Quantitative Petri net model of gene regulated metabolic networks in the cell. - Ming Chen 005; Ralf Hofestädt (Silico Biol., 2003)

An algorithm for linear metabolic pathway alignment. - Ming Chen 005; Ralf Hofestädt (Silico Biol., 2004)

STCDB: Signal Transduction Classification Database. - Ming Chen 005; Susana Lin; Ralf Hofestädt (Nucleic Acids Res., 2004)

BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network. - Xiaohui Chen; Ming Chen 005; Kaida Ning (Bioinform., 2006)

A medical bioinformatics approach for metabolic disorders: Biomedical data prediction, modeling, and systematic analysis. - Ming Chen 005; Ralf Hofestädt (J. Biomed. Informatics, 2006)

Thresholded Interference Cancellation Algorithm for the LTE Uplink Multiuser MIMO. - Xinzheng Wang; Pengcheng Zhu 001; Ming Chen 005 (GLOBECOM, 2008)

In Silico Analysis of Crop Science: Report on the First China-UK Workshop on Chips, Computers and Crops. - Ming Chen 005; Andrew P. Harrison (Genom. Proteom. Bioinform., 2008)

Antenna location design for generalized distributed antenna systems. - Xinzheng Wang; Pengcheng Zhu 001; Ming Chen 005 (IEEE Commun. Lett., 2009)

Threshold-Based OSIC Detection Algorithm for Per-Antenna-Coded TIMO-OFDM Systems. - Xinzheng Wang; Ming Chen 005; Pengcheng Zhu 001 (IEICE Trans. Commun., 2009)

Antenna Location Optimization for Circular-Layout Distributed Antenna Systems. - Xinzheng Wang; Pengcheng Zhu 001; Ming Chen 005 (IEICE Trans. Commun., 2009)

PBSK browser: Navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats. - Donglin Huang; Yiling Huang; Christian Klukas; Ralf Hofestädt; Ming Chen 005 (BIBM Workshops, 2010)

Small RNAs in angiosperms: sequence characteristics, distribution and generation. - Dijun Chen; Yijun Meng; Xiaoxia Ma; Chuanzao Mao; Youhuang Bai; Junjie Cao 002; Haibin Gu; Ping Wu; Ming Chen 005 (Bioinform., 2010)

Functional characterization of plant small RNAs based on next-generation sequencing data. - Ming Chen 005; Yijun Meng; Haibin Gu; Dijun Chen (Comput. Biol. Chem., 2010)

Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing. - Sebastian Janowski; Benjamin Kormeier; Thoralf Töpel; Klaus Hippe; Ralf Hofestädt; Nils Willassen; Rafael Friesen; Sebastian Rubert; Daniela Borck; Peik Haugen; Ming Chen 005 (Silico Biol., 2010)

Toward microRNA-mediated gene regulatory networks in plants. - Yijun Meng; Chaogang Shao; Ming Chen 005 (Briefings Bioinform., 2011)

MyBioNet: interactively visualize, edit and merge biological networks on the Web. - Donglin Huang; Yiling Huang; Youhuang Bai; Dijun Chen; Ralf Hofestädt; Christian Klukas; Ming Chen 005 (Bioinform., 2011)

PRIN, a predicted rice interactome network. - Haibin Gu; Pengcheng Zhu; Yinming Jiao; Yijun Meng; Ming Chen 005 (BMC Bioinform., 2011)

Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network. - Pengcheng Zhu; Haibin Gu; Yinming Jiao; Donglin Huang; Ming Chen 005 (Genom. Proteom. Bioinform., 2011)

PmiRKB: a plant microRNA knowledge base. - Yijun Meng; Lingfeng Gou; Dijun Chen; Chuanzao Mao; Yongfeng Jin; Ping Wu; Ming Chen 005 (Nucleic Acids Res., 2011)

Petri net models for the semi-automatic construction of large scale biological networks. - Ming Chen 005; Sridhar Hariharaputran; Ralf Hofestädt; Benjamin Kormeier; Sarah Spangardt (Nat. Comput., 2011)

Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell. - Yuriy L. Orlov; Han Xu; Dmitry A. Afonnikov; Bing Lim; Jian-Chien Heng; Ping Yuan; Ming Chen 005; Junli Yan; Neil D. Clarke; Nina Orlova; Mikael Huss; Konstantin V. Gunbin; et al. (J. Integr. Bioinform., 2012)

PlantNATsDB: a comprehensive database of plant natural antisense transcripts. - Dijun Chen; Chunhui Yuan; Jian Zhang; Zhao Zhang 012; Lin Bai; Yijun Meng; Ling-Ling Chen; Ming Chen 005 (Nucleic Acids Res., 2012)

A reversed framework for the identification of microRNA-target pairs in plants. - Chaogang Shao; Ming Chen 005; Yijun Meng (Briefings Bioinform., 2013)

An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice. - Lili Liu; Qian Mei; Zhenning Yu; Tianhao Sun; Zijun Zhang; Ming Chen 005 (J. Integr. Bioinform., 2013)

Integrative Bioinformatics. - Ming Chen 005; Ralf Hofestädt (Approaches in Integrative Bioinformatics, 2014)

Bridging Genomics and Phenomics. - Dijun Chen; Ming Chen 005; Thomas Altmann; Christian Klukas (Approaches in Integrative Bioinformatics, 2014)

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks. - Zeeshan Gillani; Muhammad Akash; Md. Matiur Rahaman; Ming Chen 005 (BMC Bioinform., 2014)

Open problems in Petri net modeling and simulation of biological systems. - Ming Chen 005; Ralf Hofestädt (it Inf. Technol., 2014)

Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques. - Björn Sommer 001; Stephen Jia Wang; Lifeng Xu; Ming Chen 005; Falk Schreiber (BDVA, 2015)

MTide: an integrated tool for the identification of miRNA-target interaction in plants. - Zhao Zhang 012; Li Jiang; Jingjing Wang; Peizhen Gu; Ming Chen 005 (Bioinform., 2015)

Toward a next-generation atlas of RNA secondary structure. - Youhuang Bai; Xiaozhuan Dai; Andrew P. Harrison; Caroline E. Johnston; Ming Chen 005 (Briefings Bioinform., 2016)

DaTo: an atlas of biological databases and tools. - Qilin Li; Yincong Zhou; Yingmin Jiao; Zhao Zhang 012; Lin Bai; Li Tong; Xiong Yang; Björn Sommer 001; Ralf Hofestädt; Ming Chen 005 (J. Integr. Bioinform., 2016)

Circular RNA: an emerging key player in RNA world. - Xianwen Meng; Xue Li; Peijing Zhang; Jingjing Wang; Yincong Zhou; Ming Chen 005 (Briefings Bioinform., 2017)

PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks. - Peijing Zhang; Xianwen Meng; Hongjun Chen; Yongjing Liu; Jitong Xue; Yincong Zhou; Ming Chen 005 (Database J. Biol. Databases Curation, 2017)

DEF: an automated dead-end filling approach based on quasi-endosymbiosis. - Lili Liu; Zijun Zhang; Taotao Sheng; Ming Chen 005 (Bioinform., 2017)

CircPro: an integrated tool for the identification of circRNAs with protein-coding potential. - Xianwen Meng; Qi Chen 010; Peijing Zhang; Ming Chen 005 (Bioinform., 2017)

Non-coding RNAs and Their Roles in Stress Response in Plants. - Jingjing Wang; Xianwen Meng; Oxana B. Dobrovolskaya; Yuriy L. Orlov; Ming Chen 005 (Genom. Proteom. Bioinform., 2017)

Biological Big Bytes: Integrative Analysis of Large Biological Datasets. - Ming Chen 005; Andrew P. Harrison; Hugh P. Shanahan; Yuriy L. Orlov (J. Integr. Bioinform., 2017)

Digital Biomass Accumulation Using High-Throughput Plant Phenotype Data Analysis. - Md. Matiur Rahaman; Md. Asif Ahsan; Zeeshan Gillani; Ming Chen 005 (J. Integr. Bioinform., 2017)

A Generalized Approach for Measuring Relationships Among Genes. - Lijun Wang; Md. Asif Ahsan; Ming Chen 005 (J. Integr. Bioinform., 2017)

PceRBase: a database of plant competing endogenous RNA. - Chunhui Yuan; Xianwen Meng; Xue Li; Nicola Illing; Robert A. Ingle; Jingjing Wang; Ming Chen 005 (Nucleic Acids Res., 2017)

Big Data Analytics in Medicine and Healthcare. - Blagoj Ristevski; Ming Chen 005 (J. Integr. Bioinform., 2018)

Versatile interactions and bioinformatics analysis of noncoding RNAs. - Qi Chen 010; Xianwen Meng; Qi Liao; Ming Chen 005 (Briefings Bioinform., 2019)

A practical guide for DNase-seq data analysis: from data management to common applications. - Yongjing Liu; Liangyu Fu; Kerstin Kaufmann; Dijun Chen; Ming Chen 005 (Briefings Bioinform., 2019)

CircFunBase: a database for functional circular RNAs. - Xianwen Meng; Dahui Hu; Peijing Zhang; Qi Chen 010; Ming Chen 005 (Database J. Biol. Databases Curation, 2019)

Bioinformatics research at BGRS-2018. - Tatiana V. Tatarinova; Ming Chen 005; Yuriy L. Orlov (BMC Bioinform., 2019)

Integrative Bioinformatics: History and Future. - Ming Chen 005; Ralf Hofestädt; Jan Taubert (J. Integr. Bioinform., 2019)

Non-Coding RNAs and their Integrated Networks. - Peijing Zhang; Wenyi Wu; Qi Chen 010; Ming Chen 005 (J. Integr. Bioinform., 2019)

PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants. - Wenyi Wu; Yan Wu; Dahui Hu; Yincong Zhou; Yanshi Hu; Yujie Chen; Ming Chen 005 (Database J. Biol. Databases Curation, 2020)

PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction. - Qiang Kang; Jun Meng; Jun Cui 004; Yushi Luan; Ming Chen 005 (Bioinform., 2020)

CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants. - Peijing Zhang; Yongjing Liu; Hongjun Chen; Xianwen Meng; Jitong Xue; Kunsong Chen; Ming Chen 005 (Genom. Proteom. Bioinform., 2020)

Bioinformatics of genome regulation and structure - 2020 papers collection. - Yuriy L. Orlov; Oxana B. Dobrovolskaya; Ming Chen 005; Ralf Hofestädt (J. Integr. Bioinform., 2020)

A novel riboswitch classification based on imbalanced sequences achieved by machine learning. - Solomon Shiferaw Beyene; Tianyi Ling; Blagoj Ristevski; Ming Chen 005 (PLoS Comput. Biol., 2020)

Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2. - Md. Asif Ahsan; Yongjing Liu; Cong Feng; Yincong Zhou; Guangyuan Ma; Youhuang Bai; Ming Chen 005 (Briefings Bioinform., 2021)

Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage. - Cong Feng; Min Dai; Yongjing Liu; Ming Chen 005 (Briefings Bioinform., 2021)

mPPI: a database extension to visualize structural interactome in a one-to-many manner. - Yekai Zhou; Hongjun Chen; Sida Li; Ming Chen 005 (Database J. Biol. Databases Curation, 2021)

A Petri nets-based framework for whole-cell modeling. - Fei Liu 006; George Assaf; Ming Chen 005; Monika Heiner (Biosyst., 2021)

OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources. - Md. Asif Ahsan; Yongjing Liu; Cong Feng; Ralf Hofestädt; Ming Chen 005 (J. Integr. Bioinform., 2021)

LBD: a manually curated database of experimentally validated lymphoma biomarkers. - Bin Tan; Saige Xin; Yanshi Hu; Cong Feng; Ming Chen 005 (Database J. Biol. Databases Curation, 2022)

CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure. - Yuhao Chen; Yanshi Hu; Xiaotian Hu; Cong Feng; Ming Chen 005 (Bioinform., 2022)

DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. - Xiaotian Hu; Cong Feng; Yincong Zhou; Andrew P. Harrison; Ming Chen 005 (Bioinform., 2022)

Editorial: Petri nets for cellular process modelling. - Hiroshi Matsuno; Fei Liu 006; Ming Chen 005 (Biosyst., 2022)

CropGF: a comprehensive visual platform for crop gene family mining and analysis. - Jingtian Xu; Can Zhu; Minzeng Su; Sida Li; Haoyu Chao; Ming Chen 005 (Database J. Biol. Databases Curation, 2023)

Early Identification of Crop Type for Smallholder Farming Systems Using Deep Learning on Time-Series Sentinel-2 Imagery. - Haseeb Rehman Khan; Zeeshan Gillani; Muhammad Hasan Jamal; Atifa Athar; Muhammad Tayyab Chaudhry; Haoyu Chao; Yong He 001; Ming Chen 005 (Sensors, 2023)

Network integration and protein structural binding analysis of neurodegeneration-related interactome. - Hongjun Chen; Yekai Zhou; Yongjing Liu; Peijing Zhang; Ming Chen 005 (Briefings Bioinform., 2023)

AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling. - Yi Shen; Liya Liu; Enyan Liu; Sida Li; Yuriy L. Orlov; Vladimir A. Ivanisenko; Ming Chen 005 (Database J. Biol. Databases Curation, 2024)

Integrating omics databases for enhanced crop breeding. - Haoyu Chao; Shilong Zhang; Yueming Hu; Qingyang Ni; Saige Xin; Liang Zhao; Vladimir A. Ivanisenko; Yuriy L. Orlov; Ming Chen 005 (J. Integr. Bioinform., 2024)

BGRS: bioinformatics of genome regulation and data integration. - Yuriy L. Orlov; Ming Chen 005; Nikolay A. Kolchanov; Ralf Hofestädt (J. Integr. Bioinform., 2024)

STCDB4ND: a signal transduction classification database for neurological diseases. - Boyan Gong; Sida Li; Yifan Chen; Liya Liu; Ralf Hofestädt; Ming Chen 005 (Database J. Biol. Databases Curation, 2025)