Junbai Wang

Summary

Affiliation: Institute for Cancer Research
Country: Norway

Publications

  1. pmc Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
    Junbai Wang
    Division of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 11:36. 2010
  2. pmc Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
    Junbai Wang
    Department of Pathology, Oslo University Hospital Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
    BMC Genomics 14:70. 2013
  3. pmc The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 11:412. 2010
  4. pmc BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
    Junbai Wang
    Division of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 10:345. 2009
  5. ncbi request reprint Computational biology of genome expression and regulation--a review of microarray bioinformatics
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Medical Faculty, University of Oslo, Oslo, Norway
    J Environ Pathol Toxicol Oncol 27:157-79. 2008
  6. pmc Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
    BMC Genomics 12:172. 2011
  7. doi request reprint Effective non-linear methods for inferring genetic regulation from time-series microarray gene expression data
    Junbai Wang
    Department of Pathology, Oslo University Hospital, Radium Hospital, Montebello, Oslo, Norway
    Methods Mol Biol 802:235-46. 2012
  8. pmc Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
    Junbai Wang
    Department of Tumor Biology, The Norwegian Radium Hospital, N0310 Oslo, Norway
    BMC Bioinformatics 4:60. 2003
  9. ncbi request reprint Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas
    Leonardo A Meza-Zepeda
    Department of Tumor Biology, Rikshospitalet Radiumhospitalet Medical Center, Oslo, Norway
    Cancer Res 66:8984-93. 2006
  10. pmc M-CGH: analysing microarray-based CGH experiments
    Junbai Wang
    Department of Tumor Biology, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    BMC Bioinformatics 5:74. 2004

Collaborators

Detail Information

Publications19

  1. pmc Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
    Junbai Wang
    Division of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 11:36. 2010
    ..Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets...
  2. pmc Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
    Junbai Wang
    Department of Pathology, Oslo University Hospital Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
    BMC Genomics 14:70. 2013
    ..It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in response to stimulation of environmental chemicals or hormones...
  3. pmc The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 11:412. 2010
    ..In addition, we divided hyperparameter (regularization constants alpha of the model) into multiple distinct classes based on either the structure of the neural networks or the property of the weights...
  4. pmc BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
    Junbai Wang
    Division of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway
    BMC Bioinformatics 10:345. 2009
    ..The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential...
  5. ncbi request reprint Computational biology of genome expression and regulation--a review of microarray bioinformatics
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Medical Faculty, University of Oslo, Oslo, Norway
    J Environ Pathol Toxicol Oncol 27:157-79. 2008
    ..This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields...
  6. pmc Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
    Junbai Wang
    Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
    BMC Genomics 12:172. 2011
    ..Here this issue was investigated by using publicly available histone modification data in yeast...
  7. doi request reprint Effective non-linear methods for inferring genetic regulation from time-series microarray gene expression data
    Junbai Wang
    Department of Pathology, Oslo University Hospital, Radium Hospital, Montebello, Oslo, Norway
    Methods Mol Biol 802:235-46. 2012
    ..Our quantitative model can not only be used to infer the regulatory relationship between TF and its downstream genes but also be applied to estimate the protein activities of TF from the expression levels of its target genes...
  8. pmc Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
    Junbai Wang
    Department of Tumor Biology, The Norwegian Radium Hospital, N0310 Oslo, Norway
    BMC Bioinformatics 4:60. 2003
    ..Then, the prediction of marker genes is accomplished by either manual feature selection (visualizing the weighted/mean SOM component plane) or automatic feature selection (by pair-wise Fisher's linear discriminant)...
  9. ncbi request reprint Array comparative genomic hybridization reveals distinct DNA copy number differences between gastrointestinal stromal tumors and leiomyosarcomas
    Leonardo A Meza-Zepeda
    Department of Tumor Biology, Rikshospitalet Radiumhospitalet Medical Center, Oslo, Norway
    Cancer Res 66:8984-93. 2006
    ..Our results show the potential of using array comparative genomic hybridization to classify histologically similar tumors such as GISTs and leiomyosarcomas...
  10. pmc M-CGH: analysing microarray-based CGH experiments
    Junbai Wang
    Department of Tumor Biology, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    BMC Bioinformatics 5:74. 2004
    ..Dedicated tools are needed to analyse the results of such experiments, which include appropriate visualisation, and to take into consideration the physical relation in the genome between the probes on the array...
  11. ncbi request reprint MGraph: graphical models for microarray data analysis
    Junbai Wang
    Tumor Biology Department, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
    Bioinformatics 19:2210-1. 2003
    ..This application may provide a valuable aid in the prediction of genetic regulatory networks, as well as in investigations of various experimental conditions that affect global gene expression profiles...
  12. doi request reprint Interleukin-33 drives a proinflammatory endothelial activation that selectively targets nonquiescent cells
    Jürgen Pollheimer
    LIIPAT, Institute of Pathology, University of Oslo, Oslo, Norway
    Arterioscler Thromb Vasc Biol 33:e47-55. 2013
    ..Interleukin (IL)-33 is a nuclear protein that is released from stressed or damaged cells to act as an alarmin. We investigated the effects of IL-33 on endothelial cells, using the prototype IL-1 family member, IL-1β, as a reference...
  13. ncbi request reprint Plasminogen activator inhibitor-1 increases the expression of VEGF in human glioma cells
    Geir Olav Hjortland
    Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, 0310 Oslo, Norway
    Exp Cell Res 294:130-9. 2004
    ..The induction of VEGF expression and thus endothelial cell proliferation may represent an as yet undiscovered mechanism whereby PAI-1 contributes to tumor neoangiogenesis...
  14. pmc POLD2 and KSP37 (FGFBP2) correlate strongly with histology, stage and outcome in ovarian carcinomas
    Bente Vilming Elgaaen
    Department of Gynaecology, Oslo University Hospital, Oslo, Norway
    PLoS ONE 5:e13837. 2010
    ....
  15. pmc Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
    Junbai Wang
    Department of Tumor Biology, Norwegian Radium Hospital, N0310 Oslo, Norway
    BMC Bioinformatics 3:36. 2002
    ..Next, hierarchical clustering and K-means clustering is used to identify patterns of gene expression useful for classification of samples...
  16. ncbi request reprint A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle
    Junbai Wang
    Department of Biological Sciences, Columbia University, 1212, Amsterdam Avenue, MC 2442, New York, NY 10027, USA
    J Biomed Inform 40:707-25. 2007
    ..The new framework may easily be extended to study other higher eukaryotes...
  17. pmc Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
    Celine Moorman
    Department of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 103:12027-32. 2006
    ..Colocalization hotspots constitute a previously uncharacterized type of feature in the genome of Drosophila, and our results provide insights into the general targeting mechanisms of transcription regulators in a higher eukaryote...
  18. ncbi request reprint New probabilistic graphical models for genetic regulatory networks studies
    Junbai Wang
    Department of Biological Sciences, Columbia University, MC 2442, New York, NY 10027, USA
    J Biomed Inform 38:443-55. 2005
    ..Additionally, we found the same common limitations in the prediction of genetic regulatory networks when using only DNA microarray data...
  19. ncbi request reprint MArray: analysing single, replicated or reversed microarray experiments
    Junbai Wang
    Department of Tumour Biology, Norwegian Radium Hospital, N0310 Oslo, Norway
    Bioinformatics 18:1139-40. 2002
    ..It is entirely platform independent, and only requires Matlab installed...