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Publications
On This Page
- Below are broad categories of recent publications concerning EPA's research using Computational Toxicology methods.
- Improve Linkages in the Source-to-Outcome Paradigm
- Provide Predictive Models for Hazard Identification
- Enhance Quantitative Risk Assessment
Bibliographic Information on EPA's
Computational Toxicology Research Programs 2000-2004
The following listing is a compilation of peer reviewed products for EPA's Computational Toxicology program from 2000-Present. To obtain a copy or for more information about the articles or research presented on this page, please visit http://www.ncbi.nlm.nih.gov/sites/entrez/ 
or contact the journal or lead investigator by using EPA's employee online directory.
Improve Linkages in the Source-to-Outcome Paradigm
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
A
Adgate, JL, Barr, D, Clayton, CA, Eberly, LE, Freeman, NCG, Lloy, PJ, Needham, L, Pellizzari, ED, Quackenboss, JJ, Roy, A, and Sexton, KG. (2001). Measurement of children's exposure to pesticides: analysis of urinary metabolite levels in a probability-based sample. Environmental Health Perspectives 109(6):583-590. EPA/600/J-01/230. [NERL]
Allis, JW, and Zhao, G. (2002). Kinetics of Bromodichloromethane Metabolism by Cytochrome P450 Isoenzymes in Human Liver Microsomes. Chemico-Biological Interactions 140:155-168. ETD-02-037. [NHEERL]
Allis, JW, and Zhao, G. (2002). Quantitative Evaluation of Bromodichloromethane Metabolism by Recombinant Rat and Human Cytochrome P450s. Chemico-Biological Interactions 140:137-153. ETD-02-009. [NHEERL]
B
Bagley, MJ, Anderson, SL, and May, BP. (2001). Choice of methodology for assessing genetic impacts of environmental stressors: Polymorphism and reproducibility of RAPD and AFLP fingerprints. Ecotoxicology 10(4):239-244. [NCER]
Bagley, MJ, Anderson, SL, and May, B. (2001). Choice of methodology for assessing genetic impacts of environmental stressors: Polymorphism and reproducibility of RAPD and AFLP fingerprints. Ecotoxicology 10:239-244. [NERL]
Bagley, MJ, Franson, SE, Christ, SA and Toth, GP. (2000). Genetic diversity indicator of ecosystem condition and sustainability. NERL Internal Document. NERL-C1-EERD-00-033. [NERL]
Bagley, MJ, Franson, SE, Christ, SA, Waits, ER, Toth, GP. (2002). Genetic diversity as an indicator of ecosystem condition and sustainability: Utility for regional assessments of stream condition in the Eastern United States. Agency document. EPA/600/R-03/056. NERL-CI-EERD-02-042. [NERL]
Ballatori N, Boyer JL, Rockett JC. (2003). Exploiting genome data to understand the function, regulation, and evolutionary origins of toxicologically relevant genes. EHP Toxicogenomics, 111:61-65 [NHEERL]
Barton, HA, Deisinger, PJ, English, JC, Gearhart, JM, Faber, WD, Tyler, TR, Banton, MI, Teeguarden, J, and Andersen, ME. (2000). Risk assessment-family approach for estimating reference concentrations/doses for series of related organic chemicals. Toxicological Sciences 54(1):251-261. [NCER]
Belfiore, NM, and Anderson, SL. (2001). Effects of contaminants on genetic patterns in aquatic organisms: a review. Mutation Research-Reviews in Mutation Research 489(2-3):97-122. [NCER]
Betowski, LD, Enlow, M, and Riddick, LA. (2002). The phototoxoicity of polycyclic aromatic hydrocarbons: A theoretical study of excited states and correlation to experiment. Environmental Forensics 2(1):61-74. EPA/600/J-01/241. [NERL]
Boorman, GA, Anderson, SP, Casey, WM, Brown, RH, Crosby, LM; Gottschalk, K, Easton, M, Ni, H, and Morgan, KT. (2001). Toxicogenomics drug discovery and the pathologist. Toxicologic Pathology 30(1):15-27. ECD-01-092. [NHEERL]
Bryant, PL, Reid, LM, Diala, ES, Buckalew, AR, and Abbott, BD. (2001). An in vitro model for murine ureteric epithelial cells. In Vitro Cellular & Developmental Biology - Animal 37(8):395-398. RTD-01-012. [NHEERL]
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C
Charlap, JH, Craig, RC, O'Hara, MF, and Knudsen, TB. (2001). Toxicogenomic characterization of a biological threshold in developmental toxicity. Teratology, 63(6):281. [NCER]
Charlap, JH, Nemeth, KR, Craig, RC, and Knudsen, TB. (2002). Microarray analysis of gene expression in the mouse embryonic headfold following exposure to Bzrp ligands. Teratology 65(6):333. [NCER]
Charlap, JC, Donahue, RJ, and Knudsen, TB. (2003) Exposure-disease continuum for 2-chloro-2'-deoxyadenosine, a prototype ocular teratogen. 3. Intervention with PK11195. Birth Defects Research (Part A) 67:108-115. [NCER]
Cohen, Y, and Cooter, EJ. (2002). Multimedia environmental distribution of toxics (mend-tox): part II, software implementation and case studies. ASCE Practice Periodical: Hazardous, Toxic, and Radioactive Waste Management 6(2):87-101. EPA/600/J-03/221. [NERL]
Collette, TW. (2001). Prediction of molecular properties with mid-infrared spectra and interferograms. Spectroscopy 55(6):1067-1078. [NERL]
Collette, TW, Williams, TL, and D'Angelo, JC. (2001). Optimization of Raman spectroscopy for speciation of organics in water. Applied Spectroscopy 55(6):750-766. [NERL]
ColÓn, D, Weber, EJ, and Baughman, GL. (2002). Sediment-associated reactions of aromatic amines. 2. QSAR development. Environmental Science & Technology, 36(11):2443-2450. [NERL]
Cooter, EJ, and Cohen, Y, (2003). Multimedia environmental distribution of toxics (mend-tox): part I, hybrid compartmental-spatial modeling framework. ASCE Practice Periodical: Hazardous, Toxic and Radioactive Waste Management 6(2):70-86. [NERL]
Costa, DL, and Kodavanti, UP. (2003). Toxic Responses of the Lung to Inhaled Pollutants: Benefits and Limitations of Lung-Disease Models. Toxicology Letters 140-141:195-203. ETD-03-097. [NHEERL]
Crosby, LM, Hyder KS, Deangelo AB, Kepler TB, Gaskill B, Benavides GR, Yoon L, Morgan KT. (2000). Morphologic analysis correlates with gene expression changes in F344 rat mesothial cells. Toxicol. Appl. Pharm. 169:205-221. [NHEERL]
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D
DeMarini, DM, Shelton, ML, Kohan, MJ, Hudgens, EE, Kleindienst, TE, Ball, LM, Walsh, DB, de Boer, JG, Lewis-Bevan, L, Rabinowitz, JR, Claxton, LD and Lewtas, J. (2000). Mutagenicity in lung of big blue (R) mice and induction of tandem-base substitutions in salmonella by the air pollutant peroxyacetyl nitrate (PAN): predicted formation of intrastrand cross-links. Mutation Research 457(1-2):41-55. ECD-00-034. [NHEERL]
Dimsoski, P, Toth, GP, and Bagley, MJ. (2000). Microsatellite characterization in central stoneroller Campostoma anomalum (Pisces: Cyprinidae). Molecular Ecology 9:2187-2189. [NERL]
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Easterling, MR, Evans, MV, and Kenyon, EM. (2002). Comparative Analysis of Software for Physiologically Based Pharmacokinetic Modeling: Simulation, Optimization and Sensitivity Analysis. Toxicology Methods 10:203-229. ETD-00-017. [NHEERL]
Easterling, MR, Styblo, M, Evans, MV, and Kenyon, EM. (2001). Pharmacokinetic Modeling of Arsenic Uptake and Metabolism in Hepatocytes - Mechanistic Insights and Implications for Further Experiments. Journal of Pharmcokinetics and Pharmacodynamics 29(3):207-34. ETD-01-102. [NHEERL]
Eaton, RW. (2001). Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B: Biotransformations of 2-substituted benzoates and their use in cloning and characterization of phthalate catabolism genes and gene products. Journal of Bacteriology 183 (12):3689-3703. EPA/600/J-01/440, GED-01-2216. [NHEERL]
Ekman, DR, Lorenz, WW, Przybyla, AE, Wolfe, NL and Dean, JFD. (2003). SAGE analysis of transcriptome responses in arabidopsis thalian roots exposed to TNT. Plant Physiology (E-Pub ahead of print). [NERL]
F
Fielden, MR, and Zacharewski, T. (2001). Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicological Sciences 60(1):6-10. [NCER]
Fielden, MR, Fertuck, KC, Matthews, JB, Halgren, R and Zacharewsk, T. (2002). In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists. Critical Reviews in Toxicology 32(2):67-112. [NCER]
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Guan, X, Segal, RA, Shearer, M, and Martonen, TB. (2000). Mathematical Model of Airflow in the Lungs of Children. II. Effects of Ventilatory Parameters. Journal of Theoretical Medicine 3:51-62. ETD-00-009. [NHEERL]
H
Halgren, RG, Fielden, MR, Fong, C, and Zacharewski, TR. (2001). Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucleic Acids Research 29(2):582-588. NOTE: When the chips are down. Highlighted in Nature 2001; 410:860-861. [NCER]
Hester, SD, Benavides, GB, Sartor, M, Yoon, L, Wolf, DC and Morgan, KT. (2001). Normal gene expression in male F344 rat nasal transitional/respiratory epithelium. Genomics 85(1-2):301-310. EPA/600/J-02/180, ECD-01-050. [NHEERL]
Hester SD, Benavides GB, Yoon L, Morgan KT, Zou F, Barry W, Wolf DC. (2003). Formaldehyde-induced gene expression in F344 rat nasal respiratory epithelium. Toxicology, 187:13-24. [NHEERL]
Holmes, M, Suarez, JD, Roberts, NL, Mole, L, Murr, AS and Klinefelter, GR (2001). Bibromoacetic acid, a prevalent disinfectant by-product of drinking water disinfection, compromises synthesis of specific seminiferous tubule proteins following both in vivo and in vitro exposures. J. Androl. 22:878-890. [NHEERL]
Hornung, MW, Ankley, GT, and Schmieder, PK. (2002). Induction of an estrogen-responsive reporter gene in rainbow trout hepatoma cells (RTH 149) at 11 or 18 degrees C. Environmental Toxicology and Chemistry 22(4):866-871. MED-02-3922. [NHEERL]
Hurst, CH, DeVito, MJ, Setzer, RW, and Birnbaum, LS. (2000). Acute administration of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in pregnant Long Evans rats: Association of measured tissue concentrations with developmental effects. Toxicological Sciences 53:411-420. MS-00-042. [NHEERL]
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I
Inglefield, JR, Mundy, WR, Meacham, CA, and Shafer, TJ. (2002). Identification of calcium-dependent and -independent signaling pathways involved in polychlorinated biphenyl-induced CREB phosphorylation in developing cortical neurons. Neuroscience 115(2):559-573. NTD-02-040. [NHEERL]
Iwata, H and Stegeman, JJ. (2000). In situ RT-PCR detection of CYP1A mRNA in pharyngeal epithelium and chondroid cells of chemically untreated fish: involvement in craniofacial skeletal development? Biochemical and Biophysical Research Communications 271:130-137. [NCER]
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K
Kenneke, JF, and Weber, EJ. (2003). Reductive dehalogenation of halomethanes in iron- and sulfate-reducing sediments. 1. Reactivity pattern analysis. Environmental Science & Technology 37(4): 713-720. [NERL]
Kenyon, EM, Fea, M, Styblo, M, and Evans, MV. (2000). Application of Modeling Techniques to the Planning of In Vitro Arsenic Pharmacokinetic Studies. Alternatives to Laboratory Animals 29:15-33. ETD-00-025. [NHEERL]
Kim, CS, Zhang, Z, and Kleinstreuer, C. (2002). Aerosol deposition efficiencies and upstream release positions for different inhalation modes in an upper bronchial airway models. Aerosol Science and Technology 36:828-844. HSD-02-022. [NHEERL]
Kittler, R, Stoneking, M, and Kayser, M. (2002). A whole genome amplification method to generate long fragments from low quantities of genomic DNA. Analytical Biochemistry 300(2):237-244. [NCER]
Kinefelter, GR, Welch JE, Perreault, SD, Moore, HD, Zucker, RM, Suarez JD, Roberts NL, Bobseine, K and Jeffay, S. (2002). Localization of the sperm protein SP22 and inhibition of of fertility in vivo and in vitro. J. Androl. 23:48-63. [NHEERL]
Kodavanti, PRS, and Tilson, HA. (2000). Neurochemical effects of environmental chemicals: in vitro and in vivo correlations on second messenger pathways. Annals of the New York Academy of Sciences 919:97-105. MS-00-001. [NHEERL]
Kovatch, CC, Schizas, NV, Chandler, GT, Coull, BC, and Quattro, JM. (2000). Tolerance and genetic relatedness of three meiobenthic copepod populations exposed to sediment-associated contaminant mixtures: Role of environmental history. Environmental Toxicology and Chemistry 19(4):912-919. [NCER]
Kuhn-Hines, A, Champlin, DM, Munns, Jr., WR, McKinney, RA, Serbst, JR and Gleason, TR. (2001). Evaluation Of The Efficacy of Extrapolation Population Modeling to Predict the Dynamics of Americamysis bahia Populations in the Laboratory. Environmental Toxicology and Chemistry 20(1):213-221. AED-98-2041. [NHEERL]
Kuhn-Hines, A, Munns, Jr. WR, Poucher, S, Champlin, DM, and Lussier, SM. (2000). Prediction of Population-level Response from Mysid Toxicity Test Data Using Population Model Techniques. Environmental Toxicology and Chemistry 19(9):2364-2371. 600/J-00/256. [NHEERL]
Kullman, SW, and Hinton, DE. (2001). Identification characterization and ontogeny of a second cytochrome P450 3A gene from the fresh water teleost medaka (Oryzias latipes). Molecular Reproduction and Development 58:149-158. [NCER]
Kullman, SW, Hamm, JT, and Hinton, DE. (2000). Identification and characterization of cDNA encoding Cytochrome P450 3A from the fresh water teleost medaka (Oryzias latipes). Archives of Biochemistry and Biophysics 380:29-38. [NCER]
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L
Lattier, DL, Gordon, DA, Burks, DJ, and Toth, GP. (2001). Vitellogenin gene transcription: A relative quantitative exposure indicator of environmental estrogens. Environmental Toxicology and Chemistry 20:1979-1985. [NERL]
Lattier, DL, Reddy, TV, Gordon, DA, Lazorchak, JM, Smith, ME, Williams, DE, Wiechman, B,
Miracle, AL, Flick, RW, and Toth GP. (2002). 17 -Ethynylestradiol induced vitellogenin gene transcription qualified in fathead minnow (pimephales promelas) adult male livers, embryo larvae and gills. Environmental Toxicology and Chemistry 21(11):2385-2393. [NERL]
Lau, CS, Andersen, ME, Crawford-Brown, DJ, Kavlock, RJ, Kimmel, CA, Knudsen, TB, Muneoka, K, Rogers, JM, Setzer, RW, Smith, G, and Tyl, R. (2000). Evaluation of biologically based dose-response modeling for developmental toxicity: A workshop report. Regulatory Toxicology and Pharmacology 31:190-199. MS-99-171. [NHEERL]
Lau, CS, Mole, ML, Copeland, FM, Rogers, JM, Kavlock, RJ, Shuey, DL, Cameron, AM, Ellis, D, Logsdon, TR, Merriman, J and Setzer, RW. (2001). Toward a biologically based dose-response model for developmental toxicity of 5-fluorouracil in the rat: Acquisition of experimental data. Toxicological Sciences 59:37-48. MS-98-217. [NHEERL]
Lau, CS, Narotsky, MG, Lui, D, Best, DS, Setzer, RW, Mann, PC, Wubah, JA and Knudsen, TB. (2002). Exposure-disease continuum for 2-Chloro-2'-deoxyadenosine (2-CdA), a prototype teratogen: Induction of lumbar hernia in the rat and species comparison for the teratogenic responses. Teratology 66(1):6-18. RTD-01-103. [NHEERL]
Leikauf, GD, McDowell, SA, Gammon, K, Wesselkamper, SC, Bachurski, CJ, Puga, A, Wiest, JS, Leikauf, JE, and Prows, DR. (2000). Functional genomics of particle-induced lung injury. Inhalation Toxicology 12:59-73. [NCER]
Lui, J, Corton, C, Dix, DJ, Liu, Y, Waalkes, MP and Klassen, CD (2001). Genetic background but not metallothionein phenotype dictates sensitivity to cadmium-induced testicular injury in mice. Toxicol. Appl. Pharm., 176:1-9. [NHEERL]
Loomis, AK, and Thomas, P. (2000). Effects of estrogens and xenoestrogens on androgen production by Atlantic croaker testes in vitro: evidence for a nongenomic action mediated by an estrogen membrane receptor. Biology of Reproduction 62(4):995-1004. [NCER]
Loux, NT. (2003). An exact method for relating zwitterionic microscopic to macroscopic acidity constants. Chemical Speciation and Bioavailability 15(2):47-51. [NERL]
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M
Makridakis, N, diSalle, E and Reichardt, JK. (2000). Biochemical and pharmacogenetic dissection of human steroid 5alpha reductase type II. Pharmacogenetics 10(5):407-413. [NCER]
MacLeod, SL, Nowell, S, Massengill, J, Jazieh, A, McClure, G, Plaxco, J, Kadlubar, FF, and Lan, NP. (2000). Cancer therapy and polymorphisms of cytochromes P450. Clinical Chemistry and Laboratory Medicine 38:883-887. [NCER]
Martonen, TB, Zhang, Z, Yu, G and Musante, CJ. (2001). Three-Dimensional Computer Modeling of the Human Upper Respiratory Tract. Cell Biophysics and Biochemistry, 35(3):255-261. ETD-02-022. [NHEERL]
McClain, JS, Oris, JT, Burton, GA Jr. and Lattier, DL. (2003). Laboratory and field validation of multiple molecular biomarkers of contaminant exposure in rainbow trout (Oncorhynchus mykiss). Environmental Toxicology and Chemistry 22(2):361-70. [NERL]
McDorman, K, and Wolf, DC. (2000). Use of the spontaneous Tsc2 knockout (Eker) rat model of hereditary renal cell carcinoma for the study of renal carcinogens. Toxicologic Pathology 30(6):675-680. EPA/600/J-03/022, ECD-00-056. [NHEERL]
McDowell, SA, Gammon, K, Bachurski, CJ, Wiest, JS, Leikauf, JE, Prows, DR, and Leikauf, GD. (2000). Differential gene expression in the initiation and progression of nickel-induced acute lung injury. American Journal of Respiratory Cell and Molecular Biology 23:466-474. [NCER]
Miracle, AL, Toth, GP, and Lattier, DL. (2003). The path from molecular indicators of exposure to describing dynamic biological systems in an aquatic organism: Microarrays and the Fathead Minnow. Ecotoxicology12(6):457-62. [NERL]
Morgan, KT, Ni, H, Brown, HR, Yoon, L, Qualls, Jr, CW, Crosby, LM, Reynolds, R, Gaskill, B, Anderson, SP, Kepler, TB, Brainard, T, Liv, N, Easton, M, Merrill, C, Creech, D, Sprenger, D, Conner, G, Johnson, PR, Fox, T, Tyler, R, Sartor, M, Richard, E, Kuruvilla, S, Casey, WM, and Benavides, G. (2001). Application of cDNA microarray technology to in vitro toxicology and the selection of genes for a real time RT-PCR-based screen for oxidative stress in Hep-G2 cells. Toxicologic Pathology 30 (4):435-451. EPA/600/J-02/370, ECD-01-093. [NHEERL]
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Nadadur SS, Schladweiler, MCJ and Kodavanti, UP (2000). Pulmonary rat gene array for screening altered expression profiles in air pollutant induced lung injury. Inhal. Toxicol. 12:1239-1254. [NHEERL]
Nadadur SS, Pinkerton KE, Kodavanti UP. (2002). Pulmonary gene expression profiles of spontaneously hypertensive rats exposed to environmental tobacco smoke. Chest, 121:83S-84S [NHEERL]
Nadadur SS, Kodavanti UP. (2002). Altered gene expression profiles of rat lung in response to an emission particulate and its metal constituents. J Toxicol Environ Health A. 65:1333-50. [NHEERL]
Nelson, GM, Swank, AE, Brooks, LR, Bailey, KC, and George, SE. (2000). Metabolism, microflora effects, and genotoxicity in haloacetic acid-treated cultures of rat cecal microbiota. Toxicological Sciences 60(2):232-241. EPA/600/J-01/386, ECD-00-054. [NHEERL]
Nowell, S, Ambrosone, CB, Ozawa, S, MacLeod, SL, Mrackova, G, Williams, S, Plaxco, J, Kadlubar, FF, and Lang, NP. (2000). Relationship of phenol sulfotransferase (SULT1A1) genotype to sulfotransferase activity phenotype in platelet cytosol. Pharmacogenetics 10(9):789-797. [NCER]
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Ostermeier, GC, Dix DJ and Kravetz, SA (2002). A bioinformatic strategy to rapidly characterize cDNA libraries. Bioinoformatics, 18:949-952. [NHEERL]
Overton, JH, Kimbell, J, Subramaniam, RP, and Miller, FJ. (2001). Dosimetry Modeling of Inhaled Formaldehyde: The Human Respiratory Tract. Toxicological Sciences 64:122-134. ETD-00-024. [NHEERL]
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Rashleigh, B. (2003). Application of AQUATOX, a process-based model for ecological assessment, to Contentnea Creek in North Carolina. Journal of Freshwater Ecology. 18: 515-522. [NERL]
Reid, R, Dix, DJ, Miller, D and Krawetz, SA (2001). Recovering microarray data for Pathways analysis using a multipoint alignment strategy. Biotechniques, 30:762-768. [NHEERL]
Richburg JH, Johnson KJ, Schoenfeld HA, Meistrich ML, Dix DJ. (2002). Defining the cellular and molecular mechanisms of toxicant action in the testis. Toxicol Lett. 135:167-83. [NHEERL]
Rigas, ML, Okino, MS, and Quackenboss, JJ. (2001). Use of pharmacokinetic model to assess chlorpyrifos exposure and dose in children based on urinary biomarker measurements. Toxicological Sciences 61:374-381. EPA/600/J-02/284. [NERL]
Rockett, JC and Dix, DJ (2000). DNA arrays: technology, options and toxicological applications. Xenobiotica 30:155-177. [NHEERL]
Rockett, JC, Kavlock, RJ, Lambright, CR, Parks, LG, Schmid, JE, Wilson, VS, and Dix, DJ. (2002). DNA arrays to monitor gene expression in rat blood and uterus following 17-beta-estradiol exposure: Biomonitoring environmental effects using surrogate tissues. Toxicological Sciences 69(1):49-59. RTD-01-124. [NHEERL]
Rockett, JC, Luft, JC, Garges, JB, Krawetz, SA, Hughes, MR, Kim, KH, Oudes, A and Dix, DJ. (2001). Development of a 950-gene DNA array for examining gene expression patterns in mouse testis. Genome Biology 2(4): research0014.1 - 0014.9 (GenomeBiology.com). RTD-01-010. [NHEERL]
Rockett, JC, Mapp, FL, Garges, JB, Luft, JC, Mori, C and Dix, DJ (2001). The effects of hyperthermia on spermatogenesis, apoptosis, gene expression and fertility in adult male mice. Biol. Reprod. 65:229-239. [NHEERL]
Rockett, JC. (2001). Genomic and proteomic techniques applied to reproductive biology. GenomoeBiol 2:4020.1-4020 (at http://genomebiology.com/2001/2/9/reports/4020/) [NHEERL]
Rockett, CJ (2001). Chipping away at the mystery of drug response. The Pharmacogenomics Journal 1:161-166 . [NHEERL]
Ross, MK, Said, B, and Shank, RC. (2000). DNA-damaging effects of genotoxins in mixture. Modulation of covalent binding to DNA. Toxicological Sciences 53(2):224-236. [NCER]
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Samet, JM, Wu, W, and Graves, LM. (2003). Mechanisms for Zn-induced signaling initiation through the epidermal growth factor receptor. Toxicology and Applied Pharmacology 191(1):86-93. [NCER]
Santo Domingo, JW, MC Meckes, JM Simpson, B Sloss, and DJ Reasoner. 2003. Molecular Characterization of Bacteria Inhabiting a Water Distribution System Simulator. Water Science and Technol. 47:149-154. [NRMRL].
Santo Domingo, JW, SD Siefring, and RA Haugland. 2003. Real-time PCR method to detect Enterococcus faecalis in water. Biotechnology Letters 25:261-265 [NRMRL]
Sawunyama, P, and Bailey, GW. (2001). Modeling the interaction of agrochemicals with environmental surfaces: pesticides on rutile and organo-rutile surfaces. Journal of Molecular Structure 54(1-3):119-129. [NERL]
Schizas, NV, Chandler, GT, Coull, BC, Klosterhaus, SL, and Quattro, JM. (2001). Differential survival of three mitochondrial lineages of a marine benthic copepod exposed to a pesticide mixture. Environmental Toxicology and Chemistry 35:(3)535-538. [NCER]
Schizas, NV, Coull, BC, Chandler, GT, and Quattro, JM. (2002). Sympatry of distinct mitochondrial DNA lineages in a copepod inhabiting estuarine creeks in the southeastern USA. Marine Biology 140: 585-594. [NCER]
Schlezinger, JJ, Blickharz, CE, Mann, KK, Doerre, S and Stegeman, JJ. (2000). Identification of NF-KappaB in the marine fish Stenotomus chrysops and examination of its activation by aryl hydrocarbon receptor agonists. Chemico-Biological Interactions 126(2):137-157. [NCER]
Schroeter, JD, Fleming, JS, Hwang, D, and Martonen, TB. (2002). A Computer Model of Lung Morphology to Analyze SPECT Images. Computerized Medical Imaging and Graphics 26:237-246. ETD-01-040. [NHEERL]
Shaughnessy, DT, Setzer, RW, and DeMarini, DM. (2001). The antimutagenic effect of vanillin and cinnamaldehyde on spontaneous mutation in salmonella TA104 is due to a reduction in mutations at GC but not AT sites. Mutation Research 480-481(1-2):55-69. ECD-01-023. [NHEERL]
Silbiger, RN, Leonard, AC, Dimsoski, Pl, Fore, S, Guttman, SI, Roth, AC, Gordon, DA Wessendarp, TK, Toth, GP, and Smith, MK. (2001). The use of molecular markers to study the effects of environmental impacts on genetic diversity in Brown Bullhead (Amerius nubulosus) populations. Environmental Toxicology and Chemistry 20:2580-2587. [NERL]
Simpson, JM, DJ Reasoner, and Santo Domingo JW. (2002). Microbial Source Tracking: State of the Science. Environmental Science and Technology 36:5279-5288. [NRMRL]
Simpson, JM, JW Santo Domingo and Reasoner DJ. (2004). Assessment of equine fecal contamination: the search for alternative bacterial source-tracking targets. FEMS Microbiology Ecology. Accepted for publication [NRMRL]
Spencer, R, Schroeter, JD, and Martonen, TB. (2001). Computer Simulations of Lung Airway Structures Using Data-Driven Surface Modeling Techniques. Computers in Biological Medicine 31:499-511. ETD-01-071. [NHEERL]
Staton, JL, Schizas, NV, Chandler, GT, Coull, BC, and Quattro, JM. (2001). Ecotoxicology and population genetics: The emergence of phylogeographic and evolutionary ecotoxicology. Ecotoxicology 10(4):217-222. [NCER]
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Tebes-Stevens, CL, Espinoza, F, and Valocchi, AJ. (2001). Evaluating the sensitivity of a subsurface multicomponent reactive transport model with respect to transport and reaction parameters. Journal of Contaminant Hydrology 52(1-4):3-27. [NERL]
Thomas, P. (2000). Chemical interference with genomic and nongenomic actions of steroids in fishes: role of receptor binding. Marine Environmental Research. 50(1-5):127-134. [NCER]
Tranah, GJ, Agresti, JJ, and May, BP. (2001). New microsatellite loci for suckers (Catostomidae): primer homology in Catostomus, Chasmites, and Deltistes. Molecular Ecology Notes 1(1-2):55-60. [NCER]
Tranah, GJ, Bagley, MJ, Agresti, JJ, and May, B. (2003). Development of codominant markers for identifying species hybrids. Conservation Genetics 4(4):537-541. EPA/600/J-03/360. [NERL]
Tratnyek, PG, Weber, EJ, and Schwarzenbach, RP. (2003). Quantitative structure-activity relationships (QSARs) for chemical reductions of organic contaminants. Environmental Toxicology and Chemistry 22(8):1733-1742. [NCER]
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W
Weber, EJ, ColÓn, D, and Baughman, GL. (2001). Sediment-associated reactions of aromatic amines: 1. Elucidation of sorption mechanisms. Environmental Science & Technology 35(12):2470-2475. [NERL]
Williams, M, J Santo Domingo, M Meckes, C Kelty and H Rochon. (2004). Phylogenetic Diversity of Drinking Water Bacteria in a Distribution System Simulator. Journal of Applied Microbiology. Accepted for publication [NRMRL]
Wilson VS, Lambright C, Furr J, Ostby J, Wood C, Held G, Gray LE. (2004). Phthalate ester-induced gubernacular lesions are associated with reduced insl3 gene expression in the fetal rat testis. Toxicol Lett. 146(3):207-15. [NHEERL]
Wu, W, Graves, LM, Gill, GN, and Samet, JM. (2002). Zn-induced EGF receptor requires Src-mediated phosphorylation of EGF receptor on tyrosine 845. American Journal of Respiratory and Critical Care Medicine 165:A426. [NCER]
Wu, W, Graves, LM, Gill, GN, Parsons, SJ, and Samet, JM. (2002). Src-dependent phosphorylation of the epidermal growth factor receptor on tyrosine 845 is required for Zn-induced ras activation. Journal of Biological Chemistry 277(27):24252-24257. [NCER]
Wu, W, Samet, J, Ghio, AJ, and Devlin, RB. (2001). Activation of the EGF receptor signaling pathway in human airway epithelial cells exposed to Utah Valley particulate matter. American Journal Physiology - Lung Cellular and Molecular Physiology 281:L483-L489. HSD-01-037. [NHEERL]
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Z
Zhang, Z, Kleinstreuer, C, and Kim, CS. (2001). Effects of curved inlet tubes on air flow and particle deposition in bifurcating lung models. Journal of Biomechanics 34(5):659-669. HSD-01-077. [NHEERL]
Zhang, Z, and Kleinstreuer, C. (2002). Effect of particle inlet distributions on deposition in a triple bifurcation lung airway model. Journal of Aerosol Medicine: The Official Journal Of The International Society For Aerosols In Medicine 14(1)13-29. HSD-01-078. [NHEERL]
Zhang, ZZ, Kleinstreuer, C, and Kim, CS. (2002). Gas-solid two-phase flow in a triple bifurcation lung airway model. International Journal of Multiphase 28:1021-1046. HSD-02-034. [NHEERL].
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Provide Predictive Models for Hazard Identification
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
A
Ankley, GT, Mekenyan, OG, Kamenska, V, Schmieder, PK, and Bradbury, SP. (2002). Reactivity profile of ligands of mammalian retinoic acid receptors: a preliminary COREPA analysis. SAR and QSAR in Environmental Research 13:365-377. EPA/600/J-02/183, MED-01-3700. [NHEERL]
B
Bradbury, SP, Kamenska, V, Schmieder, PK, Ankley, GT, and Mekenyan, OG. (2000). A computationally based identification algorithm for estrogen receptor ligands: Part 2. Evaluation of a hER-alpha binding affinity model. Toxicological Sciences 58:270-281. EPA/600/J-00/336, MED-00-3545. [NHEERL]
Bradbury, SP, Russom, CL, Ankley, GT, Schultz, TW, and Walker, JD. (2003). Overview of data and conceptual approaches for derivation of QSARs for ecotoxicological effects of organic chemicals. Environmental Toxicology and Chemistry 22(8):1789-1798. MED-01-3835. [NHEERL]
Brown, KW, Little, SB, and Rabinowitz, JR. (2002). Benzo[a]pyrene and benzo[c]phenanthrene: The effect of structure on the binding of water molecules to the diol epoxides. Chemical Research in Toxicology 15(8):1069-1079. EPA/600/J-03/190, ECD-02-035. [NHEERL]
D
DeLisle, RK, Yu, S-J, Nair, AC, and Welsh, WJ. (2001). Homology modeling of the estrogen receptor subtype Beta (ER-Beta) and calculation of ligand binding affinities. Journal of Molecular Graphics and Modeling 20(2):155-167. [NCER]
DeLisle, RK, Yu, S-J, Nair, AC, and Welsh, WJ. (2001). Homology modeling of the estrogen receptor subtype Beta (ER-Beta) and calculation of ligand binding affinities. Journal of Molecular Graphics and Modeling 20(2):155-167. [NCER]
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H
Hartig PC, Bobseine KL, Britt BH, Cardon MC, Lambright CR, Wilson VS, Gray LE Jr. (2002). Development of two androgen receptor assays using adenoviral transduction of MMTV-luc reporter and/or hAR for endocrine screening. Toxicol Sci. 66:82-90. [NHEERL].
Hilal, SH, Karickhoff, SW, and Carreira, LA. (2003). Prediction of the vapor pressure, boiling point, heat of vaporization and diffusion coefficient of organic compounds. QSAR & Combinatorial Science 22(6):565-574. [NERL]
Hilal, SH, Karickhoff, SW, Carreira, LA, and Shrestha, BP. (2004). Estimation of carboxylic acid ester hydrolysis rate constants. QSAR & Combinatorial Science (in press). [NERL]
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J
Jamal, EY, Shashidhar, NR, Adrea, M, and Slikker, W, Jr. (2001). Prediction of organophosphorus acetylcholinesterase inhibition using three-dimensional quantitative structure-activity relationship (3D-QSAR) methods. Toxicological Sciences 63:223-232. NTD-03-048. [NHEERL]
M
Martin, TM, and Young, DM. (2001). Prediction of the Acute Toxicity of Organic Compounds to the Fathead Minnow (Pimephales promelas) using a Group Contribution Method. Chemical Research in Toxicology 14(10):1378-1385. [NRMRL]
Mekenyan, OG, Kamenska, V, Schmieder, PK, Ankley, GT, and Bradbury, SP. (2000). A computationally-based identification algorithm for potential estrogen receptor ligands. Part II. An evaluation of a human receptor-based model. Toxicological Sciences 58:270-281. MED-00-3594. [NHEERL]
Moudgal, CJ, Lipscomb, JC, and Bruce, RM. (2000). Potential health effects of drinking water disinfection by-products using quantitative structure toxicity relationship. Toxicology 147(2):109-131. [NCEA]
Moudgal, CJ, Venkatapathy, R, Coudhury, H, Bruce, RM, and Lipscomb, JC. (2003). Application of QSTRs in the selection of a surrogate toxicity value for a chemical of concern. Environmental Science and Technology 37(22):5228-5235 [NCEA]
P
Perkins, R, Fang, H, Tong, W, and Welsh, WJ. (2003). Quantitative structure-activity relationship (QSAR) methods: perspectives on drug discovery and toxicology. Environmental Toxicology and Chemistry 22(8):1666-79. [NCER]
Puri, S, Chickos, JS, and Welsh, WJ. (2002). Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of sublimation. Journal of Chemical Information and Computer Sciences 42(1):109-116. [NCER]
Puri, S, Chickos, JS, and Welsh, WJ. (2002). Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpy of vaporization. Journal of Chemical Information and Computer Sciences 42(2):299-304. [NCER]
Puri, S, Chickos, JS, and Welsh, WJ. (2003). Three-dimensional quantitative structure-property relationship (3D-QSPR) models for prediction of thermodynamic properties of polychlorinated biphenyls (PCBs): enthalpies of fusion and their application to estimates of enthalpies of sublimation and aqueous solubilities. Journal of Chemical Information and Computer Sciences 43(1):55-62. [NCER]
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R
Rabinowitz, JR, Little, S, and Brown, KW. (2001). Why does 5-methyl chrysene interact with DNA like both a planar and a non-planar polycyclic aromatic hydrocarbon? Quantum Mechanical Studies. International Journal of Quantum Chemistry 88(1):99-106. EPA/600/J-02/178, ECD-02-012. [NHEERL]
Richard, AM and Williams, CR (2002). Distributed structure-searchable toxicity (DSSTox) public database network: a proposal. Mutation Research 29:27-52. [NHEERL]
Richard, AM, and Benigni, R. (2001). AI and SAR approaches for predicting chemical carcinogenicity: Survey and status report. SAR and QSAR in Environmental Research 13(1):1-19. EPA/600/J-02/179, ECD-01-021. [NHEERL]
Russom, CL, Benton, RL, Walker, JD, and Bradbury, SP. (2003). An overview of the use of QSARs for ranking and prioritizing large chemical inventories. Environmental Toxicology and Chemistry 22(8):1810-1821. MED-01-3806. [NHEERL]
S
Schmieder, PK, Ankley, GT, Mekenyan, OG, Walker, JD, and Bradbury, SP. (2003). QSAR models for prediction of ER binding of structurally diverse chemicals. Environmental Toxicology
and Chemistry 22:1844-1854. MED-01-3838. [NHEERL]
Schmieder, PK, Koleva, YK, and Mekenyan, OG. (2001). A reactivity pattern for discrimination of ER agonism and antagonism based on 3-D molecular attributes. SAR and QSAR in Environmental Research 13(2):353-364. EPA/600/J-02/11184, MED-01-3734. [NHEERL]
Schmieder, PK, Aptula, AO, Routeledge, EJ, Sumpter, JP, and Mekenyan, OG. (2000). Estrogenicity of alkylphenolic compounds: A 3-D structure-activity of gene activation. Environmental Toxicology and Chemistry 19:1727-1740. EPA/600/J-00/179, MED-99-3341. [NHEERL]
Schmieder, PK, Tapper, MA, Kolanczyk, RC, Hammermeister, DE, Sheedy, BR and Denny, JS. (2003). Discriminating redox cycling and arylation pathways of reactive chemical toxicity in trout hepatocytes. Toxicological Sciences 72:66-76. MED-03-3561. [NHEERL]
Schmieder, PK, Tapper, MA, Linnum, AL, Denny, JS, Kolanczyk, RC, and Johnson, RD. (2000). Optimization of a precision-cut trout liver tissue slice assay as a screen for vitellogenin induction: Comparison of slide incubation techniques. Aquatic Toxicology 49:251-268 (2000). EPA/600/J-00/334. Available: External, MED-99-3503. [NHEERL]
T
Tratnyek, PG, Weber, EJ, and Schwarzenbach, RP. (2003). Quantitative structure-activity relationships (QSARs) for chemical reductions of organic contaminants. Environmental Toxicology and Chemistry 22(8):1733-1742. [NERL]
W
Wilson VS, Bobseine K, Lambright CR, Gray LE Jr. (2002). A novel cell line, MDA-kb2, that stably expresses an androgen- and glucocorticoid-responsive reporter for the detection of hormone receptor agonists and antagonists. Toxicol Sci. 66:69-81. [NHEERL].
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Enhance Quantitative Risk Assessment
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
C
Clewell, H, Andersen, ME, and Barton, H. (2001). A Consistent Approach for the Application of Pharmacokinetic Modeling in Cancer Risk Assessment. Environmental Health Perspectives 110(1):85-93. ETD-01-053. [NHEERL]
D
DeWoskin, RS, Barone, Jr. S, Clewell, HJ, and Setzer, RW. (2001) Improving the development and use of biologically based dose response models (BBDR) in risk assessment. Human and Ecological Risk Assessment 7(5):1091-1120. NTD-02-021. [NHEERL], [NCEA]
E
Euling, SY, Gennings, C, Wilson, EM, Kemppainen, JA, Kelce, WR, and Kimmel, CA. (2002). Response-surface modeling of the effect of 5alpha-dihydrotestosterone and androgen receptor levels on the response to the androgen antagonist vinclozolin. Toxicological Sciences 69:332-343. [NCEA]
H
Hale, SS. Species Databases and the Bioinformatics Revolution. (2001). RI Natural History Survey, Inc Newsletter December. Agency document: EPA/600/N-02/004, AED-02-002. [NHEERL]
K
Kimbell, JS, Overton, JH, Subramaniam, RP, Schlosser, PM, Morgan, KT, Conolly, R, and Miller, FJ. (2001). Dosimetry Modeling of Inhaled Formaldehyde: Binning Nasal Flux Predictions for Quantitative Risk Assessment. Toxicological Sciences 64:111-12. ETD-01-077. [NHEERL]
Kimmel, GL, Williams, PL, Claggett, TW, and Kimmel, CA. (2002). Response-surface analysis of exposure-duration relationships: the effects of hyperthermia on embryonic development of the rat in vitro. Toxicological Sciences 69:391-399. [NCEA]
M
Morgan, KT, Ni, H, Brown, RH, Benavides, GR, Crosby, LM, Sprenger, D, Yoon, L, Easton, M, Morgan, D, Laskowitz, D, and Tyler, R. (2001). Toxicogenomics and human disease risk assessment. Health Effects in Risk Assessment 8(6):1339-1353. EPA/600/J-03/163, ECD-01-091. [NHEERL]
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R
Reeves, WR, Barhoumi, R, Burghardt, RC, Lemke, SL, Mayura, K, McDonald, TJ, Phillips, TD, and Donnelly, KC. (2001). Evaluation of methods for predicting the toxicity of polycyclic aromatic hydrocarbon mixtures. Environmental Science and Technology 35(8):1630-1636. [NCER]
S
Saghir, SA, and Schultz, IR. (2002). Low dose oral bioavailability of dichloroacetate in naive and GST-zeta depleted rats. Environmental Health Perspectives 110(8):757-63. [NCER]
Schultz, IR, and Merdink, JL, Gonzalez-Leon, AG, and Bull, RJ. (2002). Dichloroacetate toxicokinetics and disruption of tyrosine catabolism in B6C3F1 mice: dose response relationships and age as a modifying factor. Toxicology 173(3):229-247. [NCER]
Schultz, IR, and Sylvestor, S. (2001). Stereospecific toxicokinetics of bromochloro- and chlorofluoroacetate: Effect of GST-zeta depletion. Toxicology and Applied Pharmacology, 175(2):104-113. [NCER]
T
Timchalk, C, Kousba, A, and Poet, TS. (2002). Assessing the impact of human PON1 polymorphisms: sensitivity and Monte Carlo analyses using a physiologically based pharmacokinetic/ pharmacodynamic (PBPK/PD) model for chlorpyrifos. Toxicological Sciences 66(1-S):1525. [NCER]
Timchalk, C, Kousba, A, and Poet, TS. (2002). Monte Carlo analysis of the human chlorpyrifos-oxonase (PON1) polymorphism using a physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) model. Toxicology Letters 135(1-2):51-59. [NCER]
Timchalk, C, Kousba, A, and Poet, TS. (2003). Development of a neonatal rat physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model for chlorpyrifos. Toxicological Sciences 72(S-1):1483. [NCER]
W
Wang, X, Santostefano, MJ, DeVito, MJ, and Birnbaum, LS. (2000). Extrapolation of a PBPK Model for Dioxin Across Dosage, Regimens, Genders, Strains and Species. Toxicological Sciences 56:49-60. ETD-00-058. [NHEERL]