-
1
-
-
84921459862
-
Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water
-
PMID: 25605026
-
Moffat I, Chepelev NL, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, et al. Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol. 2015; 45: 1-43. doi: 10.3109/ 10408444.2014.973934 PMID: 25605026
-
(2015)
Crit Rev Toxicol.
, vol.45
, pp. 1-43
-
-
Moffat, I.1
Chepelev, N.L.2
Labib, S.3
Bourdon-Lacombe, J.4
Kuo, B.5
Buick, J.K.6
-
2
-
-
84901362871
-
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat
-
PMID: 24830643
-
Romer M, Eichner J, Metzger U, Templin MF, Plummer S, Ellinger-Ziegelbauer H, et al. Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. PLoS One. 2014; 9: e97640. doi: 10.1371/journal.pone.0097640 PMID: 24830643
-
(2014)
PLoS One.
, vol.9
, pp. e97640
-
-
Romer, M.1
Eichner, J.2
Metzger, U.3
Templin, M.F.4
Plummer, S.5
Ellinger-Ziegelbauer, H.6
-
3
-
-
84889602466
-
Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan
-
PMID: 24183702
-
Jackson AF, Williams A, Recio L, Waters MD, Lambert IB, Yauk CL. Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan. Toxicol Appl Pharmacol. 2014; 274: 63-77. doi: 10.1016/j.taap.2013.10.019 PMID: 24183702
-
(2014)
Toxicol Appl Pharmacol.
, vol.274
, pp. 63-77
-
-
Jackson, A.F.1
Williams, A.2
Recio, L.3
Waters, M.D.4
Lambert, I.B.5
Yauk, C.L.6
-
4
-
-
84870660150
-
Gene expression profiling to identify potentially relevant disease outcomes and support human health risk assessment for carbon black nanoparticle exposure
-
PMID: 23146762
-
Bourdon JA, Williams A, Kuo B, Moffat I, White PA, Halappanavar S, et al. Gene expression profiling to identify potentially relevant disease outcomes and support human health risk assessment for carbon black nanoparticle exposure. Toxicology. 2013; 303: 83-93. doi: 10.1016/j.tox.2012.10.014 PMID: 2314676
-
(2013)
Toxicology.
, vol.303
, pp. 83-93
-
-
Bourdon, J.A.1
Williams, A.2
Kuo, B.3
Moffat, I.4
White, P.A.5
Halappanavar, S.6
-
5
-
-
84887987005
-
Concordance of transcriptional and apical benchmark dose levels for conazole-induced liver effects in mice
-
PMID: 23970803
-
Bhat VS, Hester SD, Nesnow S, Eastmond DA. Concordance of transcriptional and apical benchmark dose levels for conazole-induced liver effects in mice. Toxicol Sci. 2013; 136: 205-215. doi: 10.1093/ toxsci/kft182 PMID: 23970803
-
(2013)
Toxicol Sci.
, vol.136
, pp. 205-215
-
-
Bhat, V.S.1
Hester, S.D.2
Nesnow, S.3
Eastmond, D.A.4
-
6
-
-
84878522427
-
Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species
-
Thomas R, Thomas RS, Auerbach SS, Portier CJ. Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species. PLoS ONE. 2013; 8. doi: 10.1371/journal.pone.0063308
-
(2013)
PLoS ONE.
, vol.8
-
-
Thomas, R.1
Thomas, R.S.2
Auerbach, S.S.3
Portier, C.J.4
-
7
-
-
84865723912
-
Subchronic oral exposure to benzo (a)pyrene leads to distinct transcriptomic changes in the lungs that are related to carcinogenesis
-
PMID: 22610609
-
Labib S, Yauk C, Williams A, Arlt VM, Phillips DH, White PA, et al. Subchronic oral exposure to benzo (a)pyrene leads to distinct transcriptomic changes in the lungs that are related to carcinogenesis. Toxicol Sci. 2012; 129: 213-224. doi: 10.1093/toxsci/kfs177 PMID: 22610609
-
(2012)
Toxicol Sci.
, vol.129
, pp. 213-224
-
-
Labib, S.1
Yauk, C.2
Williams, A.3
Arlt, V.M.4
Phillips, D.H.5
White, P.A.6
-
8
-
-
77049090813
-
Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning
-
PMID: 20004213
-
Auerbach SS, Shah RR, Mav D, Smith CS, Walker NJ, Vallant MK, et al. Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning. Toxicol Appl Pharmacol. 2010; 243: 300-314. doi: 10.1016/j.taap.2009.11.021 PMID: 20004213
-
(2010)
Toxicol Appl Pharmacol.
, vol.243
, pp. 300-314
-
-
Auerbach, S.S.1
Shah, R.R.2
Mav, D.3
Smith, C.S.4
Walker, N.J.5
Vallant, M.K.6
-
9
-
-
78649318364
-
Characterizing and predicting carcinogenicity and mode of action using conventional and toxicogenomics methods
-
PMID: 20399889
-
Waters MD, Jackson M, Lea I. Characterizing and predicting carcinogenicity and mode of action using conventional and toxicogenomics methods. Mutation Research-Reviews in Mutation Research. 2010; 705: 184-200. doi: 10.1016/j.mrrev.2010.04.005 PMID: 2039988
-
(2010)
Mutation Research-Reviews in Mutation Research.
, vol.705
, pp. 184-200
-
-
Waters, M.D.1
Jackson, M.2
Lea, I.3
-
10
-
-
37149025669
-
Prediction of a carcinogenic potential of rat hepatocarcinogens using toxicogenomics analysis of short-term in vivo studies
-
S0027-5107(07)00270-00279 [pii] PMID: 17689568
-
Ellinger-Ziegelbauer H, Gmuender H, Bandenburg A, Ahr HJ. Prediction of a carcinogenic potential of rat hepatocarcinogens using toxicogenomics analysis of short-term in vivo studies. Mutat Res. 2008; 637: 23-39. S0027-5107(07)00270-9 [pii]. PMID: 17689568
-
(2008)
Mutat Res.
, vol.637
, pp. 2339
-
-
Ellinger-Ziegelbauer, H.1
Gmuender, H.2
Bandenburg, A.3
Ahr, H.J.4
-
11
-
-
33847329758
-
A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays
-
kfl171 [pii] PMID: 17114358
-
Thomas RS, O'Connell TM, Pluta L, Wolfinger RD, Yang L, Page TJ. A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays. Toxicol Sci. 2007; 96: 40-46. kfl171 [pii]. PMID: 17114358
-
(2007)
Toxicol Sci.
, vol.96
, pp. 40-46
-
-
Thomas, R.S.1
O'Connell, T.M.2
Pluta, L.3
Wolfinger, R.D.4
Yang, L.5
Page, T.J.6
-
12
-
-
34347344782
-
Application of toxicogenomics to genetic toxicology risk assessment
-
PMID: 17567850
-
Thybaud V, Le Fevre AC, Boitier E. Application of toxicogenomics to genetic toxicology risk assessment. Environ Mol Mutagen. 2007; 48: 369-379. doi: 10.1002/em.20304 PMID: 1756785
-
(2007)
Environ Mol Mutagen.
, vol.48
, pp. 369-379
-
-
Thybaud, V.1
Le Fevre, A.C.2
Boitier, E.3
-
13
-
-
33747872953
-
Phenotypic anchoring of acetaminophen-induced oxidative stress with gene expression profiles in rat liver
-
PMID: 16751229
-
Powell CL, Kosyk O, Ross PK, Schoonhoven R, Boysen G, Swenberg JA, et al. Phenotypic anchoring of acetaminophen-induced oxidative stress with gene expression profiles in rat liver. Toxicol Sci. 2006; 93: 213-222. doi: 10.1093/toxsci/kfl030 PMID: 1675122
-
(2006)
Toxicol Sci.
, vol.93
, pp. 213-222
-
-
Powell, C.L.1
Kosyk, O.2
Ross, P.K.3
Schoonhoven, R.4
Boysen, G.5
Swenberg, J.A.6
-
14
-
-
84912527013
-
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
-
PMID: 25150839
-
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014; 32: 926-932. doi: 10.1038/nbt.3001 PMID: 25150839
-
(2014)
Nat Biotechnol.
, vol.32
, pp. 926-932
-
-
Wang, C.1
Gong, B.2
Bushel, P.R.3
Thierry-Mieg, J.4
Thierry-Mieg, D.5
Xu, J.6
-
15
-
-
79959958755
-
Introduction to benchmark dose methods and U.S
-
EPA's benchmark dose software (BMDS) version 2.1.1 PMID: 21034758
-
Davis JA, Gift JS, Zhao QJ. Introduction to benchmark dose methods and U.S. EPA's benchmark dose software (BMDS) version 2.1.1. Toxicol Appl Pharmacol. 2011; 254: 181-191. doi: 10.1016/j.taap. 2010.10.016 PMID: 21034758
-
(2011)
Toxicol Appl Pharmacol
, vol.254
, pp. 181-191
-
-
Davis, J.A.1
Gift, J.S.2
Zhao, Q.J.3
-
16
-
-
84893408802
-
Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments
-
PMID: 24194394
-
Black MB, Parks BB, Pluta L, Chu TM, Allen BC, Wolfinger RD, et al. Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments. Toxicol Sci. 2014; 137: 385-403. doi: 10.1093/toxsci/kft249 PMID: 24194394
-
(2014)
Toxicol Sci.
, vol.137
, pp. 385-403
-
-
Black, M.B.1
Parks, B.B.2
Pluta, L.3
Chu, T.M.4
Allen, B.C.5
Wolfinger, R.D.6
-
17
-
-
79952098323
-
Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment
-
PMID: 21097997
-
Thomas RS, Clewell HJ III, Allen BC, Wesselkamper SC, Wang NCY, Lambert JC, et al. Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment. Toxicol Sci. 2011; 120: 194-205. doi: 10.1093/toxsci/kfq355 PMID: 21097997
-
(2011)
Toxicol Sci.
, vol.120
, pp. 194-205
-
-
Thomas, R.S.1
Clewell, I.I.I.2
Allen, B.C.3
Wesselkamper, S.C.4
Wang, N.C.Y.5
Lambert, J.C.6
-
18
-
-
84880308121
-
Temporal concordance between apical and transcriptional points of departure for chemical risk assessment
-
PMID: 23596260
-
Thomas SR, Wesselkamper SC, Wang NCY, Zhao QJ, Petersen DD, Lambert JC, et al. Temporal concordance between apical and transcriptional points of departure for chemical risk assessment. Toxicol Sci. 2013; 134: 180-194. doi: 10.1093/toxsci/kft094 PMID: 23596260
-
(2013)
Toxicol Sci.
, vol.134
, pp. 180-194
-
-
Thomas, S.R.1
Wesselkamper, S.C.2
Wang, N.C.Y.3
Zhao, Q.J.4
Petersen, D.D.5
Lambert, J.C.6
-
19
-
-
84906486575
-
Transcriptional responses in the rat nasal epithelium following subchronic inhalation of naphthalene vapor
-
PMID: 24976557
-
Clewell HJ, Efremenko A, Campbell JL, Dodd DE, Thomas RS. Transcriptional responses in the rat nasal epithelium following subchronic inhalation of naphthalene vapor. Toxicol Appl Pharmacol. 2014; 280: 78-85. doi: 10.1016/j.taap.2014.06.015 PMID: 2497655
-
(2014)
Toxicol Appl Pharmacol.
, vol.280
, pp. 78-85
-
-
Clewell, H.J.1
Efremenko, A.2
Campbell, J.L.3
Dodd, D.E.4
Thomas, R.S.5
-
20
-
-
84871809302
-
STAR: Ultrafast universal RNAseq aligner
-
PMID: 23104886
-
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: Ultrafast universal RNAseq aligner. Bioinformatics. 2013; 29: 15-21. doi: 10.1093/bioinformatics/bts635 PMID: 23104886
-
(2013)
Bioinformatics.
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
-
21
-
-
84907143655
-
HTSeq-a python framework to work with high-throughput sequencing data
-
btu638 [pii]
-
Anders S, Pyl PT, Huber W. HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics. 2014. btu638 [pii].
-
(2014)
Bioinformatics
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
22
-
-
33644872577
-
-
Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, editors.: Springer New York
-
Smyth GK. Limma: Linear models for microarray data. In: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, editors.: Springer New York; 2005. pp. 397-420. doi: 10.1007/0-387-29362-0-23
-
(2005)
Limma: Linear Models for Microarray Data
, pp. 397-420
-
-
Smyth, G.K.1
-
23
-
-
84920602930
-
Gene expression analysis of livers from female B6C3F1 mice exposed to carcinogenic and non-carcinogenic doses of furan, with or without bromodeoxyuridine (BrdU) treatment
-
Webster AF, Williams A, Recio L, Yauk CL. Gene expression analysis of livers from female B6C3F1 mice exposed to carcinogenic and non-carcinogenic doses of furan, with or without bromodeoxyuridine (BrdU) treatment. Genomics Data. 2014; 2: 117-122. doi: 10.1016/j.gdata.2014.05.013
-
(2014)
Genomics Data.
, vol.2
, pp. 117-122
-
-
Webster, A.F.1
Williams, A.2
Recio, L.3
Yauk, C.L.4
-
24
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
PMID: 12538238
-
Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003; 19: 185-193. doi: 10. 1093/bioinformatics/19.2.185 PMID: 1253823
-
(2003)
Bioinformatics.
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Åstrand, M.3
Speed, T.P.4
-
25
-
-
84942880985
-
-
R: A language and environment for statistical computing... 2012;Version 2.11.1
-
R-Core-Development-Team. R: A language and environment for statistical computing... 2012;Version 2.11.1.
-
-
-
R-Core-Development-Team1
-
27
-
-
24144445705
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
PMID: 15618528
-
Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics. 2005; 6: 59-75. PMID: 15618528
-
(2005)
Biostatistics.
, vol.6
, pp. 59-75
-
-
Cui, X.1
Hwang, J.T.2
Qiu, J.3
Blades, N.J.4
Churchill, G.A.5
-
28
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Series B (Methodological)
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological). 1995; 57: 289-300.
-
(1995)
Journal of the Royal Statistical Society.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
29
-
-
38149075215
-
BMDExpress: A software tool for the benchmark dose analyses of genomic data
-
PMID: 17961223
-
Yang L, Allen BC, Thomas RS. BMDExpress: A software tool for the benchmark dose analyses of genomic data. BMC genomics. 2007; 8: 387. doi: 10.1186/1471-2164-8-387 PMID: 17961223
-
(2007)
BMC genomics.
, vol.8
, Issue.387
, pp. 8-387
-
-
Yang, L.1
Allen, B.C.2
Thomas, R.S.3
-
30
-
-
84860128867
-
Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin
-
PMID: 22298810
-
Black MB, Budinsky RA, Dombkowski A, Cukovic D, LeCluyse EL, Ferguson SS, et al. Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Sci. 2012; 127: 199-215. doi: 10.1093/toxsci/kfs069 PMID: 22298810
-
(2012)
Toxicol Sci
, vol.127
, pp. 199-215
-
-
Black, M.B.1
Budinsky, R.A.2
Dombkowski, A.3
Cukovic, D.4
LeCluyse, E.L.5
Ferguson, S.S.6
-
31
-
-
60849118640
-
Furan-induced dose-response relationships for liver cytotoxicity, cell proliferation, and tumorigenicity (furan-induced liver tumorigenicity)
-
PMID: 18809303
-
Moser GJ, Foley J, Burnett M, Goldsworthy TL, Maronpot R. Furan-induced dose-response relationships for liver cytotoxicity, cell proliferation, and tumorigenicity (furan-induced liver tumorigenicity). Experimental and Toxicologic Pathology. 2009; 61: 101-111. doi: 10.1016/j.etp.2008.06.006 PMID: 18809303
-
(2009)
Experimental and Toxicologic Pathology.
, vol.61
, pp. 101-111
-
-
Moser, G.J.1
Foley, J.2
Burnett, M.3
Goldsworthy, T.L.4
Maronpot, R.5
-
33
-
-
79960869305
-
A comparison of analog and next-generation transcriptomic tools for mammalian studies
-
PMID: 21389008
-
Roy NC, Altermann E, Park ZA, McNabb WC. A comparison of analog and next-generation transcriptomic tools for mammalian studies. Brief Funct Genomics. 2011; 10: 135-150. doi: 10.1093/bfgp/elr005 PMID: 2138900
-
(2011)
Brief Funct Genomics.
, vol.10
, pp. 135-150
-
-
Roy, N.C.1
Altermann, E.2
Park, Z.A.3
McNabb, W.C.4
-
34
-
-
84898618335
-
Comparison of RNA-seq and microarray in transcriptome profiling of activated T cells
-
PMID: 24454679
-
Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-seq and microarray in transcriptome profiling of activated T cells. PLoS One. 2014; 9: e78644. doi: 10.1371/journal.pone.0078644 PMID: 24454679
-
(2014)
PLoS One.
, vol.9
, pp. e78644
-
-
Zhao, S.1
Fung-Leung, W.P.2
Bittner, A.3
Ngo, K.4
Liu, X.5
-
35
-
-
84862802259
-
Integrating pathway-based transcriptomic data into quantitative chemical risk assessment: A five chemical case study
-
Thomas RS, Clewell HJ, Allen BC, Yang L, Healy E, Andersen ME. Integrating pathway-based transcriptomic data into quantitative chemical risk assessment: A five chemical case study. Mutat Res Genet Toxicol Environ Mutagen. 2012; 746: 135-143. doi: 10.1016/j.mrgentox.2012.01.007
-
(2012)
Mutat Res Genet Toxicol Environ Mutagen.
, vol.746
, pp. 135-143
-
-
Thomas, R.S.1
Clewell, H.J.2
Allen, B.C.3
Yang, L.4
Healy, E.5
Andersen, M.E.6
-
36
-
-
29544450979
-
Mode of action in relevance of rodent liver tumors to human cancer risk
-
PMID: 16221960
-
Holsapple MP, Pitot HC, Cohen SH, Boobis AR, Klaunig JE, Pastoor T, et al. Mode of action in relevance of rodent liver tumors to human cancer risk. Toxicol Sci. 2006; 89: 51-56. doi: 10.1093/toxsci/ kfj001 PMID: 1622196
-
(2006)
Toxicol Sci.
, vol.89
, pp. 51-56
-
-
Holsapple, M.P.1
Pitot, H.C.2
Cohen, S.H.3
Boobis, A.R.4
Klaunig, J.E.5
Pastoor, T.6
-
37
-
-
33845620001
-
The ToxCast program for prioritizing toxicity testing of environmental chemicals
-
kfl103 [pii]. PMID: 16963515
-
Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ. The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci. 2007; 95: 5-12. kfl103 [pii]. PMID: 16963515
-
(2007)
Toxicol Sci.
, vol.95
, pp. 5-12
-
-
Dix, D.J.1
Houck, K.A.2
Martin, M.T.3
Richard, A.M.4
Setzer, R.W.5
Kavlock, R.J.6
|