Grantee Research Project Results
Journal Publications Details for Grant Number R833825
Carolina Center for Computational Toxicology
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| Reference Type | Citation | Progress Report Year | Document Sources |
|---|---|---|---|
| Journal Article | Abell AN, Jordan NV, Huang W, Prat A, Midland AA, Johnson NL, Granger DA, Mieczkowski PA, Perou CM, Gomez SM, Li L, Johnson GL. MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells. Cell Stem Cell 2011;8(5):525-537. |
R833825 (Final) |
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| Journal Article | Alves VM, Muratov E, Fourches D, Strickland J, Kleinstreuer N, Andrade CH, Tropsha A. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds. Toxicology and Applied Pharmacology 2015;284(2):262-272. |
R833825 (Final) R835166 (Final) |
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| Journal Article | Alves VM, Muratov E, Fourches D, Strickland J, Kleinstreuer N, Andrade CH, Tropsha A. Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization. Toxicology and Applied Pharmacology 2015; 284(2):273-280. |
R833825 (Final) R835166 (Final) |
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| Journal Article | Artemenko AG, Muratov EN, Kuz'min VE, Muratov NN, Varlamova EV, Kuz'mina AV, Gorb LG, Golius A, Hill FC, Leszczynski J, Tropsha A. QSAR analysis of the toxicity of nitroaromatics in Tetrahymena pyriformis: structural factors and possible modes of action. SAR and QSAR in Environmental Research 2011;22(5-6):575-601. |
R833825 (Final) |
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| Journal Article | Berginski ME, Vitriol EA, Hahn KM, Gomez SM. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells. PLoS ONE 2011;6(7):e22025 (13 pp.). |
R833825 (Final) |
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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, Lock EF, Kosyk O, Kim S, Uehara T, Harbourt D, DeSimone M, Threadgill DW, Tryndyak V, Pogribny IP, Bleyle L, Koop DR, Rusyn I. Interstrain differences in the liver effects of trichloroethylene in a multistrain panel of inbred mice. Toxicological Sciences 2011;120(1):206-217. |
R833825 (Final) |
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| Journal Article | Chaki SP, Barhoumi R, Berginksi ME, Sreenivasappa H, Trache A, Gomez SM, Rivera GM. Nck enables directional cell migration through the coordination of polarized membrane protrusion with adhesion dynamics. Journal of Cell Science 2013;126(Pt 7):1637-1649. |
R833825 (Final) |
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| Journal Article | Chen Z, Lessey E, Berginski ME, Cao L, Li J, Trepat X, Itano M, Gomez SM, Kapustina M, Huang C, Burridge K, Truskey G, Jacobson K. Gleevec, an Abl family inhibitor, produces a profound change in cell shape and migration. PLoS ONE 2013;8(1):e52233 (14 pp.). |
R833825 (Final) |
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| Journal Article | Choi K, Gomez SM. Comparison of phylogenetic trees through alignment of embedded evolutionary distances. BMC Bioinformatics 2009;10:423. |
R833825 (Final) |
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| Journal Article | Doolittle JM, Gomez SM. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virology Journal 2010;7:82 (15 pp.). |
R833825 (Final) |
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| Journal Article | Doolittle JM, Gomez SM. Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Neglected Tropical Diseases 2011;5(2):e954 (15 pp.). |
R833825 (Final) |
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| Journal Article | Duncan JS, Whittle MC, Nakamura K, Abell AN, Midland AA, Zawistowski JS, Johnson NL, Granger DA, Jordan NV, Darr DB, Usary J, Kuan P-F, Smalley DM, Major B, He X, Hoadley KA, Zhou B, Sharpless NE, Perou CM, Kim WY, Gomez SM, Chen X, Jin J, Frye SV, Earp HS, Graves LM, Johnson GL. Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple negative breast cancer. Cell 2012;149(2):307-321. |
R833825 (Final) |
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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 DM, Zhao N, Chesler EJ, Bradford BU, Shabalin AA, Yordanova R, Lu L, Rusyn I. Sex-specific gene expression in the BXD mouse liver. Physiological Genomics 2010;42(3):456-468. |
R833825 (Final) |
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| Journal Article | Gatti DM, Barry WT, Nobel AB, Rusyn I, Wright FA. Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics 2010;11:574. |
R833825 (Final) |
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| Journal Article | Gatti DM, Lu L, Williams RW, Sun W, Wright FA, Threadgill DW, Rusyn I. MicroRNA expression in the livers of inbred mice. Mutation Research 2011;714(1-2):126-133. |
R833825 (Final) |
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| Journal Article | Golbraikh A, Muratov E, Fourches D, Tropsha A. Data set modelability by QSAR. Journal of Chemical Information and Modeling 2014;54(1):1-4. |
R833825 (Final) |
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| Journal Article | Ha MJ, Sun W. Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation. Biometrics 2014;70(3):765-773. |
R833825 (Final) |
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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 | Herschlag G, Garcia GJ, Button B, Tarran R, Lindley B, Reinhardt B, Elston TC, Forest MG. A mechanochemical model for auto-regulation of lung airway surface layer volume. Journal of Theoretical Biology 2013;325:42-51. |
R833825 (Final) |
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| Journal Article | Kesseler KJ, Blinov ML, Elston TC, Kaufmann WK, Simpson DA. A predictive mathematical model of the DNA damage G2 checkpoint. Journal of Theoretical Biology 2013;320:159-169. |
R833825 (Final) |
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| Journal Article | Lee S, Wright FA, Zou F. Control of population stratification by correlation-selected principal components. Biometrics 2011;67(3):967-974. |
R833825 (Final) |
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| Journal Article | Lock EF, Abdo N, Huang R, Xia M, Kosyk O, O'Shea SH, Zhou YH, Sedykh A, Tropsha A, Austin CP, Tice RR, Wright FA, Rusyn I. Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model. Toxicological Sciences 2012;126(2):578-588. |
R833825 (Final) R835166 (Final) |
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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) R834999 (Final) R835166 (2014) R835166 (2016) R835166 (Final) |
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| Journal Article | Low Y, Uehara T, Minowa Y, Yamada H, Ohno Y, Urushidani T, Sedykh A, Muratov E, Kuz’min V, Fourches D, Zhu H, Rusyn I, Tropsha A. Predicting drug-induced hepatotoxicity using QSAR and toxicogenomics approaches. Chemical Research in Toxicology 2011;24(8):1251-1262. |
R833825 (Final) R834999 (Final) |
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| Journal Article | Martinez SM, Bradford BU, Soldatow VY, Kosyk O, Sandot A, Witek R, Kaiser R, Stewart T, Amaral K, Freeman K, Black C, LeCluyse EL, Ferguson SS, Rusyn I. Evaluation of an in vitro toxicogenetic mouse model for hepatotoxicity. Toxicology and Applied Pharmacology 2010;249(3):208-216. |
R833825 (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 | O'Shea SH, Schwarz J, Kosyk O, Ross PK, Ha MJ, Wright FA, Rusyn I. In vitro screening for population variability in chemical toxicity. Toxicological Sciences 2011;119(2):398-407. |
R833825 (Final) |
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| Journal Article | Politi R, Rusyn I, Tropsha A. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods. Toxicology and Applied Pharmacology 2014;280(1):177-189. |
R833825 (Final) R835166 (2014) R835166 (2016) R835166 (Final) |
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| Journal Article | Rusyn I, Daston GP. Computational toxicology: realizing the promise of the toxicity testing in the 21st century. Environmental Health Perspectives 2010;118(8):1047-1050. |
R833825 (Final) |
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| Journal Article | Rusyn I, Gatti DM, Wiltshire T, Kleeberger SR, Threadgill DW. Toxicogenetics: population-based testing of drug and chemical safety in mouse models. Pharmacogenomics 2010;11(8):1127-1136. |
R833825 (Final) |
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| Journal Article | Rusyn I, Sedykh A, Low Y, Guyton KZ, Tropsha A. Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data. Toxicological Sciences 2012;127(1):1-9. |
R833825 (Final) R835166 (Final) |
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| Journal Article | Sedykh A, Zhu H, Tang H, Zhang L, Richard A, Rusyn I, Tropsha A. Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity. Environmental Health Perspectives 2011;119(3):364-370. |
R833825 (Final) |
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| Journal Article | Soldatow VY, LeCluyse EL, Griffith LG, Rusyn I. In vitro models for liver toxicity testing. Toxicology Research 2013;2(1):23-39. |
R833825 (Final) |
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| Journal Article | Staab JM, O’Connell TM, Gomez SM. Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). BMC Bioinformatics 2010;11:123. |
R833825 (Final) |
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| Journal Article | Strychalski W, Adalsteinsson D, Elston TC. A cut-cell method for simulating spatial models of biochemical reaction networks in arbitrary geometries. Communications in Applied Mathematics and Computational Science 2010;5(1):31-53. |
R833825 (Final) |
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| Journal Article | Sun W, Buck MJ, Patel M, Davis IJ. Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics 2009;10:173 (13 pp.). |
R833825 (2008) R833825 (Final) |
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| Journal Article | Sun W, Xie W, Xu F, Grunstein M, Li K-C. Dissecting nucleosome free regions by a segmental semi-Markov model. PLoS One 2009;4(3):e4721 (10 pp.). |
R833825 (2008) R833825 (Final) |
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| Journal Article | Sun W, Wright FA, Tang Z, Nordgard SH, Van Loo P, Yu T, Kristensen VN, Perou CM. Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Research 2009;37(16):5365-5377. |
R833825 (Final) |
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| Journal Article | Sun W, Wright FA. A geometric interpretation of the permutation p-value and its application in eQTL studies. Annals of Applied Statistics 2010;4(2):1014-1033. |
R833825 (Final) |
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| Journal Article | Sun W. A statistical framework for eQTL mapping using RNA-seq data. Biometrics 2012;68(1):1-11. |
R833825 (Final) |
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| Journal Article | Sun W, Li L. Multiple loci mapping via model-free variable selection. Biometrics 2012;68(1):12-22. |
R833825 (Final) |
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| Journal Article | Sun W, Hu Y. eQTL mapping using RNA-seq data. Statistics in Biosciences 2013;5(1):198-219. |
R833825 (Final) |
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| Journal Article | Sushko I, Novotarskyi S, Korner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Muller KR, Xi L, Liu H, Yao X, Oberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz’min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV. Applicability domains for classification problems: benchmarking of distance to models for Ames mutagenicity set. Journal of Chemical Information and Modeling 2010;50(12):2094-2111. |
R833825 (Final) |
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| Journal Article | Wright FA, Shabalin AA, Rusyn I. Computational tools for discovery and interpretation of expression quantitative trait loci. Pharmacogenomics 2012;13(3):343-352. |
R833825 (Final) R835166 (Final) |
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| Journal Article | Xia K, Shabalin AA, Huang S, Madar V, Zhou YH, Wang W, Zou F, Sun W, Sullivan PF, Wright FA. seeQTL: a searchable database for human eQTLs. Bioinformatics 2012;28(3):451-452. |
R833825 (Final) |
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| Journal Article | Xu K, Morgan KT, Todd Gehris A, Elston TC, Gomez SM. A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis. PLoS Computational Biology 2011;7(12):e1002272 (13 pp.). |
R833825 (Final) |
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| Journal Article | Zhang L, Sedykh A, Tripathi A, Zhu H, Afantitis A, Mouchlis VD, Melagraki G, Rusyn I, Tropsha A. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches. Toxicology and Applied Pharmacology 2013;272(1):67-76. |
R833825 (Final) R835166 (2013) R835166 (Final) |
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| Journal Article | Zhang X, Huang S, Sun W, Wang W. Rapid and robust resampling-based multiple-testing correction with application in a genome-wide expression quantitative trait loci study. Genetics 2012;190(4):1511-1520. |
R833825 (Final) |
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| Journal Article | Zhou Y-H, Xia K, Wright FA. A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics 2011;27(19):2672-2678. |
R833825 (Final) |
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| Journal Article | Zhou Y-H, Barry WT, Wright FA. Empirical pathway analysis, without permutation. Biostatistics 2013;14(3):573-585. |
R833825 (Final) |
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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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| Journal Article | Zou F, Lee S, Knowles MR, Wright FA. Quantification of population structure using correlated SNPs by shrinkage principal components. Human Heredity 2010;70(1):9-22. |
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.