Yang Dai

Summary

Affiliation: University of Illinois at Chicago
Country: USA

Publications

  1. pmc Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures
    Damian Roqueiro
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
    Proteome Sci 10:S15. 2012
  2. pmc MicroRNA-24 targeting RNA-binding protein DND1 in tongue squamous cell carcinoma
    Xiqiang Liu
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA
    FEBS Lett 584:4115-20. 2010
  3. ncbi Correlated Discretized Expression score: a method for identifying gene interaction networks from time course microarray expression data
    Peter Larsen
    Core Genomics Lab, Illinois Univ, Chicago, IL 60607 7058, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5842-5. 2006
  4. ncbi Sample scale-free gene regulatory network using gene ontology
    Guanrao Chen
    Department of Computer Science, University of Illinois at Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5523-6. 2006
  5. ncbi Building a meta-predictor for MHC class II-binding peptides
    Lei Huang
    Bioengineering Bioinformatics, University of Illinois at Chicago, USA
    Methods Mol Biol 409:355-64. 2007
  6. pmc Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
    Zhengdeng Lei
    Department of Bioengineering MC063, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
    BMC Bioinformatics 7:491. 2006
  7. pmc Identification and experimental validation of G protein alpha inhibiting activity polypeptide 2 (GNAI2) as a microRNA-138 target in tongue squamous cell carcinoma
    Lu Jiang
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 S Paulina Street, Room 530C, Chicago, IL 60612, USA
    Hum Genet 129:189-97. 2011
  8. pmc Polycomb group protein EZH2-mediated E-cadherin repression promotes metastasis of oral tongue squamous cell carcinoma
    Cheng Wang
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, USA
    Mol Carcinog 52:229-36. 2013
  9. pmc Molecular characterization of the microRNA-138-Fos-like antigen 1 (FOSL1) regulatory module in squamous cell carcinoma
    Yi Jin
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois, Chicago, Illinois 60612, USA
    J Biol Chem 286:40104-9. 2011
  10. pmc MicroRNA-99 family members suppress Homeobox A1 expression in epithelial cells
    Dan Chen
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, United States of America Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
    PLoS ONE 8:e80625. 2013

Research Grants

Collaborators

Detail Information

Publications39

  1. pmc Identifying transcription factors and microRNAs as key regulators of pathways using Bayesian inference on known pathway structures
    Damian Roqueiro
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, 60607, USA
    Proteome Sci 10:S15. 2012
    ..Although these methods provide a static snapshot of how genes may be regulated, they are not effective for the identification of condition-specific regulators...
  2. pmc MicroRNA-24 targeting RNA-binding protein DND1 in tongue squamous cell carcinoma
    Xiqiang Liu
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA
    FEBS Lett 584:4115-20. 2010
    ..Furthermore, the miR-24-mediated change in DND1 expression suppressed the expression of cyclin-dependent kinase inhibitor 1B (CDKN1B), and also led to enhanced proliferation and reduced apoptosis in TSCC cells...
  3. ncbi Correlated Discretized Expression score: a method for identifying gene interaction networks from time course microarray expression data
    Peter Larsen
    Core Genomics Lab, Illinois Univ, Chicago, IL 60607 7058, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5842-5. 2006
    ..The usefulness of this method is demonstrated using a set of hypothetical gene expression data and the analysis of S. cerevisiae cell cycle microarray data...
  4. ncbi Sample scale-free gene regulatory network using gene ontology
    Guanrao Chen
    Department of Computer Science, University of Illinois at Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5523-6. 2006
    ..In this paper, several network sampling strategies are explored on a set assembled from previous published gene interactions in yeast, expecting to reconstruct regulatory networks that are scale-free...
  5. ncbi Building a meta-predictor for MHC class II-binding peptides
    Lei Huang
    Bioengineering Bioinformatics, University of Illinois at Chicago, USA
    Methods Mol Biol 409:355-64. 2007
    ..The system is designed in such a way that results obtained from any number of individual predictors can be easily incorporated. This meta-predictor is expected to give users more confidence in the prediction...
  6. pmc Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
    Zhengdeng Lei
    Department of Bioengineering MC063, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
    BMC Bioinformatics 7:491. 2006
    ....
  7. pmc Identification and experimental validation of G protein alpha inhibiting activity polypeptide 2 (GNAI2) as a microRNA-138 target in tongue squamous cell carcinoma
    Lu Jiang
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 S Paulina Street, Room 530C, Chicago, IL 60612, USA
    Hum Genet 129:189-97. 2011
    ..In summary, we identified a number of high-confident miR-138 target genes, including proto-oncogene GNAI2, which may play an important role in TSCC initiation and progression...
  8. pmc Polycomb group protein EZH2-mediated E-cadherin repression promotes metastasis of oral tongue squamous cell carcinoma
    Cheng Wang
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, USA
    Mol Carcinog 52:229-36. 2013
    ..Taken together, these data suggest that EZH2 plays major roles in the progression of OTSCC, and may serve as a biomarker or therapeutic target for patients at risk of metastasis...
  9. pmc Molecular characterization of the microRNA-138-Fos-like antigen 1 (FOSL1) regulatory module in squamous cell carcinoma
    Yi Jin
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois, Chicago, Illinois 60612, USA
    J Biol Chem 286:40104-9. 2011
    ..Our results also provide evidence that microRNAs target both canonical and non-canonical targeting sites located in all areas of the mRNA molecule (e.g. 5'-UTR, coding sequences, and 3'-UTR)...
  10. pmc MicroRNA-99 family members suppress Homeobox A1 expression in epithelial cells
    Dan Chen
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, United States of America Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat Sen University, Guangzhou, China
    PLoS ONE 8:e80625. 2013
    ....
  11. ncbi A meta-predictor for MHC class II binding peptides based on Naïve Bayesian approach
    Lei Huang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5322-5. 2006
    ..The system is designed in such a way that results obtained from any number of individual predictors can be easily incorporated. This meta-predictor is expected to give users more confidence in the prediction...
  12. pmc MicroRNA-138 suppresses epithelial-mesenchymal transition in squamous cell carcinoma cell lines
    Xiqiang Liu
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA
    Biochem J 440:23-31. 2011
    ....
  13. pmc Rank-based edge reconstruction for scale-free genetic regulatory networks
    Guanrao Chen
    Department of Computer Science MC152, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
    BMC Bioinformatics 9:75. 2008
    ..Various approaches to this problem have been proposed, however, they do not take into account the topological characteristics of the targeted networks while reconstructing them...
  14. pmc A local genetic algorithm for the identification of condition-specific microRNA-gene modules
    Wenbo Mu
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    ScientificWorldJournal 2013:197406. 2013
    ..The identified regulatory modules may provide useful insights on the mechanisms of transcription factors and microRNAs...
  15. pmc An integrated bioinformatics approach identifies elevated cyclin E2 expression and E2F activity as distinct features of tamoxifen resistant breast tumors
    Lei Huang
    Department of Bioengineering, University of Illinois at Chicago, Illinois, United States of America
    PLoS ONE 6:e22274. 2011
    ....
  16. ncbi A probabilistic meta-predictor for the MHC class II binding peptides
    Oleksiy Karpenko
    Department of Bioengineering MC063, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
    Immunogenetics 60:25-36. 2008
    ..It is concluded that this integrative approach provides a clearly enhanced reliability of prediction. Moreover, this computational framework can be directly extended to MHC class I binding predictions...
  17. doi Prioritizing predicted cis-regulatory elements for co-expressed gene sets based on Lasso regression models
    Hong Hu
    Department of Bioengineering M C 063, University of Illinois at Chicago, 851 S Morgan St, SEO 218, Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 2011:6853-6. 2011
    ..We examine the ability of the Lasso model using time-course microarray data obtained from a comprehensive study of gene expression profiles in skin and mucosal wounds in mouse over all stages of wound healing...
  18. doi Analyzing mRNA and microRNA co-expression profiles to identify pathways and their potential regulators in ER+ and ER- breast tumors
    Lei Huang
    Department of Bioengineering, University of Illinois, Chicago MC063, Chicago, IL60607, USA
    Conf Proc IEEE Eng Med Biol Soc 2011:932-5. 2011
    ..We propose a method that combines these prediction data with co-expression analysis and a supervised learning algorithm to determine the main regulators in different pathways of ER+ and ER- tumors...
  19. doi Association of aldosterone concentration and mineralocorticoid receptor genotype with potassium response to spironolactone in patients with heart failure
    Larisa H Cavallari
    Department of Pharmacy Practice, University of Illinois at Chicago, 60612 7230, USA
    Pharmacotherapy 30:1-9. 2010
    ..To identify patient-specific factors associated with spironolactone-induced potassium level elevation in patients with heart failure...
  20. pmc MicroRNA-7 targets IGF1R (insulin-like growth factor 1 receptor) in tongue squamous cell carcinoma cells
    Lu Jiang
    Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, 60612, USA
    Biochem J 432:199-205. 2010
    ..Our results indicate that miR-7 plays an important role in TSCC and may serve as a novel therapeutic target for TSCC patients...
  21. doi Gene expression patterns in the human breast after pregnancy
    Szilard Asztalos
    Department of Biopharmaceutical Sciences, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
    Cancer Prev Res (Phila) 3:301-11. 2010
    ..These initial data, among the first on gene expression in samples of normal human breast, provide intriguing clues about the mechanisms behind the time-dependent effects of pregnancy on breast cancer risk...
  22. ncbi Direct prediction of T-cell epitopes using support vector machines with novel sequence encoding schemes
    Lei Huang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    J Bioinform Comput Biol 4:93-107. 2006
    ..A procedure of feature selection is also introduced to strengthen the prediction. The computational results demonstrate competitive performance over previous techniques...
  23. pmc MicroRNA-99 family targets AKT/mTOR signaling pathway in dermal wound healing
    Yi Jin
    Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 8:e64434. 2013
    ..In summary, we identified a panel of differentially expressed microRNAs which may play important roles in wound healing. We provide evidence that miR-99 family members contribute to wound healing by regulating the AKT/mTOR signaling...
  24. pmc Positive cross-talk between estrogen receptor and NF-kappaB in breast cancer
    Jonna Frasor
    Department of Physiology, University of Illinois at Chicago, Chicago, Illinois 60612, USA
    Cancer Res 69:8918-25. 2009
    ....
  25. pmc A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments
    Peter Larsen
    Core Genomics Laboratory at University of Illinois at Chicago, 845 West Taylor Street Chicago, IL 60607, USA
    BMC Bioinformatics 8:317. 2007
    ..We propose a novel method based on the statistical analysis of reported gene interactions in PubMed literature...
  26. pmc Genome-wide DNA methylation analysis predicts an epigenetic switch for GATA factor expression in endometriosis
    Matthew T Dyson
    Division of Reproductive Biology Research, Dept Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS Genet 10:e1004158. 2014
    ....
  27. pmc Genome-wide progesterone receptor binding: cell type-specific and shared mechanisms in T47D breast cancer cells and primary leiomyoma cells
    Ping Yin
    Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS ONE 7:e29021. 2012
    ..Here, we determined the interaction between common or cell-specific genome-wide binding sites of PR and mRNA expression in RU486-treated uterine leiomyoma and breast cancer cells...
  28. pmc Intrinsic differences between oral and skin keratinocytes
    ANNA TURABELIDZE
    Center for Wound Healing and Tissue Regeneration, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 9:e101480. 2014
    ..We hypothesized that oral and skin keratinocytes might have intrinsic differences at baseline as well as in the response to injury, and that such differences would be reflected in gene expression profiles. ..
  29. doi An evolutionary optimization strategy using graphics processing units to efficiently investigate gene-gene interactions in genetic association studies
    Joel B Fontanarosa
    Bioinformatics Program, Department of Bioengineering, The University of Illinois at Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 2011:5547-50. 2011
    ..The proposed GPU algorithm was shown to have improved efficiency and equivalent power relative to the CPU version...
  30. pmc Correlative Analysis of miRNA Expression and Oncotype Dx Recurrence Score in Estrogen Receptor Positive Breast Carcinomas
    Rajyasree Emmadi
    Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 10:e0145346. 2015
    ....
  31. pmc An SVM-based system for predicting protein subnuclear localizations
    Zhengdeng Lei
    Department of Bioengineering MC063, University of Illinois at Chicago, 851 South Morgan Street, Chicago IL 60607, USA
    BMC Bioinformatics 6:291. 2005
    ..In order to design a suitable predictive system, the extraction of subtle sequence signals that can discriminate among proteins with different subnuclear localizations is the key...
  32. ncbi Prediction of MHC class II binders using the ant colony search strategy
    Oleksiy Karpenko
    Department of Bioengineering MC063, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
    Artif Intell Med 35:147-56. 2005
    ..Predictions of the binding ability of antigen peptides to major histocompatibility complex (MHC) class II molecules are important in vaccine development. The variable length of each binding peptide complicates this prediction...
  33. ncbi Patterns and localization of gene expression during intramembranous bone regeneration in the rat femoral marrow ablation model
    Shinji Kuroda
    Department of Anatomy and Cell Biology, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
    Calcif Tissue Int 77:212-25. 2005
    ..Principal components analysis identified eight underlying factors that together explained over 80% of the variance in the data...
  34. pmc A prototype tobacco-associated oral squamous cell carcinoma classifier using RNA from brush cytology
    Antonia Kolokythas
    Department of Oral and Maxillofacial Surgery, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
    J Oral Pathol Med 42:663-9. 2013
    ..We sought to determine whether the identified mRNAs could be used as markers by a non-invasive detection system for OSCC using RNA from brush cytology...
  35. pmc Using LASSO regression to detect predictive aggregate effects in genetic studies
    Joel B Fontanarosa
    Bioinformatics Program, Department of Bioengineering MC 063, University of Illinois at Chicago, 851 S, Morgan Street, 218 SEO, Chicago, IL 60607 7052, USA
    BMC Proc 5:S69. 2011
    ..69-0.87 when both genotypic and phenotypic information are used. The ability of the LASSO method to find true causal markers is limited, but the method was able to discover several common variants (e.g., FLT1) under certain conditions...
  36. ncbi Effect of CYP3A5 polymorphism on tacrolimus metabolic clearance in vitro
    Yang Dai
    Department of Pharmaceutics, University of Washington, Seattle, 98195 7610, USA
    Drug Metab Dispos 34:836-47. 2006
    ..These data suggest that CYP3A5 contributes significantly to the metabolic clearance of tacrolimus in the liver and kidney...
  37. pmc Rifampin resistance, Beijing-W clade-single nucleotide polymorphism cluster group 2 phylogeny, and the Rv2629 191-C allele in Mycobacterium tuberculosis strains
    Soumitesh Chakravorty
    Division of Infectious Disease, Department of Medicine, and the Ruy V Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
    J Clin Microbiol 46:2555-60. 2008
    ..The allele appears to be an excellent marker for the Beijing-W clade/SCG-2 phylogenetic group...
  38. ncbi Local application of rhTGF-beta2 modulates dynamic gene expression in a rat implant model
    Aladino De Ranieri
    Department of Anatomy and Cell Biology, Rush Medical College, Rush University Medical Center, Chicago, IL 60612, USA
    Bone 36:931-40. 2005
    ..Thus, in addition to changes in individual transcription profiles, the regulatory connections between sets of co-expressed genes may also be affected by exogenously delivered anabolic agents during bone regeneration...
  39. ncbi [The advance of research on pathogenesis of acquired pure red cell aplastic anemia caused by cellular immune abnormalities]
    Yang Dai
    Department of Hematology, West China Hospital of Sichuan University, Chengdu 610041, China
    Zhongguo Shi Yan Xue Ye Xue Za Zhi 11:105-8. 2003
    ..This review will focus on the focus points: T lymphocytes abnormalities, change of T-cell subset phenotypes, abnormality of cellular clonality, and effects of related cytokines in PRCA...

Research Grants1

  1. Computational Prediction of MHC Class II Epitopes
    Yang Dai; Fiscal Year: 2007
    ..The computational prediction can provide a rapid method for the of pathogen molecules containing immunostimulatory sequences that can serve as targets for immune intervention or diagnostics. [unreadable] [unreadable] [unreadable]..