Ming Chen

71 papers B 1Journal 65Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins.
Database J. Biol. Databases Curation
Yanyan Zhu, Liya Liu, Yueming Hu, Sida Li, Enyan Liu, Yanshi Hu, Shilong Zhang, Haoyu Chao, Qiuyu Fang, Huan Yu, Ming Chen
2025 J jnl
STCDB4ND: a signal transduction classification database for neurological diseases.
Database J. Biol. Databases Curation
Boyan Gong, Sida Li, Yifan Chen, Liya Liu, Ralf Hofestädt, Ming Chen
2024 J jnl
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling.
Database J. Biol. Databases Curation
Yi Shen, Liya Liu, Enyan Liu, Sida Li, Yuriy L. Orlov, Vladimir A. Ivanisenko, Ming Chen
2024 J jnl
BGRS: bioinformatics of genome regulation and data integration.
J. Integr. Bioinform.
Yuriy L. Orlov, Ming Chen, Nikolay A. Kolchanov, Ralf Hofestädt
2024 J jnl
Integrating omics databases for enhanced crop breeding.
J. Integr. Bioinform.
Haoyu Chao, Shilong Zhang, Yueming Hu, Qingyang Ni, Saige Xin, Liang Zhao, Vladimir A. Ivanisenko, Yuriy L. Orlov, Ming Chen
2024 J jnl
iSeq: an integrated tool to fetch public sequencing data.
Bioinform.
Haoyu Chao, Zhuojin Li, Dijun Chen, Ming Chen
2023 J jnl
CropGF: a comprehensive visual platform for crop gene family mining and analysis.
Database J. Biol. Databases Curation
Jingtian Xu, Can Zhu, Minzeng Su, Sida Li, Haoyu Chao, Ming Chen
2023 J jnl
Early Identification of Crop Type for Smallholder Farming Systems Using Deep Learning on Time-Series Sentinel-2 Imagery.
Sensors
Haseeb Rehman Khan, Zeeshan Gillani, Muhammad Hasan Jamal, Atifa Athar, Muhammad Tayyab Chaudhry, Haoyu Chao, Yong He, Ming Chen
2023 J jnl
Network integration and protein structural binding analysis of neurodegeneration-related interactome.
Briefings Bioinform.
Hongjun Chen, Yekai Zhou, Yongjing Liu, Peijing Zhang, Ming Chen
2022 J jnl
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure.
Bioinform.
Yuhao Chen, Yanshi Hu, Xiaotian Hu, Cong Feng, Ming Chen
2022 J jnl
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks.
Bioinform.
Xiaotian Hu, Cong Feng, Yincong Zhou, Andrew P. Harrison, Ming Chen
2022 J jnl
Editorial: Petri nets for cellular process modelling.
Biosyst.
Hiroshi Matsuno, Fei Liu, Ming Chen
2022 J jnl
LBD: a manually curated database of experimentally validated lymphoma biomarkers.
Database J. Biol. Databases Curation
Bin Tan, Saige Xin, Yanshi Hu, Cong Feng, Ming Chen
2021 J jnl
A Petri nets-based framework for whole-cell modeling.
Biosyst.
Fei Liu, George Assaf, Ming Chen, Monika Heiner
2021 J jnl
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2.
Briefings Bioinform.
Md. Asif Ahsan, Yongjing Liu, Cong Feng, Yincong Zhou, Guangyuan Ma, Youhuang Bai, Ming Chen
2021 J jnl
OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources.
J. Integr. Bioinform.
Md. Asif Ahsan, Yongjing Liu, Cong Feng, Ralf Hofestädt, Ming Chen
2021 J jnl
Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage.
Briefings Bioinform.
Cong Feng, Min Dai, Yongjing Liu, Ming Chen
2021 J jnl
mPPI: a database extension to visualize structural interactome in a one-to-many manner.
Database J. Biol. Databases Curation
Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen
2020 J jnl
A novel riboswitch classification based on imbalanced sequences achieved by machine learning.
PLoS Comput. Biol.
Solomon Shiferaw Beyene, Tianyi Ling, Blagoj Ristevski, Ming Chen
2020 J jnl
Bioinformatics of genome regulation and structure - 2020 papers collection.
J. Integr. Bioinform.
Yuriy L. Orlov, Oxana B. Dobrovolskaya, Ming Chen, Ralf Hofestädt
2020 J jnl
CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants.
Genom. Proteom. Bioinform.
Peijing Zhang, Yongjing Liu, Hongjun Chen, Xianwen Meng, Jitong Xue, Kunsong Chen, Ming Chen
2020 J jnl
PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction.
Bioinform.
Qiang Kang, Jun Meng, Jun Cui, Yushi Luan, Ming Chen
2020 J jnl
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants.
Database J. Biol. Databases Curation
Wenyi Wu, Yan Wu, Dahui Hu, Yincong Zhou, Yanshi Hu, Yujie Chen, Ming Chen
2019 J jnl
A practical guide for DNase-seq data analysis: from data management to common applications.
Briefings Bioinform.
Yongjing Liu, Liangyu Fu, Kerstin Kaufmann, Dijun Chen, Ming Chen
2019 J jnl
Bioinformatics research at BGRS-2018.
BMC Bioinform.
Tatiana V. Tatarinova, Ming Chen, Yuriy L. Orlov
2019 J jnl
CircFunBase: a database for functional circular RNAs.
Database J. Biol. Databases Curation
Xianwen Meng, Dahui Hu, Peijing Zhang, Qi Chen, Ming Chen
2019 J jnl
Integrative Bioinformatics: History and Future.
J. Integr. Bioinform.
Ming Chen, Ralf Hofestädt, Jan Taubert
2019 J jnl
Non-Coding RNAs and their Integrated Networks.
J. Integr. Bioinform.
Peijing Zhang, Wenyi Wu, Qi Chen, Ming Chen
2019 J jnl
Versatile interactions and bioinformatics analysis of noncoding RNAs.
Briefings Bioinform.
Qi Chen, Xianwen Meng, Qi Liao, Ming Chen
2018 J jnl
Big Data Analytics in Medicine and Healthcare.
J. Integr. Bioinform.
Blagoj Ristevski, Ming Chen
2017 J jnl
A Generalized Approach for Measuring Relationships Among Genes.
J. Integr. Bioinform.
Lijun Wang, Md. Asif Ahsan, Ming Chen
2017 J jnl
Biological Big Bytes: Integrative Analysis of Large Biological Datasets.
J. Integr. Bioinform.
Ming Chen, Andrew P. Harrison, Hugh P. Shanahan, Yuriy L. Orlov
2017 J jnl
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential.
Bioinform.
Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen
2017 J jnl
Circular RNA: an emerging key player in RNA world.
Briefings Bioinform.
Xianwen Meng, Xue Li, Peijing Zhang, Jingjing Wang, Yincong Zhou, Ming Chen
2017 J jnl
DEF: an automated dead-end filling approach based on quasi-endosymbiosis.
Bioinform.
Lili Liu, Zijun Zhang, Taotao Sheng, Ming Chen
2017 J jnl
Digital Biomass Accumulation Using High-Throughput Plant Phenotype Data Analysis.
J. Integr. Bioinform.
Md. Matiur Rahaman, Md. Asif Ahsan, Zeeshan Gillani, Ming Chen
2017 J jnl
Non-coding RNAs and Their Roles in Stress Response in Plants.
Genom. Proteom. Bioinform.
Jingjing Wang, Xianwen Meng, Oxana B. Dobrovolskaya, Yuriy L. Orlov, Ming Chen
2017 J jnl
PceRBase: a database of plant competing endogenous RNA.
Nucleic Acids Res.
Chunhui Yuan, Xianwen Meng, Xue Li, Nicola Illing, Robert A. Ingle, Jingjing Wang, Ming Chen
2017 J jnl
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.
Database J. Biol. Databases Curation
Peijing Zhang, Xianwen Meng, Hongjun Chen, Yongjing Liu, Jitong Xue, Yincong Zhou, Ming Chen
2016 J jnl
DaTo: an atlas of biological databases and tools.
J. Integr. Bioinform.
Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
2016 J jnl
Toward a next-generation atlas of RNA secondary structure.
Briefings Bioinform.
Youhuang Bai, Xiaozhuan Dai, Andrew P. Harrison, Caroline E. Johnston, Ming Chen
2015 — conf
Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques.
BDVA
Björn Sommer, Stephen Jia Wang, Lifeng Xu, Ming Chen, Falk Schreiber
2015 J jnl
MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Bioinform.
Zhao Zhang, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen
2014 — book
Approaches in Integrative Bioinformatics - Towards the Virtual Cell
Ming Chen, Ralf Hofestädt
2014 — ch.
Bridging Genomics and Phenomics.
Approaches in Integrative Bioinformatics
Dijun Chen, Ming Chen, Thomas Altmann, Christian Klukas
2014 J jnl
CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks.
BMC Bioinform.
Zeeshan Gillani, Muhammad Akash, Md. Matiur Rahaman, Ming Chen
2014 — ch.
Integrative Bioinformatics.
Approaches in Integrative Bioinformatics
Ming Chen, Ralf Hofestädt
2014 J jnl
Open problems in Petri net modeling and simulation of biological systems.
it Inf. Technol.
Ming Chen, Ralf Hofestädt
2013 J jnl
A reversed framework for the identification of microRNA-target pairs in plants.
Briefings Bioinform.
Chaogang Shao, Ming Chen, Yijun Meng
2013 J jnl
An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice.
J. Integr. Bioinform.
Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen
2012 J jnl
Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell.
J. Integr. Bioinform.
Yuriy L. Orlov, Han Xu, Dmitry A. Afonnikov, Bing Lim, Jian-Chien Heng, Ping Yuan, Ming Chen, Junli Yan, Neil D. Clarke, Nina Orlova, Mikael Huss, Konstantin V. Gunbin, Nikolay Podkolodnyy, Huck-Hui Ng
2012 J jnl
PlantNATsDB: a comprehensive database of plant natural antisense transcripts.
Nucleic Acids Res.
Dijun Chen, Chunhui Yuan, Jian Zhang, Zhao Zhang, Lin Bai, Yijun Meng, Ling-Ling Chen, Ming Chen
2011 J jnl
Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network.
Genom. Proteom. Bioinform.
Pengcheng Zhu, Haibin Gu, Yinming Jiao, Donglin Huang, Ming Chen
2011 J jnl
MyBioNet: interactively visualize, edit and merge biological networks on the Web.
Bioinform.
Donglin Huang, Yiling Huang, Youhuang Bai, Dijun Chen, Ralf Hofestädt, Christian Klukas, Ming Chen
2011 J jnl
PRIN, a predicted rice interactome network.
BMC Bioinform.
Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng, Ming Chen
2011 J jnl
Petri net models for the semi-automatic construction of large scale biological networks.
Nat. Comput.
Ming Chen, Sridhar Hariharaputran, Ralf Hofestädt, Benjamin Kormeier, Sarah Spangardt
2011 J jnl
PmiRKB: a plant microRNA knowledge base.
Nucleic Acids Res.
Yijun Meng, Lingfeng Gou, Dijun Chen, Chuanzao Mao, Yongfeng Jin, Ping Wu, Ming Chen
2011 J jnl
Toward microRNA-mediated gene regulatory networks in plants.
Briefings Bioinform.
Yijun Meng, Chaogang Shao, Ming Chen
2010 J jnl
Functional characterization of plant small RNAs based on next-generation sequencing data.
Comput. Biol. Chem.
Ming Chen, Yijun Meng, Haibin Gu, Dijun Chen
2010 J jnl
Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing.
Silico Biol.
Sebastian Janowski, Benjamin Kormeier, Thoralf Töpel, Klaus Hippe, Ralf Hofestädt, Nils Willassen, Rafael Friesen, Sebastian Rubert, Daniela Borck, Peik Haugen, Ming Chen
2010 — conf
PBSK browser: Navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats.
BIBM Workshops
Donglin Huang, Yiling Huang, Christian Klukas, Ralf Hofestädt, Ming Chen
2010 J jnl
Small RNAs in angiosperms: sequence characteristics, distribution and generation.
Bioinform.
Dijun Chen, Yijun Meng, Xiaoxia Ma, Chuanzao Mao, Youhuang Bai, Junjie Cao, Haibin Gu, Ping Wu, Ming Chen
2009 J jnl
Antenna Location Optimization for Circular-Layout Distributed Antenna Systems.
IEICE Trans. Commun.
Xinzheng Wang, Pengcheng Zhu, Ming Chen
2009 J jnl
Antenna location design for generalized distributed antenna systems.
IEEE Commun. Lett.
Xinzheng Wang, Pengcheng Zhu, Ming Chen
2009 J jnl
Threshold-Based OSIC Detection Algorithm for Per-Antenna-Coded TIMO-OFDM Systems.
IEICE Trans. Commun.
Xinzheng Wang, Ming Chen, Pengcheng Zhu
2008 J jnl
In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops.
Genom. Proteom. Bioinform.
Ming Chen, Andrew P. Harrison
2008 B conf
Thresholded Interference Cancellation Algorithm for the LTE Uplink Multiuser MIMO.
GLOBECOM
Xinzheng Wang, Pengcheng Zhu, Ming Chen
2006 J jnl
A medical bioinformatics approach for metabolic disorders: Biomedical data prediction, modeling, and systematic analysis.
J. Biomed. Informatics
Ming Chen, Ralf Hofestädt
2004 J jnl
An algorithm for linear metabolic pathway alignment.
Silico Biol.
Ming Chen, Ralf Hofestädt
2004 J jnl
STCDB: Signal Transduction Classification Database.
Nucleic Acids Res.
Ming Chen, Susana Lin, Ralf Hofestädt
2003 J jnl
Quantitative Petri net model of gene regulated metabolic networks in the cell.
Silico Biol.
Ming Chen, Ralf Hofestädt