Jianhua Ruan

Summary

Affiliation: University of Texas at San Antonio
Country: USA

Publications

  1. pmc A Fully Automated Method for Discovering Community Structures in High Dimensional Data
    Jianhua Ruan
    Department of Computer Science University of Texas at San Antonio One UTSA Circle, San Antonio, TX 78249
    Proc IEEE Int Conf Data Min . 2009
  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 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
  9. pmc A novel algorithm for network-based prediction of cancer recurrence
    Jianhua Ruan
    Department of Computer Science, University of Texas, San Antonio, TX, USA Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA Department of Electrical Engineering and Computer Science, McNeese State University, Lake Charles, LA, USA Electronic address
    Genomics . 2016
  10. 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

Collaborators

Detail Information

Publications25

  1. pmc A Fully Automated Method for Discovering Community Structures in High Dimensional Data
    Jianhua Ruan
    Department of Computer Science University of Texas at San Antonio One UTSA Circle, San Antonio, TX 78249
    Proc IEEE Int Conf Data Min . 2009
    ..Compared with several existing approaches, our method is not only fully automatic, but also has the best accuracy overall...
  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 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...
  9. pmc A novel algorithm for network-based prediction of cancer recurrence
    Jianhua Ruan
    Department of Computer Science, University of Texas, San Antonio, TX, USA Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA Department of Electrical Engineering and Computer Science, McNeese State University, Lake Charles, LA, USA Electronic address
    Genomics . 2016
    ....
  10. 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...
  11. 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...
  12. ncbi request reprint EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition
    Ya Ting Hsu
    Departments of Molecular Medicine Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
    Cancer Res 76:6171-6182. 2016
    ..Cancer Res; 76(21); 6171-82. ©2016 AACR...
  13. 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...
  14. 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...
  15. 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...
  16. pmc Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development
    Sreejith J Nair
    Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
    Nat Commun 7:10913. 2016
    ..Thus our genetic suppression analysis uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription programme during mammary gland development. ..
  17. 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...
  18. pmc The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia
    Dawn L Lovelace
    Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
    Development 143:1893-906. 2016
    ..Together, these data reveal the full profile of PLZF and SALL4 regulatory targets in undifferentiated spermatogonia, including SSCs, which will help elucidate mechanisms controlling the earliest cell fate decisions in spermatogenesis. ..
  19. pmc An Ensemble Approach for Drug Side Effect Prediction
    Md Jamiul Jahid
    Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas 78249
    Proceedings (IEEE Int Conf Bioinformatics Biomed) . 2013
    ..The method described in this article can be useful to predict side-effects in drug design in an early stage to reduce experimental cost and time...
  20. pmc Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer
    Ya Ting Hsu
    Authors Affiliations Department of Molecular Medicine, Institute of Biotechnology Department of Urology Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin Department of Obstetrics and Gynecology, Tri Service General Hospital Laboratory of Epigenetics, Cancer Stem Cells Department and Graduate Institute of Biochemistry, National Defense Medical Center, Taiwan, Republic of China Department of Obstetrics and Gynecology, Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri Department of Obstetrics and Gynecology, Ohio State University, Columbus, Ohio
    Clin Cancer Res 19:6272-85. 2013
    ..Our goal was to investigate whether altered DNA methylation signatures associated with oncogenic signaling delineate biomarkers predictive of endometrial cancer recurrence...
  21. pmc A personalized committee classification approach to improving prediction of breast cancer metastasis
    Md Jamiul Jahid
    Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA, Department of Molecular Medicine and Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
    Bioinformatics 30:1858-66. 2014
    ..Furthermore, attempting to develop subtype-specific models is hindered by the ambiguity and stereotypical definitions of subtypes...
  22. 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
    ..Identifying approximately repeated patterns, or motifs, in DNA sequences from a set of co-regulated genes is an important step towards deciphering the complex gene regulatory networks and understanding gene functions...
  23. 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...
  24. 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...
  25. 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...