Jianhua Ruan

Weixiong Zhang, Gary D. Stormo, Jianhua Ruan, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity

K. Mitsuya, Jianhua Ruan, T. Huang, 2022, Cell reports.

Coordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance

R. Schiff, C. Glass, Jianhua Ruan, 2019 .

Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science

Yufei Huang, Zhongming Zhao, Jianhua Ruan, 2016, BMC Genomics.

Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana

Jianhua Ruan, Chengwei Lei, Joseph Perez, 2011, BMC Bioinformatics.

A randomized steiner tree approach for biomarker discovery and classification of breast cancer metastasis

Jianhua Ruan, Md. Jamiul Jahid, Jianhua Ruan, 2012 .

A novel algorithm for network-based prediction of cancer recurrence.

Jianhua Ruan, Chengwei Lei, Md. Jamiul Jahid, 2016, Genomics.

Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data

Tim Hui-Ming Huang, Fei Gu, Jianhua Ruan, 2012, BCB.

Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation

K. Mitsuya, Jianhua Ruan, L. Myatt, 2017, PloS one.

The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia

Jianhua Ruan, B. Hermann, Y. Song, 2016, Development.

Identification and Evaluation of Functional Modules in Gene Co-expression Networks

Weixiong Zhang, Jianhua Ruan, Weixiong Zhang, 2006, Systems Biology and Computational Proteomics.

A completely parameter-free method for graph-based single cell RNA-seq clustering

Jianhua Ruan, Maryam Zand, 2021, bioRxiv.

Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency

Jianhua Ruan, Maryam Zand, 2021, F1000Research.

Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency.

Jianhua Ruan, Maryam Zand, Jianhua Ruan, 2020, F1000Research.

A general co-expression network-based approach to gene expression analysis: comparison and applications

Weixiong Zhang, Jianhua Ruan, Angela K. Dean, 2010, BMC Systems Biology.

A bi-dimensional regression tree approach to the modeling of gene expression regulation

Weixiong Zhang, Jianhua Ruan, Weixiong Zhang, 2006, Bioinform..

Identification and Evaluation of Weak Community Structures in Networks

Weixiong Zhang, Jianhua Ruan, Weixiong Zhang, 2006, AAAI.

CAGER: classification analysis of gene expression regulation using multiple information sources

Weixiong Zhang, Jianhua Ruan, Weixiong Zhang, 2005, BMC Bioinformatics.

ANNC: AUC-Based Feature Selection by Maximizing Nearest Neighbor Complementarity

Jun Wang, Gang Yu, Jinmao Wei, 2018, PRICAI.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools

Genevera I. Allen, Zhongming Zhao, Zhandong Liu, 2017, BMC Bioinformatics.

Endometrial Gap Junction Expression - Early Indicators of Endometriosis and Integral to Invasiveness

Jianhua Ruan, P. Osmulski, M. Gaczynska, 2021, bioRxiv.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications

Xiaoming Liu, Lei Xie, Kai Wang, 2018, BMC Bioinformatics.

Robust edge-based biomarker discovery improves prediction of breast cancer metastasis

Jianhua Ruan, Chengwei Lei, Nahim Adnan, 2020, BMC Bioinformatics.

Comparative evaluation of network features for the prediction of breast cancer metastasis

Jianhua Ruan, Nahim Adnan, Zhijie Liu, 2020, BMC Medical Genomics.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics

Genevera I. Allen, Zhongming Zhao, Zhandong Liu, 2017, BMC Genomics.

Supplementary materials for “ Identifying network communities with a high resolution ”

Jianhua Ruan, Weixiong Zhang, Weixiong Zhang, 2007 .

Semi-Supervised Multi-Label Feature Selection by Preserving Feature-Label Space Consistency

Jun Wang, Yuanyuan Xu, Jinmao Wei, 2018, CIKM.

Probabilistic Margin-Aware Multi-Label Feature Selection by Preserving Spatial Consistency

Jianhua Ruan, Jun Wang, Shuai An, 2019, 2019 International Joint Conference on Neural Networks (IJCNN).

A particle swarm optimization-based algorithm for finding gapped motifs

Jianhua Ruan, Chengwei Lei, Jianhua Ruan, 2010, BioData Mining.

Finding Gapped Motifs by a Novel Evolutionary Algorithm

Jianhua Ruan, Chengwei Lei, Jianhua Ruan, 2010, EvoBIO.

A Particle Swarm Optimization algorithm for finding DNA sequence motifs

Jianhua Ruan, Chengwei Lei, Jianhua Ruan, 2008, 2008 IEEE International Conference on Bioinformatics and Biomeidcine Workshops.

A novel swarm intelligence algorithm for finding DNA motifs

Jianhua Ruan, Chengwei Lei, Jianhua Ruan, 2009, Int. J. Comput. Biol. Drug Des..

Network-based pathway enrichment analysis

Lu Liu, Jianhua Ruan, Jianhua Ruan, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

A Novel Multiple Classifier Generation and Combination Framework Based on Fuzzy Clustering and Individualized Ensemble Construction

Jianhua Ruan, Zhen Gao, Maryam Zand, 2019, 2019 IEEE International Conference on Data Science and Advanced Analytics (DSAA).

A personalized committee classification approach to improving prediction of breast cancer metastasis

Tim Hui-Ming Huang, Jianhua Ruan, Md. Jamiul Jahid, 2014, Bioinform..

A novel approach for cancer outcome prediction using personalized classifier

Jianhua Ruan, Md. Jamiul Jahid, Jianhua Ruan, 2012, RACS.

Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data

Jianhua Ruan, Md. Jamiul Jahid, Jianhua Ruan, 2011, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Pathway Enrichment Analysis with Networks

Jianhua Ruan, Jinmao Wei, Jianhua Ruan, 2017, Genes.

An ensemble approach for drug side effect prediction

Jianhua Ruan, Md. Jamiul Jahid, Jianhua Ruan, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

Discovering Functional Modules by Clustering Gene Co-expression Networks

Weixiong Zhang, Jianhua Ruan, Weixiong Zhang, 2006 .

Discovering Functional Modules by Clustering

Weixiong Zhang, Jianhua Ruan, 2006 .

Characterization and Identification of MicroRNA Core Promoters in Four Model Species

Weixiong Zhang, Jianhua Ruan, Xuefeng Zhou, 2007, PLoS Comput. Biol..

Probabilistic Topic and Role Model for Information Diffusion in Social Network

Jun Wang, Zhenglu Yang, Jinmao Wei, 2018, PAKDD.

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites*

Jianhua Ruan, L. Penalva, S. Burns, 2011, The Journal of Biological Chemistry.

The Aquila Digital Community The Aquila Digital Community

Jianhua Ruan, Edward J. Perkins, Youping Deng, 2022 .

A random walk based approach for improving protein-protein interaction network and protein complex prediction

Jianhua Ruan, Chengwei Lei, Jianhua Ruan, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.

Fully automated protein complex prediction based on topological similarity and community structure

Jianhua Ruan, Chengwei Lei, Saleh Tamim, 2013, Proteome Science.

Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science

Yufei Huang, Lang Li, Jianhua Ruan, 2016, BMC Genomics.

A Top-Performing Algorithm for the DREAM3 Gene Expression Prediction Challenge

Jianhua Ruan, Jianhua Ruan, 2010, PloS one.

Mutation of the conserved late element in geminivirus CP promoters abolishes Arabidopsis TCP24 transcription factor binding and decreases H3K27me3 levels on viral chromatin

Jianhua Ruan, G. Sunter, D. Bisaro, 2024, PLoS pathogens.