jianlong Wang, Xiaohua Shen, George Q. Daley, Hu Li, Jin Zhang* (2021)
LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells
Protein & Cell, 2021. (SCI=14.87; 11.279)
- Hua Yu, Lu Lu, Ming Chen, Chen Li, Jin Zhang* (2021)
Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet
npj Genomic Medicine, 6(1): 50. (SCI=8.617; 7.355)
- Jingjing Wang#, Qi Chen#, Wenyi Wu, Yujie Chen, Yincong Zhou, Guoji Guo*, Ming Chen* (2021)
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana
Functional & Integrative Genomics, 21(1): 17-30. (SCI=3.41; 3.616)
- Md Asif Ahsan, Yongjing Liu, Cong Feng, Ralf Hofestädt, Ming Chen* (2021)
OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources
Journal of Integrative Bioinformatics, 18(1): 9–17. (S(SCI=)
- Hiroshi Matsuno*, Fei Liu, Ming Chen (2022)
Petri nets for cellular process modelling
BioSystems, 212: 104603 (Editorial). (SCI=1.973; 2.063)
- Dahui Hu, Peijing Zhang, Ming Chen* (2021)
Database Resources for Functional Circular RNAs
In: RNA Bioinformatics. Methods Molecular Biology, Vol. 2284 (Ernesto Picardi, ed.) , ISBN: 978-1-0716-1306-1, Chapter 24
- Peijing Zhang, Ming Chen* (2021)
Circular RNA Databases
In: Plant Circular RNAs: Methods and Protocols, Methods in Molecular Biology, Vol. 2362 (Luis María Vaschetto ed.), ISBN: 978-1-0716-1645-1, Chapter 7
- 2021 IEEE the 9th International Conference on Bioinformatics and Compuational Biology (ICBCB 2021)
Proceeding (co-chair)
ISBN: 978-0-7381-3202-0
- 陈宇杰，吴江鸿，丽春，胡斯乐，陈铭(2021)
大数据时代下的生物信息学教学探究
内蒙古民族大学学报(自然科学版),5: 455-457.
2020
- Peijing Zhang, Yongjing Liu, Hongjun Chen, Xianwen Meng, Jitong Xue, Kunsong Chen, Ming Chen* (2020)
CircPlant: An Integrated Tool for CircRNA Detection and Functional Prediction in Plants
Genomics, Proteomics & Bioinformatics, 18: 352-358. (SCI=7.051; )
- Wenyi Wu, Yan Wu, Dahui Hu, Yincong Zhou, Yanshi Hu, Ming Chen* (2020)
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants
Database, baaa001. (SCI=2.593; 3.66)
- Qiang Kang, Jun Meng*, Jun Cui, Yushi Luan*, Ming Chen (2020)
PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction
Bioinformatics, btaa074. (SCI=5.61; 9.853)
- Xiaoping Han#,*, Ziming Zhou#, Lijiang Fei#, Huiyu Sun#, Renying Wang#, Yao Chen#, Haide Chen#, Jingjing Wang#, Huanna Tang, Wenhao Ge, Yincong Zhou, Fang Ye, Mengmeng Jiang, Junqing Wu, Yanyu Xiao, Xiaoning Jia, Tingyue Zhang, Xiaojie Ma, Qi Zhang, Xueli Bai, Shujing Lai, Chengxuan Yu, Lijun Zhu, Rui Lin, Yuchi Gao, Min Wang, Yiqing Wu, Jianming Zhang, Renya Zhan, Saiyong Zhu, Hailan Hu, Changchun Wang, Ming Chen, He Huang, Tingbo Liang, Jianghua Chen, Weilin Wang, Dan Zhang, Guoji Guo* (2020)
Construction of A Human Cell Landscape at Single Cell Level
Nature, 581(7808): 303-309. (SCI=42.778; 46.486)
- Xinjian Yu#, Siqi Lai#, Hongjun Chen#, Ming Chen* (2020)
Protein-protein interaction network with machine learning models and multiomics data reveals potential neurodegenerative disease-related proteins
Human Molecular Genetics, 29(8): 1378-1387. (SCI=5.1; 5.361)
- Peijing Zhang, Sida Li, Ming Chen* (2020)
Characterization and Function of Circular RNAs in Plants
Frontiers in Molecular Biosciences, 7: 91. (SCI=4.188; )
- Solomon Shiferaw Beyene, Tianyi Ling, Blagoj Ristevski, Ming Chen* (2020)
A Novel Riboswitch Classification based on Imbalanced Sequences achieved by Machine Learning
PLoS Computational Biology, 16(7): e1007760. ((SCI=4.7; 5.26).
- Yuriy L. Orlov*, Elena N Voropaeva, Ming Chen and Ancha V. Baranova (2020)
Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school
BMC Medical Genomics, 13(Suppl 8): 127. (Introduction) (SCI=2.570; 3.193)
- Yuriy L. Orlov*, Oxana B. Dobrovolskaya, Ming Chen and Ralf Hofestädt (2020)
Bioinformatics of genome regulation and structure – 2020 papers collection
Journal of Integrative Bioinformatics, 20202038 (Editorial). (SCI=)
- 霍颖异，徐程，吴敏，陈铭(2020)
基于问题导向的生物信息学综合实验教学设计
生物信息学, 18(2): 127-132.
2019
- Xianwen Meng, Dahui Hu, Peijing Zhang, Qi Chen, Ming Chen* (2019)
CircFunBase: a database for functional circular RNAs
Database, 2019: baz003. (SCI=3.683; 3.793)
- Md. Asif Ahsan, Md. Mamun Monir, Xianwen Meng, Md. Matiur Rahaman, Hongjun Chen, Ming Chen* (2019)
Identification of epistasis loci underlying rice flowering time by controlling population stratification and polygenic effect
DNA Research, 26(2): 193. (SCI=4; 5.016)
- Md. Matiur Rahaman, Md. Asif Ahsan, Ming Chen* (2019)
Data-mining Techniques for Image-based Plant Phenotypic Traits Identification and Classification
Scientific Reports, 9: 19526. (SCI=4.011; 4.525)
- Qi Chen, Xianwen Meng, Qi Liao, Ming Chen* (2019)
Versatile interactions and bioinformatics analysis of noncoding RNAs
Briefings in Bioinformatics, 20(5): 1781–1794. (SCI=9.101; 8.265)
- Yongjing Liu, Liangyu Fu, Kerstin Kaufmann, Dijun Chen*, Ming Chen* (2019)
A practical guide for DNase-seq data analysis: from data management to common applications
Briefings in Bioinformatics, 20(5): 1865–1877. (SCI=9.101; 8.265)
- Wenhao Yan#, Dijun Chen#,*, Julia Schumacher, Diego Durantini, Julia Engelhorn, Ming Chen, Cristel C. Carles, Kerstin Kaufmann* (2019)
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis
Nature Communication, 10: 1705. (SCI=11.878; 13.811)
- Youjun Huang#, Lihong Xiao#,*, Rui Zhang#, Zhengjia Wang, Zhongren Zhang, Chunying Huang, Ren Huang, Yumeng Luan, Jianhua Wang, Chen Shen, Shenmei Zhang, Xinwang Wang, Jennifer J. Randall, Bingsong Zheng, Jiasheng Wu, Qixiang Zhang, Guohua Xia, Chuanmei Xu, Ming Chen, Liangsheng Zhang, Lizhi Gao, Zhiduan Chen, Wenkai Jiang, Charles A. Leslie, L. J. Grauke, Jianqin Huang* (2019)
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition
GigaScience, 8(5): giz036. (SCI=4.688; 7.441)
- Jael Sanyanda Wekesa, Yushi Luan, Ming Chen, and Jun Meng* (2019)
A hybrid prediction method for Plant lncRNA-protein Interaction
cells, 8(6): 521. (SCI=5.656)
- Tatiana V. Tatarinova, Ming Chen, Yuriy L. Orlov* (2019)
Bioinformatics research at BGRS-2018
BMC Bioinformatics, 20(Suppl 1):33. (SCI=2.511; 2.97)
- Youhuang Bai, Ziding Zhang, Ming Chen (2019)
Special Issue on Plant Bioinformatics
Current Bioinformatics, 14(7): 564-565(Editorial). (SCI=1.189; 0.736)
- Ming Chen, Ralf Hofestädt, Jan Taubert (2019)
Integrative Bioinformatics: History and Future
Journal of Integrative Bioinformatics, 20192001(Editorial). (SCI=)
- Danfeng Jin, Xianwen Meng, Yue Wang, Jingjing Wang, Yuhua Zhao*, Ming Chen* (2019)
Computational Investigation of Small RNAs in the Plant-microorganism Symbionts in Medicago truncatula
In: The Model Legume Medicago truncatula, 2 Volume Set (Frans J. de Bruijn, ed.) , ISBN-13: 978-1119409168, Chapter 12.9.5
- 2019 IEEE 7th International Conference on Bioinformatics and Compuational Biology (ICBCB 2019)
Proceeding (co-chair)
ISBN: 978-1-7281-0641-0
2018
- Dijun Chen*, Rongli Shi, Jean-Michel Pape, Kerstin Neumann, Daniel Arend, Andreas Graner, Ming Chen, Christian Klukas (2018)
Predicting plant biomass accumulation from image-derived parameters
GigaScience, 7: 1-13. (SCI=7.267; 10.742)
- Dijun Chen*, Liangyu Fu, Dahui Hu, Christian Klukas, Ming Chen*, Kerstin Kaufmann* (2018)
The HTPmod Shiny application enables modeling and visualization of large-scale biological data
Communications Biology, 1: 89.
- Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang, Ming Chen* (2018)
Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development
BMC Genomics, 19: 607. (SCI=3.73; 4.257)
- Danfeng Jin, Xianwen Meng, Yue Wang, Jingjing Wang, Yuhua Zhao*, Ming Chen* (2018)
Computational Investigation of Small RNAs in the Establishment of Root Nodules and Arbuscular Mycorrhiza in Leguminous Plants
SCIENCE CHINA Life Sciences, 61(6): 706–717. (SCI=3.085; 2.328)
- Qilin Li, Md. Asif Ahsan, Hongjun Chen, Jitong Xue and Ming Chen* (2018)
Discovering Putative Peptides Encoded from Noncoding RNAs in Ribosome Profiling Data of Arabidopsis thaliana
ACS Synthetic Biology, 7(2): 655–663. (SCI=5.316; 5.253)
- Qilin Li+, Chao Zhang+, Hongjun Chen, Jitong Xue, Xiaolei Guo, Ming Liang*, Ming Chen* (2018)
BioPepDB: An integrated data platform for food-derived bioactive peptides
International Journal of Food Sciences and Nutrition, 69(8): 963-968. (SCI=2.317)
- Xiaoping Han#,*, Renying Wang#, Yincong Zhou#, Lijiang Fei#, Huiyu Sun#, Shujing Lai, Assieh Saadatpour, Zimin Zhou, Haide Chen, Fang Ye, Daosheng Huang, Yang Xu, Wentao Huang, Mengmeng Jiang, Xinyi Jiang, Jie Mao, Yao Chen, Chenyu Lu, Jin Xie, Qun Fang, Yibin Wang, Rui Yue, Tiefeng Li, He Huang, Stuart H. Orkin, Guo-Cheng Yuan, Ming Chen, Guoji Guo* (2018)
Mapping the Mouse Cell Atlas by Microwell-seq
Cell, 172: 1091-1107. (SCI=31.389; 33.796)
- Qing-Chong Qiu, Lin Wang, Shan-Shan Jin, Guan-Feng Liu, Jie Liu, Liang Ma, Rui-Fang Mao, Ying-Ying Ma, Na Zhao, Ming Chen*, Biao-Yang Lin* (2018)
CHI3L1 promotes tumor progression by activating TGF-β and PI3K/AKT signaling pathway in hepatocellular carcinoma
Scientific Reports, 8: 15029. (SCI=4.122; 4.6609)
- Lihua Jiang, Lishen Kang, Changwen Wu, Ming Chen, Zhenming Lü* (2018)
A comprehensive description and evolutionary analysis of 9 Loliginidae mitochondrial genomes
Hydrobiologia, 808(1): 115-124. (SCI=2.165; 2.444)
- Akhileshwar Namani, Md. Matiur Rahaman, Ming Chen*, Xiuwen Tang* (2018)
Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer
BMC Cancer, 18: 46. (SCI=3.288; 3.679)
- Xue Li, Xianwen Meng, Jingjing Wang, Yincong Zhou, Hongjun Chen, He Huang, Ming Chen* (2018)
Dissecting LncRNA Roles in Renal Cell Carcinoma Metastasis and Characterizing Heterogeneity by Single-cell RNA-seq
Molecular Cancer Research, 16(12): 1879-1888. (SCI=4.597; 4.605)
- Yuriy L. Orlov*, Julio R. Fernandez-Masso, Ming Chen, Ancha V. Baranova (2018)
Medical genomics at Belyaev Conference – 2017
BMC Medical Genomics, 11(Suppl 1): 11. (Editorial) (SCI=3.317; 3.364)
- Blagoj Ristevski*, Ming Chen (2018)
Big Data Analytics in Medicine and Healthcare
Journal of Integrative Bioinformatics, 15(3): 20170030.
- Integrative Bioinformatics and Systems Biology (WIBSB-2018), First Sino-Russian Workshop (Abstracts)
Proceeding (co-chair)
===>>>list
- Q. Dai, W. Liu, M. Chen*(2018)
Brief introduction of bioinformatics education in Сhina
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- T.G. Amstislavskaya*, M.A. Tikhonova, H. Bai, Y.L. Orlov, M. Chen(2018)
Systems biology approaches for analysis of dementia with Lewy bodies in mouse models
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- M. Chen*, J. Wang, O.B. Dobrovolskaya, V.N. Babenko, Y.L. Orlov, Y. Liu, L.S. Samarina*(2018)
Roles of non-coding RNAs in stress response in plants
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- Q. Chen, X. Meng, Q. Liao, M. Chen*(2018)
Versatile interactions and bioinformatics analysis of noncoding RNAs
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- M. Dai, C. Feng, M. Chen*(2018)
Quantifying genome sequence repeatability by repeater
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- O.B. Dobrovolskaya, A.M. Spitsina, A.G. Galieva, A.V. Tsukanov, A.G. Bogomolov, Y.L. Orlov*, M. Chen(2018)
Computer studies of miRNA in abiotic stress response in plants
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- Y. Hu*, J. Wang*, M. Chen(2018)
Analyzing the genes related to Alzheimer’s disease via a nework and pathway-based approach
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- J. Wang, Q. Chen, W. Wu, Y. Chen, Y. Zhou, Y. Liu, M. Chen*(2018)
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana
Integrative Bioinformatics and Systems Biology (WIBSB-2018),
- 陈铭 主编 (2018)
生物信息学(第三版)
科学出版社, 2018年6月. ISBN: 978-7-03-057681-1.字数：56.1万
2017
- Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen* (2017)
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Bioinformatics, 33(20): 3314–3316. (SCI=7.307; 5.929)
- Peijing Zhang, Xianwen Meng, Hongjun Chen, Yongjing Liu, Jitong Xue, Yincong Zhou, Ming Chen* (2017)
PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks
Database, 2017: bax089. (SCI=3.978; 3.755)
- Chunhui Yuan#, Xianwen Meng#, Xue Li, Nicola Illing, Robert Ingle, Jingjing Wang, Ming Chen* (2017)
PceRBase: A database of plant competing endogenous RNA
Nucleic Acids Research, 45 (D1): D1009-D1014. (SCI=10.162; 8.647)
- Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen* (2017)
DEF: an automated dead-end filling approach based on quasi-endosymbiosis
Bioinformatics, 33(3): 405-413. (SCI=7.307; 5.929)
- Jingjing Wang, Yincong Zhou, Xue Li, Xianwen Meng, Miao Fan, Hongjun Chen, Jitong Xue, Ming Chen* (2017)
Genome-wide analysis of the distinct types of chromatin interactions in Arabidopsis thaliana
Plant and Cell Physiology, 58(1): 57-70. (SCI=4.76; 4.847)
- Xianwen Meng, Xue Li, Peijing Zhang, Jingjing Wang, Yincong Zhou, Ming Chen* (2017)
Circular RNA: an emerging key player in RNA world
Briefings in Bioinformatics, 18(4): 547-557. (SCI=5.134; 6.778)
- Jingjing Wang, Xianwen Meng, Oxana Dobrovolskaya, Yuriy Orlov, Ming Chen * (2017)
Non-coding RNAs and Their Roles in Stress Response in Plants
Genomics, Proteomics & Bioinformatics, 15(5): 301-312. (SCI=6.615)
- Youhuang Bai+, Bin Chen+, Mingzhu Li+, Yincong Zhou, Silin Ren, Qin Xu, Ming Chen*, Shihua Wang* (2017)
FPD: A comprehensive phosphorylation database in fungi
Fungal Biology, 121(10): 869-875. (SCI=2.184)
- Yuriy L. Orlov*, Ancha V. Baranova, Ming Chen, Elena A. Salina (2017)
Plant Biology at Belyaev Conference – 2017
BMC Plant Biology, 17(Suppl 2): 257. (Editorial) (SCI=3.964; 4.541)
- Ming Chen, Andrew Harrison, Hugh Shanahan, Yuriy Orlov (2017)
Biological Big Bytes: Integrative Analysis of Large Biological Datasets
Journal of Integrative Bioinformatics, 14(3): 20170052. (Editorial)
- Qizhu Wu, Huiguang Wu, Yuriy L. Orlov*, G. Gegentana, Wenyan Huo, A.O.Bragin, Nuomin Wu, S. Suyalatu, Fuquan Zhao, Jingwen Zhao, Ludmila E. Tabikhanova, Ming Chen*, Haihua Bai* (2017)
Genetic polymorphisms and related risk factors of ischemic stroke in a Mongolian population in China
Vavilov Journal of Genetics and Breeding, 21(5): 581-587.
- A.I. Dergilev*, A.M. Spitsina, I.V. Chadaeva, A.V. Svichkarev, F.M. Naumenko, E.V. Kulakova, E.R. Galieva, E.E. Vityaev, M. Chen, Y.L. Orlov* (2017)
Computer Analysis of Colocalization of the TFs’ Binding Sites in the Genome According to the ChIP-seq Data
Russian Journal of Genetics: Applied Research, 7(5):513–522.
- Md. Matiur Rahaman, Md. Asif Ahsan, Ming Chen* (2017)
Significant traits inference approach for modelling of shoot biomass from highthroughput images of cereal plants under stress tolerance
International Conference on Bioinformatics and Biostatistics for Agriculture, Health and Environment, Rajshahi, Bangladesh, P109: 466-476.
- 翁宇豪, 陈铭* (2017)
多层网络模型在水稻与癌症PPI中的应用
浙江大学学报(农业与生命科学版), 43(1): 15-23. (cover page)
- 李锦，严潘瑶，钱飞箭，邱宝义，夏雯雯，牟晓威，邱丽娟，林忠平，陈铭，祝建波，陈贤丰* (2017)
新疆天山雪莲转录组注解知识库
植物学报, 52(4): 530-538.
2016
- Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen* (2016)
DaTo: an atlas of biological databases and tools
Journal of Integrative Bioinformatics, 13(4): 297.
- Jingjing Wang, Hongjun Chen, Chunhui Yuan, Xianwen Meng, Xue Li, Yincong Zhou, Ming Chen* (2016)
Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organization
Briefings in Functional Genomics, 15(5): 385-395. (SCI=3.124; 3.495)
- Jingjing Wang, Xianwen Meng, Chuihui Yuan, Andrew P. Harrison, Ming Chen* (2016)
The roles of cross-talk epigenetic patterns in Arabidopsis thaliana
Briefings in Functional Genomics, 15(4): 278-287. (SCI=3.124; 3.495)
- Lan Yu, Chaogang Shao, Xinghuo Ye, Yijun Meng*, Yincong Zhou, Ming Chen* (2016)
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining
Scientific Reports, 6: 18901. (SCI=5.228; 5.525)
- Youhuang Bai#, Xiaozhuan Dai#, Andrew Harrison, Caroline Johnston, Ming Chen* (2016)
Toward a next-generation atlas of RNA secondary structure
Briefings in Bioinformatics, 17(1): 63-77. (SCI=8.399; 6.778)
- Ziyang Gao, Yang Su, Chang Liu, Qianyun Zhang, Jianzhong Hu, Xintian Xu, Jiahao Gao, Hao Feng, Xukang Shen, Mengmeng Xu, Yue Zhong, Yuqing Shen, Tianning Zhang, Kunxun Qian, Yanruide Li, Ming Chen*(2016)
Termite Terminator: a genetically modified toxin proteins expression system with a cellulose nano-crystals delivery carrier for trapping termites based on trophallaxis
PLOS Collections, online.
- Lihua Jiang, Changwen Wu, Wei Liu, Ming Chen* (2016)
Complete mitochondrial genome of the Loligo beka
Mitochondrial DNA, 27(6):4278-4279. (SCI=1.209;)
- Jianqin Huang, Tong Zhang, Qixiang Zhang, Ming Chen, Zhengjia Wang, Bingsong Zheng, Guohua Xia, Xianyou Yang, Chunying Huang, Youjun Huang (2016)
The mechanism of high contents of oil and oleic acid revealed by transcriptomic and lipidomic analysis during embryogenesis in Carya cathayensis Sarg.
BMC Genomics, 17: 113. (SCI=3.867; 4.278)
- Ming-Bing Zhou, Ying Zheng, Zhi-Gang Liu, Xiang-Wan Xia, Ding-Qin Tang, Ying Fu & Ming Chen (2016)
Endo-1,4-β-glucanase gene involved into the rapid elongation of Phyllostachys heterocycla var. pubescens
Trees: structure and function, 30: 1259. (SCI=1.706; 1.931)
- A.I. Dergilev*, A.M. Spitsina, I.V. Chadaeva, A.V. Svichkarev, F.M. Naumenko, E.V. Kulakova, E.R. Galieva, E.E. Vityaev, M. Chen, Y.L. Orlov* (2016)
Computer analysis of co-localization of transcription factor binding sites in genome by ChIP-seq data
Vavilov Journal of Genetics and Breeding, 20(6):770-778. (in Russian)
- 范苗，陈铭，徐建红* (2016)
玉米新型氧甲基转移酶基因的全基因组鉴定、进化与表达研究
农业与生物技术学报， 24(8): 1109-1119.
2015
- Xianwen Meng, Jingjing Wang, Chunhui Yuan, Xue Li, Yincong Zhou, Ralf Hofestädt, Ming Chen* (2015)
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types
Oncogenesis, 4: e177. (SCI=5.021;)
- Chunhui Yuan, Jingjing Wang, Andrew P. Harrison, Xianwen Meng, Dijun Chen, Ming Chen* (2015)
Genome-wide View of Natural Antisense Transcripts in Arabidopsis thaliana
DNA Research, 22(3): 233–243. (SCI=5.477; 5.707)
- Md. Matiur Rahaman, Dijun Chen, Zeeshan Gillani, Christian Klukas, Ming Chen* (2015)
Advanced phenotyping and phenotype data analysis for the study of plant growth and development
Frontiers in Plant Science, 6: 619. (SCI=3.948; 3.99)
- Youhuang Bai, Xiaozhuan Dai, Andrew P. Harrison, Ming Chen* (2015)
RNA regulatory networks in animals and plant: a long noncoding RNA perspective
Briefings in Functional Genomics, 14(2): 91-101. (SCI=3.67; 3.565)
- Zhao Zhang, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen* (2015)
MTide: an integrated tool for the identification of miRNA-target interaction in plants
Bioinformatics, 31(2): 290-291. (SCI=4.981; 8.136)
- Chaogang Shao, Guofu Lu, Lan Yu, Qianer Wu, Ming Chen*, Yijun Meng* (2015)
Identification of novel miRNA-target pairs in rice (Oryza sativa) by a reversed approach
Plant Omics, 8(1): 62-68. (SCI=)
- A. M. Spitsina, Yu. L. Orlov, N. N. Podkolodnaya, A. V. Svichkarev, A. I. Dergilev, M. Chen, S. V. Kuchin, I. G. Chernykh, B. M. Glinskij (2015)
Supercomputer analysis of genomics and transcriptomics data revealed by high-throughput DNA sequencing
Program Systems: Theory and Applications, 6(1): 157-174. (in Russian)(SCI=)
- Björn Sommer, Stephen Wang, Lifeng Xu, Ming Chen and Falk Schreiber (2015)
Hybrid-dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques
IEEE International Symposium on Big Data Visual Analytics, 1-8.
- ZJU_China Team, Ming Chen (2015)
RNA Scaffold: Designed to Co-localize Enzymes
In RNA Scaffolds: Methods and Protocols, Methods in Molecular Biology (Luc Ponchon, ed.), vol. 1316, chapter 9, DOI: 10.1007/978-1-4939-2730-2_9.
- 陈铭 主编 (2015)
生物信息学(第二版)
科学出版社, 2015年2月. ISBN: 978-7-03-043287-2.字数：52.4万
2014
- Dijun Chen, Liang-Yu Fu, Zhao Zhang, Guoliang Li, Hang Zhang, Li Jiang, Andrew Harrison, Hugh Shanahan, Christian Klukas, Hong-Yu Zhang, Yijun Ruan*, Ling-ling Chen*, Ming Chen* (2014)
Dissecting the chromatin interactome of microRNA genes
Nucleic Acids Research, 42(5):3028-3043. (SCI=8.808; 8.378)
- Yijun Meng*, Chaogang Shao, Huizhong Wang, Ming Chen* (2014)
Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach
Journal of Experimental Botany, 65(2): 395-400. (SCI=5.794)
- Lie Tang, Zhao Zhang, Peizhen Gu, Ming Chen* (2014)
Construction and Analysis of MicroRNA-Transcription Factor Regulation Network in Arabidopsis
IET Systems Biology, 8(3):76-86. (SCI=1.672)
- Zeeshan Gillani, Muhamamd Sajid Hamid Akash, MD. Matiur Rahaman, Ming Chen* (2014)
CompareSVM: Supervised, Support Vector Machine (SVM) inference of gene regularity networks
BMC Bioinformatics, 15:395. (SCI=2.67)
- Jiasheng Wang, Ke Ding, Yujie Chen, Lifeng Zhang, Zukai Liu, Angli Xue, Wenjia Gu, Xiaoyue Yang, Xihan Li, Jin Huang, Congcong Xing, Yunlong Cao, Ming Chen* (2014)
Detection of Thrombin with an Aptamer-based Macromolecule Biosensor Using Bacterial Ghost System
ACS Synthetic Biology, 3(12): 963-965. (SCI=3.951)
- Haihua Bai, Xiaosen Guo, Dong Zhang, Narisu Narisu, Junjie Bu, Jirimutu, Fan Liang, Xiang Zhao, Yanping Xing, Dingzhu Wang, Tongda Li, Yanru Zhang, Baozhu Guan, Xukui Yang, Shuangshan, Zhe Su, Huiguang Wu, Wenjing Li, Ming Chen, Shilin Zhu, Bayinnamula , Yuqi Chang, Ying Gao, Tianming Lan, Suyalatu, Hui Huang, Yan Su, Yujie Chen, Wenqi Li, Xu Yang, Qiang Feng, Jian Wang, Huanming Yang, Jun Wang, Qizhu Wu, Ye Yin, Huanmin Zhou (2014)
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations
Genome Biology and Evolution, 6(12): 3122-3136. (SCI=4.532)
- Dijun Chen, Kerstin Neumann, Swetlana Friedel, Benjamin Kilian, Ming Chen, Thomas Altmann, Christian Klukas (2014)
Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis
Plant Cell, 26(12): 4636-4655. (SCI=9.575)
- Ming Chen, Ralf Hofestädt (2014)
Open Problems in Petri Net Modeling and Simulation of Biology Systems
Information Technology, 56(2): 76-81.
- Björn Sommer, Ming Chen (2014)
A novel Lecture Program in Bioinformatics: Interdisciplinary Cell Visualization and Modeling
Sommer, Björn (Ed.): Proceedings of the CELLmicrocosmos neXt workshop, Bielefeld, .
- Qingfeng Chen, Ming Chen (2014)
Protein Systems Biology: Method, Regulation, and Networks
Current Protein & Peptide Science, 15(6): 519-521.(Editorial) (SCI=2.328)
- Ming Chen, Ralf Hofestädt, Eds. (2014)
Approaches in Integrative Bioinformatics. Towards the Virtual Cell
Springer, 2014. ISBN: 978-3-642-41280-6.
- Ming Chen, Ralf Hofestädt (2014)
Integrative Bioinformatics
In Approaches in Integrative Bioinformatics (Chen & Hofestädt, ed.), pp. 3-19.
- Dijun Chen, Ming Chen, Thomas Altman, Christian Klukas (2014)
Bridging Genomics and Phenomics
In Approaches in Integrative Bioinformatics (Chen & Hofestädt, ed.), pp. 299-333.
2013
- Danfeng Jin, Yue Wang, Yuhua Zhao*, Ming Chen* (2013)
MicroRNAs and their cross-talks in plant development
Journal of Genetics and Genomics, 40: 161-170. (SCI=2.076; 1.874)
- Chaogang Shao, Qianer Wu, Jinjin Qiu, Shaohua Jin, Beilun Zhang, Jian Qian, Ming Chen*, Yijun Meng* (2013)
Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis
Gene, 527(2): 477-83. (SCI=2.196; 2.371)
- Yijun Meng*, Chaogang Shao, Huizhong Wang, Xiaoxia Ma, Ming Chen* (2013)
Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa)
New Phytologist, 197(2): 441-453. (SCI=6.736; 6.888)
- Chaogang Shao, Ming Chen*, Yijun Meng* (2013)
A reverse framework for the identification of microRNA—target pairs in plants
Briefings in Bioinformatics, 14(3):293-301. (SCI=5.298; 7.51)
- You-Jun Huang, Li-Li Liu, Jian-Qin Huang, Zheng-Jia Wang, Fang-Fang Chen, Qi-Xiang Zhang, Bing-Song Zheng*, Ming Chen* (2013)
Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)
BMC Genomics, 14: 691.  (SCI=4.397; 4.615)
- Lili Liu, Zijun Zhang, Qian Mei, Ming Chen* (2013)
PSI: A comprehensive and integrative approach for accurate plant subcellular localization prediction
PLoS One, 8(10): e75826. (SCI=3.730; 4.244)
- Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen* (2013)
An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice
Journal of Integrative Bioinformatics, 10(2): 223.
- Ming Chen, Lili Liu, Qian Mei and Zijun Zhang (2013)
Ricenet: Genome-scale multi-level network reconstruction of rice
Journal of Computer Science and Systems Biology, 6: 4.
- Chuan Xu, Lili Liu, Zhao Zhang, Danfeng Jin, Juanping Qiu, Ming Chen* (2013)
Genome-scale metabolic model in guiding metabolic engineering of microbial improvement
Applied Microbiology and Biotechnology, 97(2): 519-539. (SCI=3.689; 3.762)
- Xiaoduo Lu, Dijun Chen, Dengfeng Shu, Zhao Zhang, Weixuan Wang, Christian Klukas, Lingling Chen, Yunliu Fan, Ming Chen*, Chunyi Zhang* (2013)
The differential transcription network between embryo and endosperm in the early developing maize seed
Plant Physiology, 162(1):440-455. (SCI=6.555; 7.084)
- Chen, Jine; Li, Jianying; Liu, Lili; Liang, Jianshe; Chen, Ming; Jiang, Zhendong; Zhong, Boxiong; You, Zhengying; Ma, Ying-ying (2013)
Proteome Analysis of Silkworm, Bombyx mori Larval Gonads: Characterization of Proteins Involved in Sexual Dimorphism and Gametogenesis
Journal of Proteome Research, 12(6): 2422-2438. (IF=5.056; 5.223)
- Yanping Zhang, Youhuang Bai, Jian Han, Ming Chen, Emrul Kayesh, Weibing Jiang, Jinggui Fang (2013)
Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE
Journal of Plant Physiology, 170(1): 80-92. (IF=2.699; 2.960)
- Chao Feng, Chang-jie Xu, Yue Wang, Wen-li Liu, Xue-ren Yin, Xian Li, Ming Chen and Kun-song Chen (2013)
Codon usage patterns in Chinese bayberry
(Myrica rubra) based on RNA-Seq data
BMC Genomics, 14: 732. (SCI=4.397; 4.615)
- Wei Zou, Dijun Chen, Min Xiong, Jiping Zhu, Xian Lin, Lun Wang, Jun Zhang, Lingling Chen,
Hongyu Zhang, Huanchun Chen, Ming Chen, Meilin Jin (2013)
Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus
Scientific Reports, 3: 1601. (IF=2.927)
- 陈铭，包家立，黄炳顶 译；T.Charlie Hodgman, Andrew French, David R.Westhead, Ed. (2013)
生物信息学（第二版）；Bioinformatics (2nd Edition)
科学出版社, 2013. ISBN: 7-03-038812-4/Q 3212.
2012
- Yijun Meng*, Chaogang Shao, Xiaoxia Ma, Huizhong Wang*, Ming Chen* (2012)
Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis
PLoS One, 7(11): e50870. (SCI=4.092; 4.537)
- Dijun Chen, Chun-hui Yuan, Jian Zhang, Zhao Zhang, Lin Bai, Yijun Meng, Ling-ling Chen*, Ming Chen* (2012)
PlantNATsDB: a comprehensive database of plant natural antisense transcripts
Nucleic Acids Research, 40(1): D1187-D1193. (SCI=8.026; 7.417)
- Yijun Meng*, Chaogang Shao, Huizhong Wang, Ming Chen* (2012)
Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants
RNA Biology, 9(3): 249-253. (SCI=4.933; )
- Chaogang Shao, Xiaoxia Ma, Ming Chen*, Yijun Meng* (2012)
Characterization of expression patterns of small RNAs among various organs in Arabidopsis
and rice based on 454 platform-generated high-throughput sequencing data
Plant Omics Journal, 5(3): 298-304. (SCI=1.734; 1.681)
- Chao Feng+, Ming Chen+, Chang-jie Xu, Lin Bai, Xue-ren Yin, Xian Li, Andrew C. Allan, Ian B. Ferguson and Kun-song Chen (2012)
Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq
BMC Genomics, 13: 19. (SCI=4.073; 4.328 )
- Xiaoying Li, Nicholas kibet Korir, Lili Liu, Lingfei Shangguan, Yuzhu Wang, Jian Han, Ming Chen, Jinggui Fang (2012)
Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca
Journal of Plant Physiology, 169(17): 1776-1788. (IF=2.791; 3.057)
- Yuriy Orlov, Han Xu, Dmitri Afonnikov, Bing Lim, Jian-Chien Heng, Ping Yuan, Ming Chen, Junli Yan, Neil Clarke, Nina Orlova, Mikael Huss, Konstantin Gunbin, Nikolay Podkolodnyy, Huck-Hui Ng (2012)
Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq Data in Embryonic Stem Cell
Journal of Integrative Bioinformatics, 9(2): 211.
- Orlov Y.L., O. Dobrovolskaya, C.H. Yuan, D.A. Afonnikov, Y. Zhu, M. Chen* (2012)
Integrative Computer Analysis of Antisense Transcripts and miRNA Targets in Plant Genomes
Journal of Stress Physiology & Biochemistry, 8(3): S7.
- Zhisong He, Dijun Chen, Kuangyu Wang, Ming Chen* (2012)
miRPreditor: a Novel MiRNA Target Predictor Based on SVM with Feature Analysis
Electronic Journal of Biology, 8(4): 79-89.
- 李燕，陈铭 (2012)
国际整合生物信息学
国际学术动态, 183(6): 33-35.
- 陈铭 主编 (2012)
生物信息学
科学出版社, 2012年1月. ISBN: 978-7-03-033205-9.字数：46万
2011
- Donglin Huang, Yiling Huang, Youhuang Bai, Dijun Chen, Ralf Hofestädt, Christian Klukas, Ming Chen* (2011)
MyBioNet: interactively visualize, edit and merge biological networks on the Web
Bioinformatics, 27(23): 3321-3322. (SCI=4.877; 6.325)
- Yijun Meng, Chaogang Shao, Ming Chen* (2011)
Toward microRNA-mediated gene regulatory networks in plants
Briefings in Bioinformatics, 12(6): 645-659. (SCI=9.283; 7.395)
- Dijun Chen, Yijun Meng, Chunhui Yuan, Lin Bai, Donglin Huang, Shaolei Lv, Ping Wu, Lingling Chen, Ming Chen* (2011)
Plant siRNAs from introns mediate DNA methylation of host genes
RNA, 17(6): 1012-1024. (SCI=6.051; 5.486)
- Yijun Meng*, Chaogang Shao, Huizhong Wang, Ming Chen* (2011)
The regulatory activities of plant microRNAs: a more dynamic perspective
Plant Physiology, 157(4): 1583-1595. (SCI=6.451; 7.016)
- Yijun Meng, Chaogang Shao, Lingfeng Gou, Yongfeng Jin, Ming Chen* (2011)
Construction of microRNA- and microRNA*-mediated regulatory networks in plants
RNA Biology, 8(6): 1124-1148. (SCI=5.597; )
- Yijun Meng, Lingfeng Gou, Dijun Chen, Chuanzao Mao, Yongfeng Jin, Ping Wu, Ming Chen* (2011)
PmiRKB: a plant microRNA knowledge base
Nucleic Acids Research, 39(Database issue): D181-D187. (SCI=7.836; 7.314)
- Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng and Ming Chen* (2011)
PRIN, a predicted rice interactome network
BMC Bioinformatics, 12:161. (SCI=3.028; 3.786)
- 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 (2011)
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. (IF=5.328; 5.498)
- Youhuang Bai, Yijun Meng, Donglin Huang, Yanhua Qi, Ming Chen* (2011)
Origin and Evolutionary Analysis of the Plant-specific TIFY Transcription Factor Family
Genomics, 98: 128-136. (SCI=3.327; 3.214) (cover page)
- Lili Liu, Lin Bai, Cong Luo, Donglin Huang, Ming Chen* (2011)
Systematic Annotation and Bioinformatics Analyses of Large-scale Oryza sativa Proteome
Current Protein & Peptide Science, 12(7): 621-630. (SCI=3.830; 3.695)
- Yu ZhiMing, Kang Bo, He XiaoWei, Lv ShaoLei, Bai YouHuang, Ding WoNa, Chen Ming, Cho Hyung-Taeg and Wu Ping (2011)
Root hair-specific EXPANSINs modulate root hair elongation in rice
The Plant Journal, 66(5):725-734. (IF=6.948; 7.325)
- Jian-ying Li, Hui-juan Yang, Tian-yun Lan, Hao Wei, Hua-rong Zhang, Ming Chen, Wei Fan, Ying-ying Ma, Bo-xiong Zhong (2011)
Expression Profiling and Regulation of Genes Related to Silkworm Posterior Silk Gland Development and Fibroin Synthesis
Journal of Proteome Research, 10(8):3551-3564. (IF=5.460; 5.617)
- Yong Min, Xiaogang Jin*, Ming Chen*, Zhengzheng Pan, Ying Ge, Jie Chang (2011)
Pathway knockout and redundancy in metabolic networks
Journal of Theoretical Biology, 270: 63-69. (SCI=2.371; 2.491)
- Ming Chen, Minjie Hu, Ralf Hofestädt (2011)
A Systematic Petri Net Approach for Multiple Scale Modeling and Simulation of Biochemical Processes
Applied Biochemistry and Biotechnology, 164(3): 338-352. (SCI=1.879; 2.053)
- Ming Chen, Sridhar Hariharaputran, Ralf Hofestädt, Benjamin Kormeier, Sarah Spangardt (2011)
Petri Net Models for the Semi-automatic Construction of Large Scale Biological Networks
Natural Computing, 10(3): 1077-1097.
- Ming Chen et al. (2011)
Two articles selected for Series "Studies in Health Technology and Informatics" (Volume 162)
===>>>list
- Ming Chen, Ralf Hofestädt (2011)
Quantitative Petri Net Model of Gene Regulated Metabolic Networks in the Cell
Studies in Health Technology and Informatics, pp. 38-55
- Sebastian Janowski, Benjamin Kormeier, Thoralf Töpel, Klaus Hippe, Ralf Hofestädt, Nils Willassen, Rafael Friesen, Sebastian Rubert, Daniela Borck, Peik Haugen and Ming Chen (2011)
Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing
Studies in Health Technology and Informatics, pp. 182-203.
In Biological Petri Nets (Edgar Wingender ed.), ISBN 978-1-60750-703-1
- Yijun Meng, Ping Wu, Ming Chen (2011)
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.
- 曹俊杰, 郑利斌, 陈铭* (2011)
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.
- 陈铭, 张子丁 (2011)
基因芯片、计算机与作物研究新进展
国际学术动态, 176(5): 36-37.
2010
- Yijun Meng, Lingfeng Gou, Dijun Chen, Ping Wu, Ming Chen* (2010)
High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism
Journal of Experimental Botany, 61(14): 3833-3837. (SCI=4.271)
- Dijun Chen, Yijun Meng, Xiaoxia Ma, Chuanzao Mao, Youhuang Bai, Junjie Cao, Haibin Gu, Ping Wu, Ming Chen* (2010)
Small RNAs in angiosperms: sequence characteristics, distribution, and generation
Bioinformatics, 26(11): 1391-1394. (SCI=4.926)
- Ming Chen, Yijun Meng, Haibin Gu, Dijun Chen (2010)
Functional characterization of plant small RNAs based on next-generation sequencing data
Computational Biology and Chemistry, 34: 308–312. (SCI=1.370)
- Chaogang Shao, Yijun Meng, Shaolei Lv, Wei Zhong, Zheyu Wang, Ming Chen* (2010)
CloneAssistant 1.0: a stand-alone software for automated cloning primer design
Journal of Biotechnology, 150: 294-298. (SCI=2.881)
- Yijun Meng, Dijun Chen, YongFeng Jin, Chuanzao Mao, Ping Wu, Ming Chen* (2010)
RNA editing of nuclear transcripts in Arabidopsis thaliana
BMC Genomics, 10(S4): S12. (SCI=3.759)
- ChenJia Shen, YouHuang Bai, SuiKang Wang, SaiNa Zhang, YunRong Wu, Ming Chen, Tom J Guilfoyle, Ping Wu, YanHua Qi (2010)
Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.)
Journal of Experimental Botany, 61(14): 3971-3981. (IF=4.271)
- ChenJia Shen, YouHuang Bai, SuiKang Wang, SaiNa Zhang, YunRong Wu, Ming Chen, DeAn Jiang, YanHua Qi (2010)
Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress
FEBS Journal, 277(14): 2954-2969. (IF=3.042)
- SuiKang Wang, YouHuang Bai, ChenJia Shen, YunRong Wu, SaiNa Zhang, DeAn Jiang, Tom J Guilfoyle, Ming Chen*, YanHua Qi* (2010)
Auxin-related gene families in abiotic stress response in Sorghum bicolor
Functional & Integrative Genomics, 10: 533-546. (SCI=3.825)
- Ming Chen, Shaolei Lv, Yijun Meng (2010)
The Epigenetic Performers in Plants
Development, Growth and Differentiation, 52(6): 555-566. (SCI=2.280)
- Yijun Meng, Xiaoxia Ma, Dijun Chen, Ping Wu, Ming Chen* (2010)
MicroRNA-mediated signaling involved in plant root development
Biochemical and Biophysical Research Communications, 393: 345-349. (SCI=2.548)
- Ming Chen, Yijun Meng, Chuanzao Mao, Dijun Chen, Ping Wu (2010)
Methodological framework for functional characterization of plant microRNAs
Journal of Experimental Botany, 61(9): 2271-2280. (SCI=4.271)
- Jianying Li, S. Hossein Hosseini Moghaddam, Xiang Chen, Ming Chen, Boxiong Zhong (2010)
Shotgun strategy-based proteome profiling analysis on the head of silkworm Bombyx mori
Amino Acids, 39(3): 751-761. (IF=3.877)
- Jian-ying Li, S. Hossein Hosseini Moghaddam, Jin-e Chen, Ming Chen, Bo-xiong Zhong (2010)
Shotgun proteomic analysis on the embryos of silkworm Bombyx mori at the end of organogenesis
Insect Biochemistry and Molecular Biology, 40: 293-302. (IF=3.117)
- Qingyun Shi, Yijun Meng, Dijun Chen, Fei He, Haibin Gu, Ping Wu, Ming Chen* (2010)
OsCAS: a comprehensive web-based annotation platform for rice microarray data
BioChip Journal, 4(1): 9-15. (SCI=1.840)
- CHEN DiJun, ZHANG Fan, YUAN ChunHui, LU Jing, LI Xia, CHEN Ming* (2010)
A web-based platform for rice microarray annotation and data analysis
Science in China Series C: Life Sciences, 53(12): 1459-1466. (SCI=0.691)
- Yijun Meng, Dijun Chen, Xiaoxia Ma, Chuanzao Mao, Junjie Cao, Ping Wu, Ming Chen* (2010)
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 (2010)
Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing
In Silico Biology, 10(1,2): 27-48.
- Donglin Huang, Yiling Huang, Christian Klukas, Ralf Hofestaedt, Ming Chen* (2010)
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.
- 陈铭 (2010)
2009计算与整合生物学国际学术会议暨基因芯片、计算机和作物国际暑期研习班
国际学术动态, 171(6): 48-49.
2009
- Xiang Chen, Cong Luo, Xiaoxia Ma, Ming Chen* (2009)
VIRS: a visual tool for identifying restriction sites in multiple DNA sequences
Biotechnology Progress, 25(5): 1525-1527. (SCI=2.108)
- Yijun Meng, Fangliang Huang, Qingyun Shi, Junjie Cao, Dijun Chen, Jinwei Zhang, Jun Ni, Ping Wu, Ming Chen* (2009)
Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant
Planta, 230: 883-898. (SCI=3.088)
- Huijuan Yang, Zhonghua Zhou, Huarong Zhang, Ming Chen, Jianying Li, Yingying Ma, Boxiong Zhong (2009)
Shotgun proteomic analysis of the fat body during metamorphosis of domesticated silkworm (Bombyx mori)
Amino Acids, 38(5): 1333-1342. (IF=4.132)
- 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 (2009)
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. (IF=5.684)
- J.-Y. Li, X. Chen, S. H. Hosseini Moghaddam, M. Chen, H. Wei and B.-X. Zhong (2009)
Shotgun proteomics approach to characterizing the embryonic proteome of the silkworm, Bombyx mori, at labrum appearance stage
Insect Molecular Biology, 18(5): 649-60. (IF=2.871)
- Shuangyan Chen, Xiu-Qing Li, Aiguo Zhao, Lijuan Wang, Xiaofeng Li, Qingyun Shi, Ming Chen, Juan Guo, Jichong Zhang, Dongmei Qi, Gongshe Liu (2009)
Genes and Pathways Induced in Early Response to Simulated-Grazing Defoliation in Rice Seedlings
Current Issues in Molecular Biology, 11(2): 81-100. (IF=3.176)
- Zhaoyuan Fang, Chuan Shao, Yijun Meng, Ping Wu, Ming Chen* (2009)
Phosphate Signaling in Arabidopsis and Oryza sativa (update)
Plant Science, 176(2): 170-180. (SCI=1.974)
- 罗依惠，陈铭，李立伟，钱景，严杰 (2009)
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* (2009)
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.
- 陈铭 (2009)
2008基因芯片、计算机和作物国际学术会议
国际学术动态, 165(6): 52.
2008
- Ming Chen, Andrew Harrison (2008)
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 (2008)
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. (IF=5.675)
- Hao Tian, Weiren Cui, Tao Wan, Ming Chen* (2008)
A Computational Approach for Recognition of Electronic Microscope Plant Pollen Images
2008 Congress on Image and Signal Processing, pp. 259-263.
- Siyan Cao, Xubin Meng, Yang Liu, Chuan Shao, Stefan Grünewald, Chengxin Fu, Ming Chen (2008)
Genetic Variation and Biodiversity of Paeonia lactiflora in China as Determined by Analysis of ISSR Using Phylogenetic Trees and Split Networks
Electronic Journal of Biology, 4(4): 134-141.
- 陈铭，王祎萍，罗聪 (2008)
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* (2007)
The Two-component Signal System in Rice (Oryza sativa L.): A Genome-Wide Study of Cytokinin Signal Perception and Transduction
Genomics, 89: 697-707. (SCI=3.558)
- He Fei, Shi Qing-yun, Chen Ming, Wu Ping (2007)
RiceDB: A Web-Based Integrated Database for Annotating Rice Microarray
Rice Science, 14(4): 256-264.
- Jiaofang Shao, Qichao Tu, Ming Chen* (2007)
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 (2007)
Genomic survey of sequence features for ultraviolet tolerance in haloarchaea (family Halobacteriaceae)
Genomics, 90: 103-109. (IF=3.558)
- 何飞，施清芸，陈铭*，吴平* (2007)
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.
- 陈铭 (2007)
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 (2006)
BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian network
Bioinformatics, 22: 2952-2954. (SCI=6.019)
- Ming Chen, Ralf Hofestaedt (2006)
A Medical Bioinformatics Approach for Metabolic Disorders: Biomedical Data Prediction, Modeling and Systematic Analysis
Journal of Biomedical Informatics, 39(2): 147-159.
- Ming Chen, Fei He, Qingyun Shi, Ping Wu (2006)
A novel and integrative approach for rice gene expression an annotation and functional analysis
2nd International Rice Congress, Oct. 9-13, New Delhi, India.
- Ming Chen, Ralf Hofestaedt (2006)
Prediction and Alignment of Metabolic Pathways
In Bioinformatics of Genome Regulation and Structure II (Nikolay Kolchanov ed.), pp.355-365.
- 陈晓辉，宁开达，陈铭* (2006)
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.
- 陈铭 (2006)
整合生物信息学
计算机教育, 9: 7-10.
2005
- Ming Chen (2005)
Systems Biology Brings Life Sciences Closer
Genomics, Proteomics & Bioinformatics, 3(3): 194-196.
- Ming Chen, Ralf Hofestaedt (2005)
An algorithm for linear metabolic pathway alignment
In Silico Biology, 5: 111-128.
- Ming Chen, Ralf Hofestädt (2005)
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.
- Zheng Ye, Huan Xu, Qichao Tu, Shu Hong, Tiansheng Xie, Di Xia, Ming Chen* (2005)
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 (2005)
Alignment and Classification of Signaling Pathways
German Conference on Bioinformatics, Oct. 5th-7th, Hamburg, Germany.
- Ming Chen (2005)
Structural Analysis of Generalized and Specific Biological Networks
Metabolic Pathway Analysis, MPA'05, 2005, March 3-4, Jena, Germany.
- Ming Chen, Andreas Freier, Ralf Hofestaedt (2005)
Bioinformatics Approaches for Metabolic Pathways
In Handbook of Genome Research (Christoph W. Sensen ed.), pp.461-490.
- 罗辽复，陈铭，张文广 (2005)
生物信息学培训班讲义
内蒙古农业大学.
- 张文广，陈铭 (2005)
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.
2004
- Ming Chen, Ralf Hofestaedt (2004)
PathAligner: Metabolic Pathway Retrieval and Alignment
Applied Bioinformatics, 3(4), 241-252.
- Ming Chen, Susana Lin and Ralf Hofestaedt (2004)
STCDB: Signal Transduction Classification Database
Nucleic Acids Research, 32(1), D456-D458.
- Ming Chen, Ralf Hofestaedt (2004)
Web-based information retrieval system for the prediction of metabolic pathways
IEEE Transactions on Nanobioscience, 3(3), 192-199.
- Ming Chen (2004)
A Systems Analysis of Urea Cycle Disorders
3rd BREW: Bioinformatics Research & Education Workshop, 2004, April 26-28, Helsinki, Finland.
- Ralf Hofestaedt, Ming Chen (2004)
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 (2004)
In Silico Systems Analysis of Biopathways
PhD Thesis (Dr. rer. nat), Faculty of Technology, Bielefeld University, Bielefeld, Germany.
- 陈铭 (2004)
后基因组时代的生物信息学
生物信息学, 2(2): 29-34.
2003
- Ming Chen and Ralf Hofestaedt (2003)
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 (2003)
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 (2003)
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 (2003)
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 (2002)
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 (2002)
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 (2002)
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 (2002)
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 (2002)
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 (2002)
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 (2002)
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 (2001)
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 (2001)
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 (2000)
MetabSim - Regelbasierte Simulation Metabolischer Prozesse
DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und genomischer Datenmengen, 2000, Mai 19-20, Magdeburg, Germany.
Patents
Up to Top |
