Jianhua Ruan

Summary

Affiliation: University of Texas at San Antonio
Country: USA

Publications

  1. pmc A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis
    Md Jamiul Jahid
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Genomics 13:S8. 2012
  2. pmc Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases
    Monika Ray
    Washington University School of Engineering, Department of Computer Science and Engineering, 1 Brookings Drive, Saint Louis, Missouri 63130, USA
    Genome Biol 9:R148. 2008
  3. pmc Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
    BMC Bioinformatics 12:S2. 2011
  4. pmc A top-performing algorithm for the DREAM3 gene expression prediction challenge
    Jianhua Ruan
    Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas, United States of America
    PLoS ONE 5:e8944. 2010
  5. pmc A general co-expression network-based approach to gene expression analysis: comparison and applications
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Syst Biol 4:8. 2010
  6. pmc An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    BMC Genomics 10:S8. 2009
  7. pmc Building and analyzing protein interactome networks by cross-species comparisons
    Amy M Wiles
    Greehey Children s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
    BMC Syst Biol 4:36. 2010
  8. pmc A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks
    Zhen Gao
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Genomics 14:S4. 2013
  9. pmc A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
    Chengwei Lei
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    Bioinformatics 29:355-64. 2013
  10. pmc A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes
    Angela K Dean
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    BMC Bioinformatics 10:S5. 2009

Collaborators

Detail Information

Publications17

  1. pmc A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis
    Md Jamiul Jahid
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Genomics 13:S8. 2012
    ..Due to the unavailability of complete pathways, protein-protein interaction (PPI) network is becoming more popular to researcher and opens a new way to investigate the developmental process of breast cancer...
  2. pmc Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases
    Monika Ray
    Washington University School of Engineering, Department of Computer Science and Engineering, 1 Brookings Drive, Saint Louis, Missouri 63130, USA
    Genome Biol 9:R148. 2008
    ....
  3. pmc Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA
    BMC Bioinformatics 12:S2. 2011
    ..In this study, we propose a completely parameter-free and systematic method for constructing gene co-expression networks and predicting functional modules as well as cis-regulatory elements...
  4. pmc A top-performing algorithm for the DREAM3 gene expression prediction challenge
    Jianhua Ruan
    Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas, United States of America
    PLoS ONE 5:e8944. 2010
    ....
  5. pmc A general co-expression network-based approach to gene expression analysis: comparison and applications
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Syst Biol 4:8. 2010
    ..However, co-expression networks are often constructed by ad hoc methods, and network-based analyses have not been shown to outperform the conventional cluster analyses, partially due to the lack of an unbiased evaluation metric...
  6. pmc An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data
    Jianhua Ruan
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    BMC Genomics 10:S8. 2009
    ....
  7. pmc Building and analyzing protein interactome networks by cross-species comparisons
    Amy M Wiles
    Greehey Children s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
    BMC Syst Biol 4:36. 2010
    ..We also developed a confidence score for interactions based on available experimental evidence and conservation across species...
  8. pmc A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks
    Zhen Gao
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    BMC Genomics 14:S4. 2013
    ..Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previous approaches...
  9. pmc A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
    Chengwei Lei
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    Bioinformatics 29:355-64. 2013
    ..The key idea of our algorithm is that two proteins sharing some higher-order topological similarities, measured by a novel random walk-based procedure, are likely interacting with each other and may belong to the same protein complex...
  10. pmc A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes
    Angela K Dean
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    BMC Bioinformatics 10:S5. 2009
    ..Identifying the regulatory networks in osteocytes may lead to new therapies for osteoporosis and loss of bone...
  11. pmc A novel swarm intelligence algorithm for finding DNA motifs
    Chengwei Lei
    Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
    Int J Comput Biol Drug Des 2:323-39. 2009
    ..Applications to several sets of real promoter sequences also show that our approach is able to detect known transcription factor binding sites, and outperforms two of the most popular existing algorithms...
  12. pmc Cell density-dependent transcriptional activation of endocrine-related genes in human adipose tissue-derived stem cells
    Sagar Ghosh
    Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas, Health Science Center at San Antonio, San Antonio, TX 78245, USA
    Exp Cell Res 316:2087-98. 2010
    ..Thus, our work suggests that cell density is an important determinant of the endocrine potential of ASCs...
  13. doi request reprint Regulation of adipose oestrogen output by mechanical stress
    Sagar Ghosh
    Department of Molecular Medicine Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
    Nat Commun 4:1821. 2013
    ..This novel mechanotransduction pathway underlies communications between extracellular matrix, stromal hormone output, and cancer cell growth within the same microenvironment...
  14. pmc A particle swarm optimization-based algorithm for finding gapped motifs
    Chengwei Lei
    Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    BioData Min 3:9. 2010
    ..abstract:..
  15. pmc Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth
    Jianlong Sun
    Department of Molecular Medicine Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA
    J Biol Chem 286:36248-57. 2011
    ..Furthermore, Nelf-b deletion also resulted in increased apoptosis. Thus, the genetic and genomic studies provide new physiological and molecular insight into Nelf-mediated pol II pausing...
  16. pmc A network of conserved damage survival pathways revealed by a genomic RNAi screen
    Dashnamoorthy Ravi
    Greehey Children s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
    PLoS Genet 5:e1000527. 2009
    ..A biologically intuitive, highly interconnected MMS survival network was revealed after we incorporated pathway data in our interactome analysis...
  17. ncbi request reprint An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    Jianhua Ruan
    Department of Computer Science, Washington University in St Louis, St Louis, MO 63130, USA
    Bioinformatics 20:58-66. 2004
    ..Maximum weighted matching, an algorithm for pseudoknot prediction with comparative analysis, suffers from low-prediction accuracy in many cases...