Dr. Jianhua Ruan, Department of Computer Science, UTSA

Publications

#: Student supervised by Dr. Ruan
IF: ISI Journal Impact Factor

Journal publications

  1. J Sun, H Pan, C Lei# (joint first author), B Yuan, SJ Nair, C April, B Parameswaran, B Klotzle, JB Fan, J Ruan (co-corresponding author) and R Li. Genetic and genomic analyses of an RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth, Journal of Biological Chemistry, in press (IF=5.328)
  2. P.J. Uren, S.C. Burns, J Ruan, K.K. Singh, A.D. Smith and L.O.F. Penalva, 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, Journal of Biological Chemistry, in press (IF=5.328)
  3. J. Ruan, J. Perez#, B. Hernandez#, C. Lei#, G. Sunter and V.M. Sponsel. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana, BMC Bioinformatics, to appear.
  4. C. Lei# and J. Ruan, A particle swarm optimization-based algorithm for finding gapped motifs, BioData Mining, 3:9, 2010
  5. J. Ruan, A.K. Dean# and W. Zhang, A general co-expression network-based approach to gene expression analysis: Comparison and applications, BMC Systems Biology, 4:8, 2010. (IF = 4.06)
  6. AM Wiles*, M Doderer*, J Ruan (*joint-first author), TT Gu, D Ravi, B Blackman and AJR Bishop, Building and Analyzing Protein Interactome Networks by Cross-species Comparisons, BMC Systems Biology, 4:36, 2010. (IF = 4.06) web server
  7. J. Ruan, A top-performing algorithm for the DREAM3 gene expression prediction challenge, PLoS ONE 5(2): e8944, 2010 (IF = 4.38)
  8. S Ghosh, AK Dean#, M Walter, Y Bao, Y Hu, J Ruan and Rong Li, Cell Density-Dependent Transcriptional Activation of Endocrine-Related Genes in Human Adipose Tissue-Derived Stem Cells, Experimental Cell Research, 316(13):2087-2098, 2010. (IF = 3.71)
  9. 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, 10 (S9):S5, 2009 (IF = 3.78)
  10. 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. (IF = 8.88)
  11. 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. (IF = 3.93)
  12. C. Lei# and J. Ruan, A novel swarm intelligence algorithm for finding DNA motifs, International Journal of Computational Biology and Drug Design, 2(4):323 - 339, 2009
  13. 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. (IF = 6.15)
  14. 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. (21 Citations)
  15. J. Ruan and W Zhang, Identifying network community structures with a high resolution, Physical Review E, 77:016104, 2008.(49 Citations)
    Supplemental file     | Matlab code | In the news | Selected by Virtual Journal of Biological Physics Research.
  16. 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. (114 Citations)
  17. J. Ruan and W. Zhang, A Bi-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulation, Bioinformatics, 22(3):332-40, 2006. (16 Citations) Supplementary file
  18. 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. (68 Citations)
  19. J. Ruan and W. Zhang, CAGER: Classification Analysis for Gene Expression Regulation, BMC Bioinformatics, 6:114, 2005. (IF = 4.96) web server
  20. 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. (29 Citations) web server
  21. 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. (155 Citations) Download software

Peer-reviewed conference / workshop publications

  1. M. J. Jahid and J. Ruan, Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11), Dec 4-6 2011, San Antonio, TX
  2. J. Ruan, J. Perez#, B. Hernandez#, G. Sunter and V.M. Sponsel. Systematic construction and analysis of co-expression networks for identification of functional modules and cis-regulatory elements, 9th International Workshop on Data Mining in Bioinformatics (BIOKDD'10) , July 25-28 2010, Washington DC, USA, accepted as a full paper. Acceptance rate: 7/29=24%.
  3. C. Lei# and J. Ruan, Finding gapped motifs by a novel evolutionary algorithm, Proc. of the 8th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBio'10), Istanbul, Turkey, April 7-9 2010. Acceptance rate: 15/40=38%. Best paper award nominee.
  4. X. Zhou, J. Ruan, W. Zhang, Promoter prediction based on a multiple instance learning scheme , ACM Intern. Conf. on Bioinformatics and Computational Biology (ACM-BCB), Aug. 2-4, 2010, Niagara Falls, NY, USA, accepted as a full paper. Acceptance rate: 37/136=28%.
  5. 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%.
  6. A.K. Dean#, S.E. Harris and J. Ruan, A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes, AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 2009. acceptance rate 17/68 = 25%. (An extended version appared in BMC Bioinformatics, 10 (S9):S5, 2009.)
  7. 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 (BIBM'08 workshops), Philadelphia, PA, USA, Nov. 5-7, 2008. Acceptance rate: 12/24=50%. (An extended version appeared in International Journal of Computational Biology and Drug Design, 2(4):323 - 339, 2009.)
  8. 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%
  9. 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).
  10. J. Ruan and W. Zhang, Identification and evaluation of functional modules in gene co-expression networks, Proc. of RECOMB Satellite Conference on Systems Biology, San Diego, CA, Dec 2006. Acceptance rate: 40%.
  11. 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 Conference on Regulatory Genomics, San Diego, CA, Dec. 2005. Acceptance rate: 50%. (An extended version appared in PLoS Computational Biology, 3(3):e37, 2007.)

 

©2008 Jianhua Ruan