Research Topics
Species | Jae LeeSummaryAffiliation: University of Virginia Country: USA Publications
Research Grants
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Detail Information
Publications
A strategy for predicting the chemosensitivity of human cancers and its application to drug discoveryJae K Lee
Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
Proc Natl Acad Sci U S A 104:13086-91. 2007..Furthermore, we used COXEN for in silico screening of 45,545 compounds and identify an agent with activity against human bladder cancer...- Enhanced peptide quantification using spectral count clustering and cluster abundanceSeungmook Lee
Department of Statistics, Seoul National University, Korea
BMC Bioinformatics 12:423. 2011.... - Response projected clustering for direct association with physiological and clinical response dataSung Gon Yi
Department of Statistics, Seoul National University, Silim Dong, Kwanak gu, Seoul, 151 747, Korea
BMC Bioinformatics 9:76. 2008.... - Boolean networks using the chi-square test for inferring large-scale gene regulatory networksHaseong Kim
Interdisciplinary Program in Bioinformatics, Seoul National University, South Korea
BMC Bioinformatics 8:37. 2007..We propose a variable selection method that are not only reduces BN computation times significantly but also obtains optimal network constructions by using chi-square statistics for testing the independence in contingency tables... - Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray dataNitin Jain
Division of Biostatistics and Epidemiology, Department of Health Evaluation Sciences, University of Virginia School of Medicine, Hospital West Complex, Charlottesville, VA 22908 0717, USA
BMC Bioinformatics 6:187. 2005..Several statistical approaches have been used to estimate and control FDR, but these may not provide reliable FDR estimation when applied to microarray data sets with a small number of replicates... - Data mining in genomicsJae K Lee
Division of Biostatistics and Epidemiology, Department of Public Health Sciences, Box 800717, University of Virginia, Charlottesville, VA 22908, USA
Clin Lab Med 28:145-66, viii. 2008..The last section briefly summarizes various genomic data mining approaches in biomedical pathway analysis and patient outcome or chemotherapeutic response prediction... - Performance of Markov chain-Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of lociJ K Lee
Department of Health Evaluation Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
Am J Hum Genet 67:1232-50. 2000..Our MCMC algorithm was shown to be significantly more efficient than LOKI (Heath 1997) in our simulation study using nuclear-family data... - GeneX Va: VBC open source microarray database and analysis softwareJae K Lee
Department of Health Evaluation Sciences, Hospital West Complex, Room 3181, University of Virginia School of Medicine, P O Box 800717, Charlottesville, VA 22908 0717, USA
Biotechniques 36:634-8, 640, 642. 2004..The VBC GeneX Va sites, which include documentation, are at http://genes.med.virginia.edu/ of the University of Virginia and at http://genex.csbc.vcu.edu/ of the Virginia Commonwealth University... - Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cellsJae K Lee
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 8322, USA
Genome Biol 4:R82. 2003..Global concordance is parameterized by a 'correlation of correlations' coefficient... - Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray studyUma T Shankavaram
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute NIH, Bethesda, MD 20892, USA
Mol Cancer Ther 6:820-32. 2007..71). Because the transcript-based technologies are more mature and are currently able to assess larger numbers of genes at one time, they continue to be useful, even when the ultimate aim is information about proteins... - Bayesian hierarchical error model for analysis of gene expression dataHyungJun Cho
Department of Health Evaluation Sciences, University of Virginia School of Medicine, Hospital West Complex, Charlottesville, VA 22908 0717, USA
Bioinformatics 20:2016-25. 2004.... - Developing optimal prediction models for cancer classification using gene expression dataMat Soukup
Department of Statistics, University of Virginia, Halsey Hall, Charlottesville, VA 22904 4135, USA
J Bioinform Comput Biol 1:681-94. 2004..The methodology is implemented and developed by the procedures in R and Splus. The source code can be obtained at http://hesweb1.med.virginia.edu/bioinformatics... - IL-2-controlled expression of multiple T cell trafficking genes and Th2 cytokines in the regulatory T cell-deficient scurfy mice: implication to multiorgan inflammation and control of skin and lung inflammationRahul Sharma
Department of Medicine, Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, VA 22908, USA
J Immunol 186:1268-78. 2011..Thus, IL-2 is potentially a master regulator for multiorgan inflammation and an underlying etiological factor for various diseases associated with skin and lung inflammation... - Gene expression profile of mouse myocardium with transgenic overexpression of A1 adenosine receptorsAmy R Lankford
Department of Pediatrics and Cardiovascular Research Center, University of Virginia Health System, Charlottesville Virginia 22908, USA
Physiol Genomics 11:81-9. 2002..These data illustrate genes with chronically altered patterns of expression in A(1) transgenic mouse myocardium that may be related to adenosine receptor overexpression-mediated cardioprotection... - Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarraysNitin Jain
Hospital West Complex, Rm 3181, P O Box 800717, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
Bioinformatics 19:1945-51. 2003.... - Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agentsSteven C Smith
Department of Urology, University of Virginia, Charlottesville, VA, USA
Neoplasia 13:72-80. 2011..Coupling COXEN and yeast chemigenomics provides rational combinations with C1311 and tumor genomic signatures that can be used to select bladder cancer patients for clinical trials with this agent... - The COXEN principle: translating signatures of in vitro chemosensitivity into tools for clinical outcome prediction and drug discovery in cancerSteven C Smith
Department of Molecular Physiology, University of Virginia, Charlottesville, Virginia 22908, USA
Cancer Res 70:1753-8. 2010.... - The bioinformatics of microarray gene expression profilingJohn N Weinstein
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, USA
Cytometry 47:46-9. 2002 - Concerted transcriptional regulation by BRCA1 and COBRA1 in breast cancer cellsSarah E Aiyar
1 Department of Biochemistry, Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
Int J Biol Sci 3:486-92. 2007..The data shown herein support the notion that COBRA1 and BRCA1 may engage in common gene regulatory pathways to suppress breast cancer progression... - Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profilingSatoshi Nishizuka
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, NIH, Bethesda, Maryland 20814, USA
Cancer Res 63:5243-50. 2003..The multistep process introduced here has the potential to produce additional markers for cancer diagnosis, prognosis, and therapy... - Concordant gene expression signatures predict clinical outcomes of cancer patients undergoing systemic therapyPaul D Williams
Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22908, USA
Cancer Res 69:8302-9. 2009..Use of such in vitro-based GEMs may provide a robust and generalizable approach to personalized cancer therapy... - Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replicationYoungchul Kim
Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
Bioinformatics 25:2486-91. 2009..We also showed the superior performance of DES compared with other commonly used methods for detecting actual protein binding sites... - Molecular credentialing of rodent bladder carcinogenesis modelsPaul D Williams
Department of Public Health Sciences, Division of Biostatistics, University of Virginia School of Medicine, Charlottesville, VA 22908 0717, USA
Neoplasia 10:838-46. 2008..Finally, we provide a list of genes that are likely candidates for driving this disease process by virtue of their concordant regulation in tumors of all three species... - Comparison of global versus epidermal growth factor receptor pathway profiling for prediction of lapatinib sensitivity in bladder cancerDmytro M Havaleshko
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
Neoplasia 11:1185-93. 2009..These results have significant implications for the use of such tools in personalizing the approach to cancers treated with EGFR-directed targeted therapies... - Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancerJae K Lee
Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
Clin Cancer Res 16:711-8. 2010..Our goal was to compare the performance of four conceptually different predictors in an independent cohort of patients... - Multi-gene expression-based statistical approaches to predicting patients' clinical outcomes and responsesFeng Cheng
Department of Biophysics, University of Virginia, Charlottesville, VA, USA
Methods Mol Biol 620:471-84. 2010.... - Utilizing the molecular gateway: the path to personalized cancer managementJonathan B Overdevest
Departments of Molecular Physiology and Biological Physics and Public Health Sciences, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA
Clin Chem 55:684-97. 2009.... - Induction of dendritic cell-like phenotype in macrophages during foam cell formationHyung Jun Cho
Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22908, USA
Physiol Genomics 29:149-60. 2007..Our findings suggest that LDL and oxLDL, but not mmLDL, induce a dendritic cell-like phenotype in macrophages, suggesting that these cells may be able to present antigens and support an immune response... - Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarraysSatoshi Nishizuka
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 100:14229-34. 2003.... - Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arraysTaesung Park
Department of Statistics, Seoul National University, Korea
Nucleic Acids Res 35:e69. 2007..Thus, our improved analysis approaches specifically designed for high-density tiling array data enabled us to reliably and sensitively identify many novel temporal replication patterns on human chromosomes... - Robust classification modeling on microarray data using misclassification penalized posteriorMat Soukup
Division of Biometrics III, Food and Drug Administration 9201 Corporate Blvd, Rm. N-250, Rockville, MD 20850, USA
Bioinformatics 21:i423-30. 2005..AVAILABILITY: Our MiPP software program is available at the Bioconductor website (http://www.bioconductor.org)... - Diagnostic plots for detecting outlying slides in a cDNA microarray experimentTaesung Park
Department of Statistics, Seoul National University, Korea
Biotechniques 38:463-71. 2005..A 3840-gene microarray experiment for neuronal differentiation of cortical stem cells and a 2076-gene microarray experiment for anticancer compound time-course expression of the NCI-60 cancer cell lines... - Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometryHyungJun Cho
Department of Statistics, Korea University, Seoul, Korea
Proteomics 7:3681-92. 2007.... - Genetic mouse models for studying inhibitors of spinal axon regenerationBinhai Zheng
Department of Neurosciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0691, USA
Trends Neurosci 29:640-6. 2006.... - Stable in vivo imaging of densely populated glia, axons and blood vessels in the mouse spinal cord using two-photon microscopyDimitrios Davalos
Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
J Neurosci Methods 169:1-7. 2008..This simplified technique can greatly expand the application of in vivo imaging to study spinal cord injury, regeneration, physiology and disease...
Research Grants
- Genome Integrative Pathway Modeling of Diabetic AtherosclerosisJae K Lee; Fiscal Year: 2010..Our GIPaM technology will also greatly enhance pathway discovery/modeling capability in other fields of the biomedical science. ..