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The Carolina Environmental Bioinformatics Research Center

Grant Number R832720


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  • Journal Article (10)
  • Presentation (30)
  • Proceedings (10)
  • Reference Type Reference Title Journal Author Citation Progress Report Year Document Sources
    Journal Article Genome-level analysis of genetic regulation of liver gene expression networks. HEPATOLOGY Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I. Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 2007;46(2):548-557. R832720 (2007)
  • Abstract from PubMed
  • Full-text: InterScience Full Text
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  • Journal Article Analysis of the transcriptome of Group A Streptococcus in mouse soft tissue infection. AMERICAN JOURNAL OF PATHOLOGY Graham MR, Virtaneva K, Porcella SF, Gardner DJ, Long RD, Welty DM, Barry WT, Johnson CA, Parkins LD, Wright FA, Musser JM Graham MR, Virtaneva K, Porcella SF, Gardner DJ, Long RD, Welty DM, Barry WT, Johnson CA, Parkins LD, Wright FA, Musser JM. Analysis of the transcriptome of Group A Streptococcus in mouse soft tissue infection. American Journal of Pathology 2006;169(3):927-942. R832720 (2007)
  • Abstract from PubMed
  • Full-text: American Journal of Pathology Full Text
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  • Journal Article Estimation of expression indexes for oligonucleotide arrays using the singular value decomposition. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION Hu J, Wright FA, Zou F Hu J, Wright FA, Zou F. Estimation of expression indexes for oligonucleotide arrays using the singular value decomposition. Journal of the American Statistical Association 2006;101(473):41-50. R832720 (2006)
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    Journal Article Large-scale gene expression differences across brain regions and inbred strains correlates with a behavioral phenotype. GENETICS Nadler JJ, Zou F, Huang H, Moy SS, Lauder J, Crawley JN, Threadgill DW, Wright FA, Magnuson TR Nadler JJ, Zou F, Huang H, Moy SS, Lauder J, Crawley JN, Threadgill DW, Wright FA, Magnuson TR. Large-scale gene expression differences across brain regions and inbred strains correlates with a behavioral phenotype. Genetics 2006;174(3):1229-1236. R832720 (2006)
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    Journal Article The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. MAMMALIAN GENOME Roberts A, Pardo-Manuel de Villena F, Wang W, McMillan L, Threadgill DW Roberts A, Pardo-Manuel de Villena F, Wang W, McMillan L, Threadgill DW. The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. Mammalian Genome 2007;18(6-7):473-481. R832720 (2007)
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  • Journal Article Predictive QSAR modeling workflow, model applicability domains, and virtual screening. CURRENT PHARMACEUTICAL DESIGN Tropsha A, Golbraikh A Tropsha A, Golbraikh A. Predictive QSAR modeling workflow, model applicability domains, and virtual screening. Current Pharmaceutical Design 2007;13(34):3494-3504. R832720 (2007)
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  • Journal Article Genomic profiling in nuclear receptor-mediated toxicity. TOXICOLOGIC PATHOLOGY Woods CG, Vanden Heuvel JP, Rusyn I Woods CG, Vanden Heuvel JP, Rusyn I. Genomic profiling in nuclear receptor-mediated toxicity. Toxicologic Pathology 2007;35(4):474-494. R832720 (2007)
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  • Other: Toxicologic Pathology PDF
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  • Journal Article Time course investigation of PPARα-and Kupffer cell-dependent effects of WY-14,643 in mouse liver using microarray gene expression. TOXICOLOGY AND APPLIED PHARMACOLOGY Woods CG, Kosyk O, Bradford BU, Ross PK, Burns AM, Cunningham ML, Qu P, Ibrahim JG, Rusyn I Woods CG, Kosyk O, Bradford BU, Ross PK, Burns AM, Cunningham ML, Qu P, Ibrahim JG, Rusyn I. Time course investigation of PPARα-and Kupffer cell-dependent effects of WY-14,643 in mouse liver using microarray gene expression. Toxicology and Applied Pharmacology 2007;225(3):267-277. R832720 (2007)
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  • Full-text: Science Direct Full Text
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  • Journal Article Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. BIOINFORMATICS Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, Pardo-Manuel de Villena F, Sullivan PF, Wilhelmsen KC, Zou F Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, Pardo-Manuel de Villena F, Sullivan PF, Wilhelmsen KC, Zou F. Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics 2007;23(19):2581-2588. R832720 (2007)
  • Abstract from PubMed
  • Full-text: Bioinformatics Full Text
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  • Journal Article The use of cell viability assay data improves the prediction accuracy of conventional quantitative structure activity relationship models of animal carcinogenicity. ENVIRONMENTAL HEALTH PERSPECTIVES Zhu H, Rusyn I, Richard A, Tropsha A Zhu H, Rusyn I, Richard A, Tropsha A. The use of cell viability assay data improves the prediction accuracy of conventional quantitative structure activity relationship models of animal carcinogenicity. Environmental Health Perspectives 2008 Jan 4 [Epub ahead of print] doi:10.1289/ehp.10573. R832720 (2007)
  • Abstract: Environmental Health Perspectives Abstract
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  • Presentation Metabolomic analysis of urine and liver after chronic alcohol treatment in C57BL/6J mice. None Bradford BU, Han J, Kosyk O, Shymonyak S, Winnike J, Kono H, O’Connell T, Rusyn I Bradford BU, Han J, Kosyk O, Shymonyak S, Winnike J, Kono H, O’Connell T, Rusyn I. Metabolomic analysis of urine and liver after chronic alcohol treatment in C57BL/6J mice. Presented at the American Association for Studies of Liver Disease Annual Meeting, Boston, MA, 2007. R832720 (2007)
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    Presentation Approximate Bayesian approaches for quantitative trait loci estimation. None Chang Y-L, Zou F, Wright FA Chang Y-L, Zou F, Wright FA. Approximate Bayesian approaches for quantitative trait loci estimation. Presented at ENAR, Atlanta, GA, 2007 (contributed presentation). R832720 (2007)
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    Presentation Approximate Bayesian approaches for quantitative trait loci estimation. None Chang Y-L, Zou F, Wright FA Chang Y-L, Zou F, Wright FA. Approximate Bayesian approaches for quantitative trait loci estimation. Presented at the UNC Biostatistics Colloquium, Department of Biostatistics, UNC, Chapel Hill, NC, 2007. R832720 (2007)
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    Presentation Multi-strain study of trichoroethylene toxicity in mice. None DeSimone MC, Harbourt D, Boysen G, Collins L DeSimone MC, Harbourt D, Boysen G, Collins L, et al. Multi-strain study of trichoroethylene toxicity in mice. Presented at the Superfund Basic Research Program Annual Meeting: New Technologies to Assess Environmental Exposure, San Diego, CA, December 10-12, 2006. R832720 (2006)
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    Presentation Development of EPA’s ToxCast program for prioritizing the toxicity testing of environmental chemicals. None Dix D, Martin MT, Li Z, Judson R, Houck KA Dix D, Martin MT, Li Z, Judson R, Houck KA. Development of EPA’s ToxCast program for prioritizing the toxicity testing of environmental chemicals. Presented at the Annual Meeting of Society for Biomolecular Sciences, Montreal, Canada, 2007. R832720 (2007)
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    Presentation EPA’s ToxCast program for predicting hazard and prioritizing toxicity testing of environmental chemicals. None Dix D, Judson R, Kavlock R, Li Z, Martin M, Richard A, Setzer W, Houck K Dix D, Judson R, Kavlock R, Li Z, Martin M, Richard A, Setzer W, Houck K. EPA’s ToxCast program for predicting hazard and prioritizing toxicity testing of environmental chemicals. Presented at the International Science Forum on Computational Toxicology, Research Triangle Park, NC, 2007. R832720 (2007)
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    Presentation Examination of genetic networks that regulate gene expression in liver using complex trait analysis. None Gatti D, Maki A, Chesler EJ, Kirova R Gatti D, Maki A, Chesler EJ, Kirova R, et al. Examination of genetic networks that regulate gene expression in liver using complex trait analysis. To be presented at the 46th Society of Toxicology Annual Meeting, Charlotte, NC, March 25-29, 2007. R832720 (2006)
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    Presentation QSAR/QSTR analysis of imbalanced datasets using k-Nearest Neighbors approach. None Golbraikh A, Zhu H, Ye L, Wang-Bell M, Tang H, Tropsha A Golbraikh A, Zhu H, Ye L, Wang-Bell M, Tang H, Tropsha A. QSAR/QSTR analysis of imbalanced datasets using k-Nearest Neighbors approach. Presented at the Fourth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Moscow, Russia, 2007. R832720 (2007)
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    Presentation High-throughput metabolite profiling of serum from trichloroethylene-exposed mice by direct infusion FTICR-MS. None Han J, Harbourt D, Danell RM, Borchers CH Han J, Harbourt D, Danell RM, Borchers CH, et al. High-throughput metabolite profiling of serum from trichloroethylene-exposed mice by direct infusion FTICR-MS. Presented at the Superfund Basic Research Program Annual Meeting: New Technologies to Assess Environmental Exposure, San Diego, CA, December 10-12, 2006. R832720 (2006)
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    Presentation Toxicogenetic dimension in studies of the mechanisms of liver injury. None Hege A, Ross P, Su S, Stylianou I Hege A, Ross P, Su S, Stylianou I, et al. Toxicogenetic dimension in studies of the mechanisms of liver injury. Presented at the U.S. Environmental Protection Agency Science Forum, Washington, DC, May 16-18, 2006. R832720 (2006)
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    Presentation Cross-species association mapping identifies genetic risk factors for liver toxicity. None Hege A, Ross P, Balletta L, Bradford B Hege A, Ross P, Balletta L, Bradford B, et al. Cross-species association mapping identifies genetic risk factors for liver toxicity. To be presented at the 46th Society of Toxicology Annual Meeting, Charlotte, NC, March 25-29, 2007. R832720 (2006)
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    Presentation Phenotypic anchoring of gene expression data from acetaminophen hepatotoxicity studies in the mouse model of the human population reveals biomarkers of response. None Hege A, Ross PK, Threadgill DW, Rusyn I Hege A, Ross PK, Threadgill DW, Rusyn I. Phenotypic anchoring of gene expression data from acetaminophen hepatotoxicity studies in the mouse model of the human population reveals biomarkers of response. Presented at the Society of Toxicology Annual Meeting, Seattle, WA, 2008. R832720 (2007)
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    Presentation U.S. EPA’s ToxCast program for predicting hazard and prioritizing toxicity testing of environmental chemicals. None Kavlock RJ, Dix D, Judson R, Li Z, Martin M, Richard A, Setzer W, Houck K Kavlock RJ, Dix D, Judson R, Li Z, Martin M, Richard A, Setzer W, Houck K. U.S. EPA’s ToxCast program for predicting hazard and prioritizing toxicity testing of environmental chemicals. Presented at the 6th World Congress on Alternatives and Animal Use in the Life Sciences, Tokyo, 2007. R832720 (2007)
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    Presentation Analysis of trichloroethylene metabolism in a genetically diverse panel of mouse inbred strains. None Kim S-K, DeSimone MC, Harbourt D, Boysen G, Collins L, Waidyanatha S, Bradford BU, Threadgill DW, Rusyn I Kim S-K, DeSimone MC, Harbourt D, Boysen G, Collins L, Waidyanatha S, Bradford BU, Threadgill DW, Rusyn I. Analysis of trichloroethylene metabolism in a genetically diverse panel of mouse inbred strains. Presented at the Society of Toxicology Annual Meeting, Seattle, WA, 2008. R832720 (2007)
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    Presentation Using aspects to create interconnected analysis tool networks. None Lee K, Stotts D Lee K, Stotts D. Using aspects to create interconnected analysis tool networks. To be presented at the International Symposium on Bioinformatics Research and Applications, Athens, GA, May 6-8, 2008 (submitted). R832720 (2007)
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    Presentation Visualization of features in curve estimates and application to genetic loci mapping. None Lee MH, Rusyn I, Threadgill DW, Marron JS Lee MH, Rusyn I, Threadgill DW, Marron JS. Visualization of features in curve estimates and application to genetic loci mapping. Presented at the Joint Statistical Meeting of the American Statistical Association, Seattle, WA, August 6-10, 2006. R832720 (2006)
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    Presentation Age-dependent heterogeneity of gene expression in Fisher 344 rat retina. None Li Z, Wright FA, Royland JE Li Z, Wright FA, Royland JE. Age-dependent heterogeneity of gene expression in Fisher 344 rat retina. Presented at the 46th Annual Meeting of the Society of Toxicology, Charlotte, NC, 2007. R832720 (2007)
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    Presentation Discovering relevant pathways in microarray experiments-a tutorial on honest testing methods. None Li Z, Wright FA Li Z, Wright FA. Discovering relevant pathways in microarray experiments-a tutorial on honest testing methods. Presented at the EPA Info on Informatics Series, EPA RTP Facility, 2007. R832720 (2007)
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    Presentation Significance analysis of variation change in gene expression studies. None Li Z, Wright FA, Royland JE Li Z, Wright FA, Royland JE. Significance analysis of variation change in gene expression studies. Presented at the 15th Annual International Conference on Intelligent Systems for Molecular Biology and 6th Annual European Conference on Computational Biology, Vienna, Austria, 2007. R832720 (2007)
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    Presentation Chemical toxicity prediction for ToxCast Phase I. None Li Z, Wright FA, Elloumi F Li Z, Wright FA, Elloumi F. Chemical toxicity prediction for ToxCast Phase I. To be presented at the 47th Annual Meeting of the Society of Toxicology, Seattle, WA, 2008 (accepted). R832720 (2007)
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    Presentation A fast Bayesian method for eQTL linkage analysis in experimental crosses. None Liu J, Chang Y-L, Zou F, Wright FA Liu J, Chang Y-L, Zou F, Wright FA. A fast Bayesian method for eQTL linkage analysis in experimental crosses. Presented at JSM, Salt Lake City, UT, 2007. R832720 (2007)
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    Presentation Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. None Tropsha A Tropsha A. Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. Presented at the Fourth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Moscow, Russia, 2007. R832720 (2007)
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    Presentation Toxico-cheminformatics and QSPR modeling of the carcinogenic potency database. None Wang K, Richard A, Rusyn I, Tropsha A Wang K, Richard A, Rusyn I, Tropsha A. Toxico-cheminformatics and QSPR modeling of the carcinogenic potency database. Presented at the 46th Society of Toxicity Annual Meeting, Charlotte, NC, March 25-29, 2007. R832720 (2006)
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    Presentation Pharmaco-metabolomics and the prediction of hepatotoxicity. None Winnike JH, Li Z, Wright FA, Macdonald JM, O’Connell TM, Watkins PB Winnike JH, Li Z, Wright FA, Macdonald JM, O’Connell TM, Watkins PB. Pharmaco-metabolomics and the prediction of hepatotoxicity. Presented to the Research Triangle Park Drug Metabolism Discussion Group, Research Triangle Park, NC, 2007. R832720 (2007)
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    Presentation Hypothesis tests of functional categories in microarray data–a new approach. None Wright FA, Nobel AB, Barry WT Wright FA, Nobel AB, Barry WT. Hypothesis tests of functional categories in microarray data–a new approach. Presented at the UIUC Bioinformatics Seminar Series, Urbana-Champaign, IL, 2007. R832720 (2007)
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    Presentation Enhanced kNN-QSAR modeling of aquatic toxicity of diverse organic compounds tested by fathead minnow. None Ye L, Zhu H, Golbraikh A, Tropsha A Ye L, Zhu H, Golbraikh A, Tropsha A. Enhanced kNN-QSAR modeling of aquatic toxicity of diverse organic compounds tested by fathead minnow. Presented at the Microsoft eScience Workshop, Chapel Hill, NC, 2007. R832720 (2007)
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    Presentation Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. None Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV. Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. Presented at the Microsoft eScience Workshop, Chapel Hill, NC, 2007. R832720 (2007)
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    Presentation Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. None Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV. Combinational QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. Presented at the US EPA International Science Forum on Computational Toxicology, Research Triangle Park, NC, 2007. R832720 (2007)
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    Presentation The utilization of NTP-HTS data in predictive ADME/tox modeling. None Zhu H, Wang K, Rusyn I, Richard A, Tropsha A Zhu H, Wang K, Rusyn I, Richard A, Tropsha A. The utilization of NTP-HTS data in predictive ADME/tox modeling. To be presented at the 46th Society of Toxicity Annual Meeting, Charlotte, NC, March 25-29, 2007. R832720 (2006)
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    Presentation The utilization of NTP-HTS data in predictive ADME/tox modeling. None Zhu H, Rusyn I, Richard A, Tropsha A Zhu H, Rusyn I, Richard A, Tropsha A. The utilization of NTP-HTS data in predictive ADME/tox modeling. Presented at the US EPA International Science Forum on Computational Toxicology, Research Triangle Park, NC, 2007. R832720 (2007)
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    Proceedings Clustering pair-wise dissimilarity data into partially ordered sets. None Liu J, Zhang Q, Wang W, McMillan L, Prins J Liu J, Zhang Q, Wang W, McMillan L, Prins J. Clustering pair-wise dissimilarity data into partially ordered sets. In: Proceedings of the 12th Association for Computer Machinery Special Interest Group on Knowledge Discovery and Data Mining, International Conference on Knowledge Discovery and Data Mining, Philadelphia, PA, August 20-23, 2006:637-642. R832720 (2006)
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    Proceedings Mining approximate frequent itemset in the presence of noise: algorithm and analysis. None Liu J, Paulsen S, Xu X, Wang W Liu J, Paulsen S, Xu X, Wang W, et al. Mining approximate frequent itemset in the presence of noise: algorithm and analysis. In: Proceedings of the Sixth Society for Industrial and Applied Mathematics Conference on Data Mining, Bethesda, MD, April 20-22, 2006:405-416. R832720 (2006)
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    Proceedings PoClustering: lossless clustering of dissimilarity data. None Liu J, Zhang Q, Wang W, McMillan L, Prins J Liu J, Zhang Q, Wang W, McMillan L, Prins J. PoClustering: lossless clustering of dissimilarity data. In: Proceedings of the 2007 SIAM International Conference on Data Mining, Radisson University Hotel, Minneapolis, MN, April 26-28, 2007. R832720 (2007)
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    Proceedings Sample selection for maximal diversity. None Pan F, Roberts A, McMillan L, Pardo-Manuel de Villena F, Threadgill D, Wang W Pan F, Roberts A, McMillan L, Pardo-Manuel de Villena F, Threadgill D, Wang W. Sample selection for maximal diversity. In: Proceedings of the IEEE International Conference on Data Mining, Ohama, NE, October 28-31, 2007, pp. 262-271. R832720 (2007)
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    Proceedings Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. None Roberts A, McMillan L, Wang W, Parker J, Rusyn I, Threadgill D Roberts A, McMillan L, Wang W, Parker J, Rusyn I, Threadgill D. Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. In: ISMB/ECCB 2007 Conference Proceedings 21-25 July 2007, Vienna, Italy. Bioinformatics 2007;23(13):i401-i407. R832720 (2007)
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    Proceedings CARE: finding local linear correlations in high dimensional data. None Wang W, Zhang X, Pan F Wang W, Zhang X, Pan F. CARE: finding local linear correlations in high dimensional data. To appear in Proceedings of the 24th International Conference on Data Engineering, Cancun, Mexico, April 7-12, 2008. R832720 (2007)
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    Proceedings Mining approximate order preserving clusters in the presence of noise. None Zhang M, Wang W, Liu J Zhang M, Wang W, Liu J. Mining approximate order preserving clusters in the presence of noise. To appear in Proceedings of the 24th International Conference on Data Engineering, Cancun, Mexico, April 7-12, 2008. R832720 (2007)
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    Proceedings Mining coherent patterns from heterogeneous microarray data. None Zhang X, Wang W Zhang X, Wang W. Mining coherent patterns from heterogeneous microarray data. In: Proceedings of the 15th Association for Computer Machinery Conference on Information and Knowledge Management, Arlington, VA, November 6-11, 2006. R832720 (2006)
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    Proceedings On demand phenotype ranking through subspace clustering. None Zhang X, Wang W, Huan J Zhang X, Wang W, Huan J. On demand phenotype ranking through subspace clustering. In: Proceedings of the 2007 SIAM International Conference on Data Mining, Radisson University Hotel, Minneapolis, MN, April 26-28, 2007. R832720 (2007)
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    Proceedings An efficient algorithm for mining coherent patterns from heterogeneous microarrays. None Zhang X, Wang W Zhang X, Wang W. An efficient algorithm for mining coherent patterns from heterogeneous microarrays. In: Proceedings of the 19th International Conference on Statistical and Scientific Database Management (SSDBM) 2007, Banff, Canada, July 9-11, 2007. R832720 (2007)
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    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.


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