Publications
2009
- J. Ruan, A top-performing algorithm for the DREAM3 gene expression prediction challenge, submitted
- J. Ruan, A.K. Dean and W. Zhang, A general co-expression network-based approach to gene expression analysis: Comparison and applications, submitted
- J. Ruan, A fully automated method for discovering community structures in high dimensional data, Proc. of IEEE International Conference on Data Mining (ICDM-09), Miami, FL, USA, Dec. 6-9, 2009. Acceptance rate: 140/786=18%. PDF
- A.K. Dean, S.E. Harris, I. Kalajzic and J. Ruan, A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes, BMC Bioinformatics (Supplemental issue for AMIA Translational Bioinformatics 2009), 10 (S9):S5, 2009 Link
- D. Ravi, A.M. Wiles, S. Bhavani, J. Ruan, P. Leder, and A.J.R. Bishop, A network of conserved damage survival pathways revealed by a genomic RNAi screen, PLoS Genetics, 5(6): e1000527, 2009. Link
- J. Ruan, Y Deng, E.J. Perkins and W. Zhang, An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data, BMC Genomics, 10(S1):S8, 2009. Link
2008
- C. Lei and J. Ruan, A Particle Swarm Optimization Algorithm for Finding DNA Sequence Motifs, 1st Workshop on Data Mining in Functional Genomics, in Conjunction with IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, PA, USA, Nov. 5-7, 2008. PDF
- M. Ray, J. Ruan (joint first author) and W. Zhang, Variations in the transcriptome of Alzheimer's disease reveal modular networks involved in cardiovascular diseases, Genome Biology, 9:R148, 2008. Link
- J. Ruan and W Zhang, Identifying network community structures with a high resolution, Physical Review E, 77:016104, 2008. link | Supplemental file | Matlab code | In the news
- J.E. McDunn, K.D. Husain, A.D. Polpitiya, A. Burykin, J. Ruan, Q. Li, W. Schierding, N. Lin, D. Dixon, W. Zhang, C.M. Coopersmith, W.M. Dunne, M. Colonna, B.K. Ghosh, and P. Cobb. Plasticity of the systemic inflammatory response to acute infection during critical illness: Development of the Riboleukogram, PLoS ONE, 3(2):e1564, 2008. link
2007
- J. Ruan and W. Zhang, An efficient spectral algorithm for network community discovery and its applications to biological and social networks, Proc. of IEEE International Conference on Data Mining ( ICDM-07), Omaha, NE, USA, Oct. 28-31, 2007. Acceptance rate: 19% Proceeding version | Complete version
- X. Zhou, J. Ruan (joint first author), G. Wang and W. Zhang, Characterization and identification of microRNA core promoters in four model species, PLoS Computational Biology, 3(3):e37, 2007. link
2006
- J. Ruan and W. Zhang, Identification and evaluation of weak community structures in networks, Proc. of National Conference on Artificial Intelligence (AAAI-06), Boston, MA, July 2006. Acceptance rate: 22% (oral presentation). preprint
- J. Ruan and W. Zhang, A Bi-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulation, Bioinformatics, 22(3):332-40, 2006. preprint | supplementary files
- J. Ruan and W. Zhang, Identification and evaluation of functional modules in gene co-expression networks, Proc. of RECOMB Satellite Conferences on Systems Biology and Computational Proteomics, San Diego, CA, Dec 2006. Acceptance rate: 40% preprint .
2005
- X. Zhou, J. Ruan (joint first author), G. Wang and W. Zhang, Characterization of the promoters of microRNA genes: A genome-scale analysis on C. elegans, A. thaliana and H. sapiens, Proc. of RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics, San Diego, CA, Dec. 2005. preprint
- W. Zhang, J. Ruan , T-h. D. Ho, Y. You, T. Yu and R.S. Quatrano, Cis-regulatory element based targeted gene finding: Genome-wide identification of ABA- and abiotic stress-responsive genes in Arabidopsis thaliana, Bioinformatics, 21(14):3074-81, 2005. link
- J. Ruan and W. Zhang, CAGER: Classification Analysis for Gene Expression Regulation, BMC Bioinformatics, 6:114, 2005. link | Web server
2004
- J. Ruan , G.D. Stormo and W. Zhang, ILM: a web server for predicting RNA secondary structures with pseudoknots, Nucleic Acids Research, 32, W146-9, 2004. link | web server
- J. Ruan , G.D. Stormo and W. Zhang, An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots, Bioinformatics, 20(1), 58-66, 2004. link | software