Grantee Research Project Results
Journal Publications Details for Grant Number R832720
Carolina Environmental Bioinformatics Center
RFA:
Computational Toxicology: Environmental Bioinformatics Research Center (2004)
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Reference Type | Citation | Progress Report Year | Document Sources |
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Journal Article | Borysov P, Hannig J, Marron JS, Muratov E, Fourches D, Tropsha A. Activity prediction and identification of mis-annotated chemical compounds using extreme descriptors. Journal of Chemometrics 2016;30(3):99-108. |
R832720 (2009) R833825 (Final) |
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Journal Article | Bradford BU, O'Connell TM, Han J, Kosyk O, Shymonyak S, Ross PK, Winnike J, Kono H, Rusyn I. Metabolomic profiling of a modified alcohol liquid diet model for liver injury in the mouse uncovers new markers of disease. Toxicology and Applied Pharmacology 2008;232(2):236-243. |
R832720 (2008) |
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Journal Article | Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. Journal of Statistical Planning and Inference 2008;138(2):387-404. |
R832720 (2006) R832720 (2008) |
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Journal Article | Fourches D, Barnes JC, Day NC, Bradley P, Reed JZ, Tropsha A. Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species. Chemical Research in Toxicology 2010;23(1):171-183. |
R832720 (2009) R833825 (Final) |
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Journal Article | Fourches D, Muratov E, Tropsha A. Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. Journal of Chemical Information and Modeling 2010;50(7):1189-1204. |
R832720 (2009) R833825 (Final) |
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Journal Article | Fourches D, Muratov E, Ding F, Dokholyan NV, Tropsha A. Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches. Journal of Chemical Information and Modeling 2013;53(8):1915-1922. |
R832720 (2009) R833825 (Final) |
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Journal Article | Gatti DM, Shabalin AA, Lam T-C, Wright FA, Rusyn I, Nobel AB. FastMap: fast eQTL mapping in homozygous populations. Bioinformatics 2009;25(4):482-489. |
R832720 (2008) R833825 (2008) R833825 (Final) |
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Journal Article | Gatti DM, Sypa M, Rusyn I, Wright FA, Barry WT. SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. Bioinformatics 2009;25(4):541-542. |
R832720 (2008) R833825 (Final) |
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Journal Article | Gatti DM, Harrill AH, Wright FA, Threadgill DW, Rusyn I. Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mammalian Genome 2009;20(7):437-446. |
R832720 (2009) R833825 (Final) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Gelfond JAL, Ibrahim JG, Zou F. Proximity model for expression quantitative trait loci (eQTL) detection. Biometrics 2007;63(4):1108-1116. |
R832720 (2006) R832720 (2008) |
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Journal Article | Ghosh A, Zou F, Wright FA. Estimating odds ratios in genome scans: an approximate conditional likelihood approach. The American Journal of Human Genetics 2008;82(5):1064-1074. |
R832720 (2008) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Gupta M, Ibrahim JG. Variable selection in regression mixture modeling for the discovery of gene regulatory networks. Journal of the American Statistical Association 2007;102(479):867-880. |
R832720 (2006) R832720 (2008) |
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Journal Article | Gupta M. Generalized hierarchical Markov models for the discovery of length-constrained sequence features from genome tiling arrays. Biometrics 2007;63(3):797-805. |
R832720 (2006) R832720 (2008) |
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Journal Article | Han J, Danell RM, Patel JR, Gumerov DR, Scarlett CO, Speir JP, Parker CE, Rusyn I, Zeisel S, Borchers CH. Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. Metabolomics 2008;4(2):128-140. |
R832720 (2008) |
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Journal Article | Harrill AH, Rusyn I. Systems biology and functional genomics approaches for the identification of cellular responses to drug toxicity. Expert Opinion on Drug Metabolism & Toxicology 2008;4(11):1379-1389. |
R832720 (2008) |
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Journal Article | Harrill AH, Ross PK, Gatti DM, Threadgill DW, Rusyn I. Population-based discovery of toxicogenomics biomarkers for hepatotoxicity using a laboratory strain diversity panel. Toxicological Sciences 2009;110(1):235-243. |
R832720 (2009) R833825 (2008) R833825 (Final) |
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Journal Article | Harrill AH, Watkins PB, Su S, Ross PK, Harbourt DE, Stylianou IM, Boorman GA, Russo MW, Sackler RS, Harris SC, Smith PC, Tennant R, Bogue M, Paigen K, Harris C, Contractor T, Wiltshire T, Rusyn I, Threadgill DW. Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans. Genome Research 2009;19(9):1507-1515. |
R832720 (2009) |
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Journal Article | Harrill JA ,Li Z, Wright FA, Radio NM, Mundy WR, Tornero-Velez R, Crofton KM. Transcriptional response of rat frontal cortex following acute in vivo exposure to the pyrethroid insecticides permethrin and deltamethrin. BMC Genomics 2008;9:546. |
R832720 (2008) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Hu J, Wright FA. Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model. Biometrics 2007;63(1):41-49. |
R832720 (2006) R832720 (2008) |
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Journal Article | Judson R, Elloumi F, Setzer RW, Li Z , Shah I. A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model. BMC Bioinformatics 2008;9:241-256. |
R832720 (2008) |
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Journal Article | Li Z, Wright FA, Royland J. Age-dependent variability in gene expression in male Fischer 344 rat retina. Toxicological Sciences 2009;107(1):281-292. |
R832720 (2008) |
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Journal Article | Liu Y, Hayes D, Nobel A, Marron J. Statistical Significance of Clustering for High-Dimension, Low–Sample Size Data. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 2012;103(483):1281-1293. |
R832720 (2009) |
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Journal Article | Low YS, Sedykh AY, Rusyn I, Tropsha A. Integrative approaches for predicting in vivo effects of chemicals from their structural descriptors and the results of short-term biological assays. Current Topics in Medicinal Chemistry 2014;14(11):1356-1364. |
R832720 (2009) R833825 (Final) R835166 (2014) R835166 (2016) R835166 (Final) |
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Journal Article | Muratov EN, Varlamova EV, Artemenko AG, Khristova T, Kuz'min VE, Makarov VA, Riabova OB, Wutzler P, Schmidtke M. QSAR analysis of [(biphenyloxy)propyl] isoxazoles: agents against coxsackievirus B3. Future Medicinal Chemistry 2011;3(1):15-27. |
R832720 (2009) R833825 (Final) |
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Journal Article | Muratov EN, Varlamova EV, Artemenko AG, Polishchuk PG, Kuz'min VE. Existing and developing approaches for QSAR analysis of mixtures. Molecular Informatics 2012;31(3-4):202-221. |
R832720 (2009) R833825 (Final) |
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Journal Article | Muratov EN, Varlamova EV, Artemenko AG, Polishchuk PG, Nikolaeva-Glomb L, Galabov AS, Kuz'min VE. QSAR analysis of poliovirus inhibition by dual combinations of antivirals. Structural Chemistry 2013;24(5):1665-1679. |
R832720 (2009) R833825 (Final) |
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Journal Article | 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 correlate with a behavioral phenotype. Genetics 2006;174(3):1229-1236. |
R832720 (2006) R832720 (2008) |
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Journal Article | Pogribny IP, Tryndyak VP, Bagnyukova TV, Melnyk S, Montgomery B, Ross SA, Latendresse JR, Rusyn I, Beland FA. Hepatic epigenetic phenotype predetermines individual susceptibility to hepatic steatosis in mice fed a lipogenic methyl-deficient diet. Journal of Hepatology 2009;51(1):176-186. |
R832720 (2009) |
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Journal Article | Polishchuk PG, Kuz'min VE, Artemenko AG, Muratov EN. Universal approach for structural interpretation of QSAR/QSPR models. Molecular Informatics 2013;32(9-10):843-853. |
R832720 (2009) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Scharph R, Tjelmeland H, Parmigiani G, Nobel A. A Bayesian Model for Cross-Study Differential Gene Expression. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 2012;104(488):1295-1310 |
R832720 (2009) |
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Journal Article | Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches D, Varnek A. Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection. Journal of Chemical Information and Modeling 2008;48(9):1733-1746. |
R832720 (2008) |
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Journal Article | Tropsha A, Golbraikh A. Predictive QSAR modeling workflow, model applicability domains, and virtual screening. Current Pharmaceutical Design 2007;13(34):3494-3504. |
R832720 (2007) R832720 (2008) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Woods CG, Vanden Heuvel JP, Rusyn I. Genomic profiling in nuclear receptor-mediated toxicity. Toxicologic Pathology 2007;35(4):474-494. |
R832720 (2007) R832720 (2008) |
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Journal Article | 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) R832720 (2008) |
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Journal Article | Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV. Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. Journal of Chemical Information and Modeling 2008;48(4):766-784. |
R832720 (2008) |
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Journal Article | Zhu H, Rusyn I, Richard A, Tropsha A. Use of cell viability assay data improves the prediction accuracy of conventional quantitative structure-activity relationship models of animal carcinogenicity. Environmental Health Perspectives 2008;116(4):506-513. |
R832720 (2007) R832720 (2008) R833825 (2008) R833825 (Final) |
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Journal Article | Zhu H, Ye L, Richard A, Golbraikh A, Wright FA, Rusyn I, Tropsha A. A novel two-step hierarchical quantitative structure-activity relationship modeling work flow for predicting acute toxicity of chemicals in rodents. Environmental Health Perspectives 2009;117(8):1257-1264. |
R832720 (2009) R833825 (2008) R833825 (Final) |
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Journal Article | Zhu H, Martin TM, Ye L, Sedykh A, Young DM, Tropsha A. Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure. Chemical Research in Toxicology 2009;22(12):1913-1921. |
R832720 (2009) R833825 (Final) |
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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.