An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru. - Jianhua Ruan; Gary D. Stormo; Weixiong Zhang (CSB, 2003)

An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. - Jianhua Ruan; Gary D. Stormo; Weixiong Zhang (Bioinform., 2004)

ILM: a web server for predicting RNA secondary structures with pseudoknots. - Jianhua Ruan; Gary D. Stormo; Weixiong Zhang (Nucleic Acids Res., 2004)

Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans , H. sapiens and A. thaliana. - Xuefeng Zhou; Jianhua Ruan; Guandong Wang; Weixiong Zhang (Systems Biology and Regulatory Genomics, 2005)

Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana. - Weixiong Zhang; Jianhua Ruan; Tuan-hua David Ho; Youngsook You; Taotao Yu; Ralph S. Quatrano (Bioinform., 2005)

CAGER: classification analysis of gene expression regulation using multiple information sources. - Jianhua Ruan; Weixiong Zhang (BMC Bioinform., 2005)

Identification and Evaluation of Weak Community Structures in Networks. - Jianhua Ruan; Weixiong Zhang (AAAI, 2006)

Identification and Evaluation of Functional Modules in Gene Co-expression Networks. - Jianhua Ruan; Weixiong Zhang (Systems Biology and Computational Proteomics, 2006)

A bi-dimensional regression tree approach to the modeling of gene expression regulation. - Jianhua Ruan; Weixiong Zhang (Bioinform., 2006)

An Efficient Spectral Algorithm for Network Community Discovery and Its Applications to Biological and Social Networks. - Jianhua Ruan; Weixiong Zhang (ICDM, 2007)

Characterization and Identification of MicroRNA Core Promoters in Four Model Species. - Xuefeng Zhou; Jianhua Ruan; Guandong Wang; Weixiong Zhang (PLoS Comput. Biol., 2007)

A Fully Automated Method for Discovering Community Structures in High Dimensional Data. - Jianhua Ruan (ICDM, 2009)

A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes. - Angela K. Dean; Stephen E. Harris; Ivo Kalajzic; Jianhua Ruan (BMC Bioinform., 2009)

A novel swarm intelligence algorithm for finding DNA motifs. - Chengwei Lei; Jianhua Ruan (Int. J. Comput. Biol. Drug Des., 2009)

Promoter prediction based on a multiple instance learning scheme. - Xuefeng Zhou; Jianhua Ruan; Weixiong Zhang (BCB, 2010)

Finding Gapped Motifs by a Novel Evolutionary Algorithm. - Chengwei Lei; Jianhua Ruan (EvoBIO, 2010)

A particle swarm optimization-based algorithm for finding gapped motifs. - Chengwei Lei; Jianhua Ruan (BioData Min., 2010)

A general co-expression network-based approach to gene expression analysis: comparison and applications. - Jianhua Ruan; Angela K. Dean; Weixiong Zhang (BMC Syst. Biol., 2010)

Building and analyzing protein interactome networks by cross-species comparisons. - Amy M. Wiles; Mark Doderer; Jianhua Ruan; Tingting Gu; Ravi Dashnamoorthy; Barron Blackman; Alexander J. R. Bishop (BMC Syst. Biol., 2010)

Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data. - Md. Jamiul Jahid; Jianhua Ruan (GENSiPS, 2011)

Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. - Jianhua Ruan; Joseph Perez; Brian Hernandez; Chengwei Lei; Garry Sunter; Valerie M. Sponsel (BMC Bioinform., 2011)

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data. - Jianhua Ruan; Md. Jamiul Jahid; Fei Gu; Chengwei Lei; Yi-Wen Huang; Ya-Ting Hsu; David G. Mutch; Chun-Liang Chen; Nameer B. Kirma; Tim Hui-Ming Huang (BCB, 2012)

A random walk based approach for improving protein-protein interaction network and protein complex prediction. - Chengwei Lei; Jianhua Ruan (BIBM, 2012)

A novel approach for cancer outcome prediction using personalized classifier. - Md. Jamiul Jahid; Jianhua Ruan (RACS, 2012)

Functional evaluation and analysis of predicted miRNA-mRNA regulatory network. - Saleh Tamim; Jianhua Ruan (RACS, 2012)

An ensemble approach for drug side effect prediction. - Md. Jamiul Jahid; Jianhua Ruan (BIBM, 2013)

Network-based pathway enrichment analysis. - Lu Liu; Jianhua Ruan (BIBM, 2013)

A structure-based approach to predicting in vitro transcription factor-DNA interaction. - Zhen Gao; Jianhua Ruan (GENSiPS, 2013)

A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. - Chengwei Lei; Jianhua Ruan (Bioinform., 2013)

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. - Zhen Gao; Ruizhe Zhao; Jianhua Ruan (BMC Genom., 2013)

A personalized committee classification approach to improving prediction of breast cancer metastasis. - Md. Jamiul Jahid; Tim Hui-Ming Huang; Jianhua Ruan (Bioinform., 2014)

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. - Zhongming Zhao; Yunlong Liu; Yufei Huang 001; Kun Huang; Jianhua Ruan (BMC Syst. Biol., 2016)

Structure-based prediction of drug side effects using a novel classification algorithm. - Md. Jamiul Jahid; Jianhua Ruan (Int. J. Comput. Biol. Drug Des., 2016)

Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning. - Zhen Gao; Jianhua Ruan (Bioinform., 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. - Zhandong Liu; W. Jim Zheng; Genevera I. Allen; Yin Liu; Jianhua Ruan; Zhongming Zhao (BMC Bioinform., 2017)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. - W. Jim Zheng; Jianhua Ruan; Hua Xu 001; Zhongming Zhao; Zhangdong Liu (BMC Syst. Biol., 2017)

Utilizing networks for differential analysis of chromatin interactions. - Lu Liu; Jianhua Ruan (J. Bioinform. Comput. Biol., 2017)

Semi-Supervised Multi-Label Feature Selection by Preserving Feature-Label Space Consistency. - Yuanyuan Xu 002; Jun Wang 023; Shuai An; Jinmao Wei 001; Jianhua Ruan (CIKM, 2018)

An integrative approach to transcriptional co-regulatory network construction and characterization in Arabidopsis. - Maryam Zand; Zhen Gao; Jinmao Wei 001; Garry Sunter; Jianhua Ruan (ICCABS, 2018)

Probabilistic Topic and Role Model for Information Diffusion in Social Network. - Hengpeng Xu; Jinmao Wei 001; Zhenglu Yang; Jianhua Ruan; Jun Wang 023 (PAKDD (2), 2018)

ANNC: AUC-Based Feature Selection by Maximizing Nearest Neighbor Complementarity. - Xuemeng Jiang; Jun Wang 023; Jinmao Wei 001; Jianhua Ruan; Gang Yu (PRICAI (1), 2018)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. - Xiaoming Liu; Lei Xie 006; Zhijin Wu; Kai Wang 063; Zhongming Zhao; Jianhua Ruan; Degui Zhi (BMC Bioinform., 2018)

A Novel Multiple Classifier Generation and Combination Framework Based on Fuzzy Clustering and Individualized Ensemble Construction. - Zhen Gao; Maryam Zand; Jianhua Ruan (DSAA, 2019)

Probabilistic Margin-Aware Multi-Label Feature Selection by Preserving Spatial Consistency. - Yu Yin; Shuai An; Jun Wang 023; Jinmao Wei 001; Jianhua Ruan (IJCNN, 2019)

Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. - Nahim Adnan; Chengwei Lei; Jianhua Ruan (BMC Bioinform., 2020)

Construction and Evaluation of Robust Interpretation Models for Breast Cancer Metastasis Prediction. - Nahim Adnan; Maryam Zand; Tim Hui-Ming Huang; Jianhua Ruan (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A Novel Feature Space Augmentation Method to Improve Classification Performance and Evaluation Reliability. - Sakhawat Hossain Saimon; Tanzira Najnin; Jianhua Ruan (KDD, 2024)