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Jianhua Ruan

TitleDr
Faculty RankAssociate Professor
InstitutionUniversity of Texas at San Antonio
DepartmentComputer Science
AddressOne UTSA Circle
San Antonio TX 78249
Phone2104586819
Fax2104584437
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    Collapse Overview 
    Collapse overview
    My research interests lie in the broad area of bioinformatics, computational systems biology, and data mining. More specifically, my current research is focused on the following three directions: (1) module discovery and analysis in complex networks, with applications in protein complex prediction and microarray data clustering; (2) modeling and analysis of transcriptional/post-transcriptional regulatory networks (e.g. DNA motif finding and ChIP-seq data analysis); and (3) network-based biomarker discovery and disease classification via integrated analysis of heterogonous functional genomics data such as gene expression, protein-protein interactions, and microRNA-mRNA interactions. My research has been sponsored by NIH, NSF, and the San Antonio Life Sciences Institute.

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Adnan N, Lei C, Ruan J. Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. BMC Bioinformatics. 2020 Sep 30; 21(Suppl 14):359. PMID: 32998692.
      Citations:    Fields:    Translation:Humans
    2. Guerrero J, Regedanz E, Lu L, Ruan J, Bisaro DM, Sunter G. Manipulation of the Plant Host by the Geminivirus AC2/C2 Protein, a Central Player in the Infection Cycle. Front Plant Sci. 2020; 11:591. PMID: 32508858.
      Citations:    
    3. Bi M, Zhang Z, Jiang YZ, Xue P, Wang H, Lai Z, Fu X, De Angelis C, Gong Y, Gao Z, Ruan J, Jin VX, Marangoni E, Montaudon E, Glass CK, Li W, Huang TH, Shao ZM, Schiff R, Chen L, Liu Z. Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. Nat Cell Biol. 2020 06; 22(6):701-715. PMID: 32424275.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    4. Adnan N, Liu Z, Huang THM, Ruan J. Comparative evaluation of network features for the prediction of breast cancer metastasis. BMC Med Genomics. 2020 04 03; 13(Suppl 5):40. PMID: 32241278.
      Citations: 1     Fields:    
    5. Zand M, Ruan J. Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification. Genes (Basel). 2020 03 31; 11(4). PMID: 32244427.
      Citations: 1     Fields:    
    6. Liu X, Xie L, Wu Z, Wang K, Zhao Z, Ruan J, Zhi D. The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinformatics. 2018 Dec 28; 19(Suppl 17):492. PMID: 30591012.
      Citations:    Fields:    Translation:HumansCells
    7. Mitsuya K, Parker AN, Liu L, Ruan J, Vissers MCM, Myatt L. Alterations in the placental methylome with maternal obesity and evidence for metabolic regulation. PLoS One. 2017; 12(10):e0186115. PMID: 29045485.
      Citations: 9     Fields:    Translation:HumansCells
    8. Zheng WJ, Ruan J, Xu H, Zhao Z, Liu Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst Biol. 2017 Oct 03; 11(Suppl 5):88. PMID: 28984194.
      Citations:    Fields:    
    9. Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Jim Zheng W, Ruan J. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics. 2017 Oct 03; 18(Suppl 6):703. PMID: 28984207.
      Citations:    Fields:    
    10. Gao Z, Liu L, Ruan J. Logo2PWM: a tool to convert sequence logo to position weight matrix. BMC Genomics. 2017 Oct 03; 18(Suppl 6):709. PMID: 28984206.
      Citations:    Fields:    Translation:Cells
    11. Gao Z, Ruan J. Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning. Bioinformatics. 2017 Jul 15; 33(14):2097-2105. PMID: 28334224.
      Citations: 2     Fields:    Translation:HumansCells
    12. Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH. EGFR-Dependent Regulated Intramembrane Proteolysis of EpCAM-Response. Cancer Res. 2017 04 01; 77(7):1777. PMID: 28330931.
      Citations:    Fields:    Translation:HumansCells
    13. Hsu YT, Osmulski P, Wang Y, Huang YW, Liu L, Ruan J, Jin VX, Kirma NB, Gaczynska ME, Huang TH. EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition. Cancer Res. 2016 11 01; 76(21):6171-6182. PMID: 27569206.
      Citations: 9     Fields:    Translation:HumansCells
    14. Zhao Z, Liu Y, Huang Y, Huang K, Ruan J. Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. BMC Syst Biol. 2016 08 26; 10 Suppl 3:61. PMID: 27587087.
      Citations:    Fields:    Translation:HumansAnimals
    15. Ruan J, Jahid MJ, Gu F, Lei C, Huang YW, Hsu YT, Mutch DG, Chen CL, Kirma NB, Huang TH. A novel algorithm for network-based prediction of cancer recurrence. Genomics. 2019 01; 111(1):17-23. PMID: 27453286.
      Citations: 2     Fields:    Translation:HumansCells
    16. Lovelace DL, Gao Z, Mutoji K, Song YC, Ruan J, Hermann BP. The regulatory repertoire of PLZF and SALL4 in undifferentiated spermatogonia. Development. 2016 06 01; 143(11):1893-906. PMID: 27068105.
      Citations: 14     Fields:    Translation:AnimalsCells
    17. Nair SJ, Zhang X, Chiang HC, Jahid MJ, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan JB, Parvin JD, Jin VX, Hu Y, Li R. Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nat Commun. 2016 Mar 04; 7:10913. PMID: 26941120.
      Citations: 6     Fields:    Translation:AnimalsCells
    18. Zhao Z, Jin VX, Huang Y, Guda C, Ruan J. Frontiers in Integrative Genomics and Translational Bioinformatics. Biomed Res Int. 2015; 2015:725491. PMID: 26605336.
      Citations: 1     Fields:    Translation:HumansAnimals
    19. Jahid MJ, Huang TH, Ruan J. A personalized committee classification approach to improving prediction of breast cancer metastasis. Bioinformatics. 2014 Jul 01; 30(13):1858-66. PMID: 24618465.
      Citations: 5     Fields:    Translation:Humans
    20. Hsu YT, Gu F, Huang YW, Liu J, Ruan J, Huang RL, Wang CM, Chen CL, Jadhav RR, Lai HC, Mutch DG, Goodfellow PJ, Thompson IM, Kirma NB, Huang TH. Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer. Clin Cancer Res. 2013 Nov 15; 19(22):6272-85. PMID: 24077349.
      Citations: 17     Fields:    Translation:HumansCells
    21. Gao Z, Zhao R, Ruan J. A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. BMC Genomics. 2013; 14 Suppl 1:S4. PMID: 23368633.
      Citations: 6     Fields:    Translation:AnimalsCells
    22. Liu L, Ruan J. Network-based Pathway Enrichment Analysis. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013; 218-221. PMID: 25327472.
      Citations:    
    23. Jahid MJ, Ruan J. An Ensemble Approach for Drug Side Effect Prediction. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2013; 440-445. PMID: 25327524.
      Citations:    
    24. Ghosh S, Ashcraft K, Jahid MJ, April C, Ghajar CM, Ruan J, Wang H, Foster M, Hughes DC, Ramirez AG, Huang T, Fan JB, Hu Y, Li R. Regulation of adipose oestrogen output by mechanical stress. Nat Commun. 2013; 4:1821. PMID: 23652009.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    25. Lei C, Ruan J. A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics. 2013 Feb 01; 29(3):355-64. PMID: 23235927.
      Citations: 19     Fields:    Translation:Humans
    26. Jahid MJ, Ruan J. A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. BMC Genomics. 2012; 13 Suppl 6:S8. PMID: 23134806.
      Citations: 13     Fields:    Translation:Humans
    27. Ruan J, Perez J, Hernandez B, Lei C, Sunter G, Sponsel VM. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. BMC Bioinformatics. 2011 Nov 24; 12 Suppl 12:S2. PMID: 22168340.
      Citations: 5     Fields:    Translation:AnimalsCells
    28. Uren PJ, Burns SC, Ruan J, Singh KK, Smith AD, Penalva LO. 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. J Biol Chem. 2011 Oct 28; 286(43):37063-6. PMID: 21890634.
      Citations: 37     Fields:    Translation:HumansCells
    29. Sun J, Pan H, Lei C, Yuan B, Nair SJ, April C, Parameswaran B, Klotzle B, Fan JB, Ruan J, Li R. Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth. J Biol Chem. 2011 Oct 21; 286(42):36248-57. PMID: 21865163.
      Citations: 14     Fields:    Translation:AnimalsCells
    30. Lei C, Ruan J. A particle swarm optimization-based algorithm for finding gapped motifs. BioData Min. 2010 Dec 13; 3:9. PMID: 21144057.
      Citations:    
    31. Ghosh S, Dean A, Walter M, Bao Y, Hu Y, Ruan J, Li R. Cell density-dependent transcriptional activation of endocrine-related genes in human adipose tissue-derived stem cells. Exp Cell Res. 2010 Aug 01; 316(13):2087-98. PMID: 20420826.
      Citations: 13     Fields:    Translation:HumansCells
    32. Wiles AM, Doderer M, Ruan J, Gu TT, Ravi D, Blackman B, Bishop AJ. Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol. 2010 Mar 30; 4:36. PMID: 20353594.
      Citations: 30     Fields:    Translation:HumansAnimals
    33. Ruan J. A top-performing algorithm for the DREAM3 gene expression prediction challenge. PLoS One. 2010 Feb 04; 5(2):e8944. PMID: 20140212.
      Citations: 5     Fields:    Translation:Animals
    34. Ruan J, Dean AK, Zhang W. A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol. 2010 Feb 02; 4:8. PMID: 20122284.
      Citations: 73     Fields:    Translation:Cells
    35. Dean AK, Harris SE, Kalajzic I, Ruan J. A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S5. PMID: 19761575.
      Citations: 4     Fields:    Translation:Cells
    36. Ruan J, Deng Y, Perkins EJ, Zhang W. An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S8. PMID: 19594885.
      Citations: 3     Fields:    Translation:AnimalsCells
    37. Ravi D, Wiles AM, Bhavani S, Ruan J, Leder P, Bishop AJ. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet. 2009 Jun; 5(6):e1000527. PMID: 19543366.
      Citations: 28     Fields:    Translation:AnimalsCells
    38. Lei C, Ruan J. A novel swarm intelligence algorithm for finding DNA motifs. Int J Comput Biol Drug Des. 2009; 2(4):323-39. PMID: 20090174.
      Citations: 2     Fields:    Translation:Cells
    39. Ruan J. A Fully Automated Method for Discovering Community Structures in High Dimensional Data. Proc IEEE Int Conf Data Min. 2009; 968-973. PMID: 25296858.
      Citations:    
    40. Ray M, Ruan J, Zhang W. Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases. Genome Biol. 2008 Oct 08; 9(10):R148. PMID: 18842138.
      Citations: 35     Fields:    Translation:Humans
    41. McDunn JE, Husain KD, Polpitiya AD, Burykin A, Ruan J, Li Q, Schierding W, Lin N, Dixon D, Zhang W, Coopersmith CM, Dunne WM, Colonna M, Ghosh BK, Cobb JP. Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram. PLoS One. 2008 Feb 13; 3(2):e1564. PMID: 18270561.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    42. Ruan J, Zhang W. Identifying network communities with a high resolution. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jan; 77(1 Pt 2):016104. PMID: 18351912.
      Citations: 44     Fields:    
    43. Patrick KL, Luz PM, Ruan JP, Shi H, Ullu E, Tschudi C. Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei. Mol Microbiol. 2008 Jan; 67(2):435-47. PMID: 18067542.
      Citations: 15     Fields:    Translation:AnimalsCells
    44. Ruan JP, Shen S, Ullu E, Tschudi C. Evidence for a capping enzyme with specificity for the trypanosome spliced leader RNA. Mol Biochem Parasitol. 2007 Dec; 156(2):246-54. PMID: 17949828.
      Citations: 13     Fields:    Translation:AnimalsCells
    45. Ruan JP, Ullu E, Tschudi C. Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol. 2007 Sep; 155(1):66-9. PMID: 17610965.
      Citations: 12     Fields:    Translation:AnimalsCells
    46. Zhou X, Ruan J, Wang G, Zhang W. Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol. 2007 Mar 09; 3(3):e37. PMID: 17352530.
      Citations: 116     Fields:    Translation:HumansAnimalsCells
    47. Ruan J, Zhang W. A bi-dimensional regression tree approach to the modeling of gene expression regulation. Bioinformatics. 2006 Feb 01; 22(3):332-40. PMID: 16303796.
      Citations: 8     Fields:    Translation:AnimalsCells
    48. Zhang W, Ruan J, Ho TH, You Y, Yu T, Quatrano RS. Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana. Bioinformatics. 2005 Jul 15; 21(14):3074-81. PMID: 15890746.
      Citations: 67     Fields:    Translation:AnimalsCells
    49. Ruan J, Zhang W. CAGER: classification analysis of gene expression regulation using multiple information sources. BMC Bioinformatics. 2005 May 12; 6:114. PMID: 15890068.
      Citations: 2     Fields:    Translation:AnimalsCells
    50. Ruan JP, Arhin GK, Ullu E, Tschudi C. Functional characterization of a Trypanosoma brucei TATA-binding protein-related factor points to a universal regulator of transcription in trypanosomes. Mol Cell Biol. 2004 Nov; 24(21):9610-8. PMID: 15485927.
      Citations: 27     Fields:    Translation:AnimalsCells
    51. Ruan J, Stormo GD, Zhang W. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W146-9. PMID: 15215368.
      Citations: 11     Fields:    Translation:Cells
    52. Ruan J, Stormo GD, Zhang W. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics. 2004 Jan 01; 20(1):58-66. PMID: 14693809.
      Citations: 60     Fields:    Translation:Cells
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