-
1
-
-
0035213686
-
Identification of toxicologically predictive gene sets using cDNA microarrays
-
Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, Glover E, Silander T, Craven MW, Reddy JK, Jovanovich SB et al: Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol (2001) 60(6):1189-1194. Provides one of the first published examples of the application of a classification algorithm for deriving a class predictor of toxicological mechanism using a large microarray dataset.
-
(2001)
Mol Pharmacol
, vol.60
, Issue.6
, pp. 1189-1194
-
-
Thomas, R.S.1
Rank, D.R.2
Penn, S.G.3
Zastrow, G.M.4
Hayes, K.R.5
Pande, K.6
Glover, E.7
Silander, T.8
Craven, M.W.9
Reddy, J.K.10
Jovanovich, S.B.11
-
2
-
-
0142065599
-
Prediction of compound signature using high density gene expression profiling
-
Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, Tennant R, Stoll R, Barrett JC, Paules RS, Blanchard K et al: Prediction of compound signature using high density gene expression profiling. Toxicol Sci (2002) 67(2):232-240.
-
(2002)
Toxicol Sci
, vol.67
, Issue.2
, pp. 232-240
-
-
Hamadeh, H.K.1
Bushel, P.R.2
Jayadev, S.3
DiSorbo, O.4
Bennett, L.5
Li, L.6
Tennant, R.7
Stoll, R.8
Barrett, J.C.9
Paules, R.S.10
Blanchard, K.11
-
3
-
-
0037255214
-
Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base
-
Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B et al: Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base. EHP Toxicogenomics (2003) 111(1T):15-28.
-
(2003)
EHP Toxicogenomics
, vol.111
, Issue.1 T
, pp. 15-28
-
-
Waters, M.1
Boorman, G.2
Bushel, P.3
Cunningham, M.4
Irwin, R.5
Merrick, A.6
Olden, K.7
Paules, R.8
Selkirk, J.9
Stasiewicz, S.10
Weis, B.11
-
4
-
-
1542331973
-
Toxicogenomics in risk assessment: An overview of an HESI collaborative research program
-
Pennie W, Pettit SD, Lord PG: Toxicogenomics in risk assessment: An overview of an HESI collaborative research program. Environ Health Perspect (2004) 112(4):417-419.
-
(2004)
Environ Health Perspect
, vol.112
, Issue.4
, pp. 417-419
-
-
Pennie, W.1
Pettit, S.D.2
Lord, P.G.3
-
5
-
-
0042923097
-
Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: Curses, caveats, cautions
-
Somorjai RL, Dolenko B, Baumgartner R: Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: Curses, caveats, cautions. Bionformatics (2003) 19(12):1484-1491. Provides an evaluation of the effect of dataset sparsity and the curve of dimensionality in microarray data, and casting doubt on the relevance of optimal classifiers.
-
(2003)
Bionformatics
, vol.19
, Issue.12
, pp. 1484-1491
-
-
Somorjai, R.L.1
Dolenko, B.2
Baumgartner, R.3
-
6
-
-
0042822243
-
Using DNA microarrays for diagnostic and prognostic prediction
-
Simon R: Using DNA microarrays for diagnostic and prognostic prediction. Expert Rev Mol Diagnostics (2003) 3(5):587-595.
-
(2003)
Expert Rev Mol Diagnostics
, vol.3
, Issue.5
, pp. 587-595
-
-
Simon, R.1
-
7
-
-
21144462902
-
Classification of a large microarray dataset: Algorithm comparison and analysis of drug signatures
-
Natsoulis G, El Ghaoui L, Lanckriet GR, Tolley AM, Leroy F, Dunlea S, Eynon BP, Pearson CI, Tugendreich S, Jamagin K: Classification of a large microarray dataset: Algorithm comparison and analysis of drug signatures. Genome Res (2005) 15(5):724-736. Provides a comparison of the classification performance and interpretability of various linear and non-linear classifiers for pharmacological and toxicological classification of a large microarray dataset.
-
(2005)
Genome Res
, vol.15
, Issue.5
, pp. 724-736
-
-
Natsoulis, G.1
El Ghaoui, L.2
Lanckriet, G.R.3
Tolley, A.M.4
Leroy, F.5
Dunlea, S.6
Eynon, B.P.7
Pearson, C.I.8
Tugendreich, S.9
Jamagin, K.10
-
8
-
-
19644365314
-
Comparison of supervised clustering methods to discriminate genotoxic from non-genotoxic carcinogens by gene expression profiling
-
van Delft JH, van Agen E, van Breda SG, Herwijnen MH, Staal YC, Kleinjans JC: Comparison of supervised clustering methods to discriminate genotoxic from non-genotoxic carcinogens by gene expression profiling. Mutat Res (2005) 575(1-2):17-33.
-
(2005)
Mutat Res
, vol.575
, Issue.1-2
, pp. 17-33
-
-
Van Delft, J.H.1
Van Agen, E.2
Van Breda, S.G.3
Herwijnen, M.H.4
Staal, Y.C.5
Kleinjans, J.C.6
-
9
-
-
3242791873
-
Discrimination of genotoxic from non-genotoxic carcinogens by gene expression profiling
-
van Delft JH, van Agen E, van Breda SG, Herwijnen MH, Staal YC, Kleinjans JC: Discrimination of genotoxic from non-genotoxic carcinogens by gene expression profiling. Carcinogenesis(2004) 25(7):1265-1276.
-
(2004)
Carcinogenesis
, vol.25
, Issue.7
, pp. 1265-1276
-
-
Van Delft, J.H.1
Van Agen, E.2
Van Breda, S.G.3
Herwijnen, M.H.4
Staal, Y.C.5
Kleinjans, J.C.6
-
10
-
-
1542361729
-
Database development in toxicogenomics: Issues and efforts
-
Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD: Database development in toxicogenomics: Issues and efforts. Environ Health Perspect (2004) 112(4):495-505. Provides a review of the issues and efforts involved in constructing a public toxicogenomic database and data standards.
-
(2004)
Environ Health Perspect
, vol.112
, Issue.4
, pp. 495-505
-
-
Mattes, W.B.1
Pettit, S.D.2
Sansone, S.A.3
Bushel, P.R.4
Waters, M.D.5
-
11
-
-
26944440912
-
Hepatic gene expression changes throughout the day in the Fischer rat: Implications for toxicogenomic experiments
-
Boorman GA, Blackshear PE, Parker JS, Lobenhofer EK, Malarkey DE, Valiant MK, Gerken DK, Irwin RD: Hepatic gene expression changes throughout the day in the Fischer rat: Implications for toxicogenomic experiments. Toxicol Sci (2005) 86(1):185-193.
-
(2005)
Toxicol Sci
, vol.86
, Issue.1
, pp. 185-193
-
-
Boorman, G.A.1
Blackshear, P.E.2
Parker, J.S.3
Lobenhofer, E.K.4
Malarkey, D.E.5
Valiant, M.K.6
Gerken, D.K.7
Irwin, R.D.8
-
12
-
-
13444267972
-
Transcriptional profiling of the left and median liver lobes of male f344/n rats following exposure to acetaminophen
-
Irwin RD, Parker JS, Lobenhofer EK, Burka LT, Blackshear PE, Vallant MK, Lebetkin EH, Gerken DF, Boorman GA: Transcriptional profiling of the left and median liver lobes of male f344/n rats following exposure to acetaminophen. Toxicol Pathol (2005) 33(1):111-117.
-
(2005)
Toxicol Pathol
, vol.33
, Issue.1
, pp. 111-117
-
-
Irwin, R.D.1
Parker, J.S.2
Lobenhofer, E.K.3
Burka, L.T.4
Blackshear, P.E.5
Vallant, M.K.6
Lebetkin, E.H.7
Gerken, D.F.8
Boorman, G.A.9
-
13
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-Toward standards for microarray data
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T et al: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 29(4):365-371.
-
(2001)
Nat Genet
, vol.29
, Issue.4
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
Gaasterland, T.11
-
14
-
-
0037163144
-
Design and Implementation of microarray gene expression markup language (MAGE-ML)
-
RESEARCH0046
-
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M et al: Design and Implementation of microarray gene expression markup language (MAGE-ML). Genome Biol (2002) 3(9):RESEARCH0046.
-
(2002)
Genome Biol
, vol.3
, Issue.9
-
-
Spellman, P.T.1
Miller, M.2
Stewart, J.3
Troup, C.4
Sarkans, U.5
Chervitz, S.6
Bernhart, D.7
Sherlock, G.8
Ball, C.9
Lepage, M.10
Swiatek, M.11
-
15
-
-
4444360916
-
Discriminating different classes of toxicants by transcript profiling
-
Steiner G, Suter L, Boess F, Gasser R, de Vera MC, Albertini S, Ruepp S: Discriminating different classes of toxicants by transcript profiling. Environ Health Perspect (2004) 112(12):1236-1248. Describes the application of a supervised classification algorithm on a large volume of microarray data for the identification, characterization and validation of signatures to predict hepatotoxicity.
-
(2004)
Environ Health Perspect
, vol.112
, Issue.12
, pp. 1236-1248
-
-
Steiner, G.1
Suter, L.2
Boess, F.3
Gasser, R.4
De Vera, M.C.5
Albertini, S.6
Ruepp, S.7
-
16
-
-
2342564918
-
Inverse gene expression patterns for macrophage activating hepatotoxicants and peroxisome proliferators in rat liver
-
McMillian M, Nie AY, Parker JB, Leone A, Kemmerer M, Bryant S, Herlich J, Yieh L, Bittner A, Liu X, Wan J et al: Inverse gene expression patterns for macrophage activating hepatotoxicants and peroxisome proliferators in rat liver. Biochem Pharmacol (2004) 67(11):2141-2165.
-
(2004)
Biochem Pharmacol
, vol.67
, Issue.11
, pp. 2141-2165
-
-
McMillian, M.1
Nie, A.Y.2
Parker, J.B.3
Leone, A.4
Kemmerer, M.5
Bryant, S.6
Herlich, J.7
Yieh, L.8
Bittner, A.9
Liu, X.10
Wan, J.11
-
17
-
-
11144355440
-
Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro
-
Kier LD, Neft R, Tang L, Suizu R, Cook T, Onsurez K, Tiegler K, Sakai Y, Ortiz M, Nolan T, Sankar U et al: Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro. Mutat Res (2004) 649(1-2):101-113.
-
(2004)
Mutat Res
, vol.649
, Issue.1-2
, pp. 101-113
-
-
Kier, L.D.1
Neft, R.2
Tang, L.3
Suizu, R.4
Cook, T.5
Onsurez, K.6
Tiegler, K.7
Sakai, Y.8
Ortiz, M.9
Nolan, T.10
Sankar, U.11
-
18
-
-
20944433525
-
Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action
-
Ganter B, Tugendreich S, Pearson CI, Ayanoglu E, Baumhueter S, Bostian KA, Brady L, Browne LJ, Calvin JT, Day GJ, Breckenridge N et a: Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. J Biotechnol (2005) 119(3):219-244. Describes the methods used to construct, standardize and control quality in one of the largest chemogenomic databases for drug discovery and development applications.
-
(2005)
J Biotechnol
, vol.119
, Issue.3
, pp. 219-244
-
-
Ganter, B.1
Tugendreich, S.2
Pearson, C.I.3
Ayanoglu, E.4
Baumhueter, S.5
Bostian, K.A.6
Brady, L.7
Browne, L.J.8
Calvin, J.T.9
Day, G.J.10
Breckenridge, N.11
-
19
-
-
22244444195
-
Preclinical drug safety analysis by chemogenomic profiling in the liver
-
Fielden MR, Pearson C, Brennan R, Kolaja KL: Preclinical drug safety analysis by chemogenomic profiling in the liver. Am J Pharmacogenomics (2005) 5(3):161-171.
-
(2005)
Am J Pharmacogenomics
, vol.5
, Issue.3
, pp. 161-171
-
-
Fielden, M.R.1
Pearson, C.2
Brennan, R.3
Kolaja, K.L.4
-
20
-
-
17844378132
-
A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity
-
Fielden MR, Eynon BP, Natsoulis G, Jamagin K, Banas D, Kolaja KL: A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicol Pathol (2005) 33(6):675-683. Provides the first published example demonstrating the derivation and validation of a signature that predicts histopathological renal tubular injury weeks before it is detected histologically.
-
(2005)
Toxicol Pathol
, vol.33
, Issue.6
, pp. 675-683
-
-
Fielden, M.R.1
Eynon, B.P.2
Natsoulis, G.3
Jamagin, K.4
Banas, D.5
Kolaja, K.L.6
-
21
-
-
29744452906
-
-
Computer Science Division (EECS), University of California, Berkeley, CA, USA
-
El Ghaoui L, Lanckriet GRG, Natsoulis G: Robust classifiers with interval data: Computer Science Division (EECS), University of California, Berkeley, CA, USA (2003). http://www.eecs.berkeley.edu/Pubs/TechRpts/2003/CSD-03-1279.pdf
-
(2003)
Robust Classifiers with Interval Data
-
-
El Ghaoui, L.1
Lanckriet, G.R.G.2
Natsoulis, G.3
-
22
-
-
20944440313
-
Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers
-
Thukral SK, Nordone PJ, Hu R, Sullivan L, Galambos E, Fitzpatrick VD, Healy L, Bass MB, Cosenza ME, Afshari CA: Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers. Toxicol Pathol (2005) 33(3):343-355.
-
(2005)
Toxicol Pathol
, vol.33
, Issue.3
, pp. 343-355
-
-
Thukral, S.K.1
Nordone, P.J.2
Hu, R.3
Sullivan, L.4
Galambos, E.5
Fitzpatrick, V.D.6
Healy, L.7
Bass, M.B.8
Cosenza, M.E.9
Afshari, C.A.10
-
23
-
-
0034602774
-
Knowledge-based analysis of microarray gene expression data by using support vector machines
-
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA (2000) 97(1):262-267.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.1
, pp. 262-267
-
-
Brown, M.P.1
Grundy, W.N.2
Lin, D.3
Cristianini, N.4
Sugnet, C.W.5
Furey, T.S.6
Ares Jr., M.7
Haussler, D.8
-
24
-
-
12144290763
-
Identification of putative gene-based markers of renal toxicity
-
Amin RP, Vickers AE, Sistare F, Thompson KL, Roman RJ, Lawton M, Kramer J, Hamadeh HK, Collins J, Grissom S, Bennett L et al: Identification of putative gene-based markers of renal toxicity. Environ Health Perspect (2004) 112(4):465-479.
-
(2004)
Environ Health Perspect
, vol.112
, Issue.4
, pp. 465-479
-
-
Amin, R.P.1
Vickers, A.E.2
Sistare, F.3
Thompson, K.L.4
Roman, R.J.5
Lawton, M.6
Kramer, J.7
Hamadeh, H.K.8
Collins, J.9
Grissom, S.10
Bennett, L.11
-
25
-
-
19644386887
-
Assessment of hepatotoxic liabilities by transcript profiling
-
Ruepp S, Boess F, Suter L, de Vera MC, Steiner G, Steele T, Weiser T, Albertini S: Assessment of hepatotoxic liabilities by transcript profiling. Toxicol Appl Pharmacol(2005) 207(2 Suppl):161-170.
-
(2005)
Toxicol Appl Pharmacol
, vol.207
, Issue.2 SUPPL.
, pp. 161-170
-
-
Ruepp, S.1
Boess, F.2
Suter, L.3
De Vera, M.C.4
Steiner, G.5
Steele, T.6
Weiser, T.7
Albertini, S.8
-
26
-
-
0038172423
-
Gene expression in two hepatic cell lines, cultured primary hepatocytes and liver slices compared to the in vivo liver gene expression in rats: Possible implications for toxicogenomics use of in vitro systems
-
Boess F, Kamber M, Romer S, Gasser R, Muller D, Albertini S, Suter L: Gene expression in two hepatic cell lines, cultured primary hepatocytes and liver slices compared to the in vivo liver gene expression in rats: Possible implications for toxicogenomics use of in vitro systems. Toxicol Sci (2003) 73(2):386-402.
-
(2003)
Toxicol Sci
, vol.73
, Issue.2
, pp. 386-402
-
-
Boess, F.1
Kamber, M.2
Romer, S.3
Gasser, R.4
Muller, D.5
Albertini, S.6
Suter, L.7
-
27
-
-
0035977845
-
Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity
-
Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG: Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett (2001) 120(1-3):359-368.
-
(2001)
Toxicol Lett
, vol.120
, Issue.1-3
, pp. 359-368
-
-
Waring, J.F.1
Ciurlionis, R.2
Jolly, R.A.3
Heindel, M.4
Ulrich, R.G.5
-
28
-
-
13644258653
-
A toxicogenomic approach to drug-induced phospholipidosis: Analysis of its induction mechanism and establishment of a novel in vitro screening system
-
Sawada H, Takami K, Asahi S: A toxicogenomic approach to drug-induced phospholipidosis: Analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol Sci (2005) 83(2):282-292. Describes the identification of 12 genes in HepG2 cells that diagnose the ability of a compound to induce phospholipidosis, and discusses validation and application in an in vitro screening assay.
-
(2005)
Toxicol Sci
, vol.83
, Issue.2
, pp. 282-292
-
-
Sawada, H.1
Takami, K.2
Asahi, S.3
-
29
-
-
9444256954
-
Toxicogenomics and systems toxicology: Aims and prospects
-
Waters MD, Fostel JM: Toxicogenomics and systems toxicology: Aims and prospects. Nat Rev Genet (2004) 5(12):936-948.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.12
, pp. 936-948
-
-
Waters, M.D.1
Fostel, J.M.2
|