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Results: 1 to 20 of 188

1.

CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, Stegman N, Nehls G, Yost KJ, Johnson CH, Gustafson SF, Xirasagar S, Xiao N, Huang CC, Boyer P, Chan DD, Pan Q, Gong H, Taylor J, Choi D, Rashid A, Ahmed A, Howle R, Selkirk J, Tennant R, Fostel J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D892-900. Epub 2007 Oct 25.

PMID:
17962311
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD.

Bioinformatics. 2006 Apr 1;22(7):874-82. Epub 2006 Jan 12.

PMID:
16410321
[PubMed - indexed for MEDLINE]
Free Article
3.

CEBS object model for systems biology data, SysBio-OM.

Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, Yost KJ 3rd, Yates JR 3rd, Sumner S, Xiao N, Waters MD.

Bioinformatics. 2004 Sep 1;20(13):2004-15. Epub 2004 Mar 25.

PMID:
15044233
[PubMed - indexed for MEDLINE]
Free Article
4.

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data.

Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, Frade C, Garcia A, Heinloth A, Irwin R, Madenspacher J, Merrick BA, Papoian T, Paules R, Rocca-Serra P, Sansone AS, Stevens J, Tomer K, Yang C, Waters M.

Toxicol Sci. 2005 Dec;88(2):585-601. Epub 2005 Sep 8.

PMID:
16150882
[PubMed - indexed for MEDLINE]
Free Article
5.

Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems).

Fostel JM.

Toxicol Appl Pharmacol. 2008 Nov 15;233(1):54-62. doi: 10.1016/j.taap.2008.06.015. Epub 2008 Jul 2.

PMID:
18680759
[PubMed - indexed for MEDLINE]
6.

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, Van Houten B, Walker N, Tennant R.

EHP Toxicogenomics. 2003 Jan;111(1T):15-28.

PMID:
12735106
[PubMed - indexed for MEDLINE]
7.

The genopolis microarray database.

Splendiani A, Brandizi M, Even G, Beretta O, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S21.

PMID:
17430566
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Toxicogenomic approach for assessing toxicant-related disease.

Waters MD, Olden K, Tennant RW.

Mutat Res. 2003 Nov;544(2-3):415-24. Review.

PMID:
14644344
[PubMed - indexed for MEDLINE]
9.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

Li F, Li M, Xiao Z, Zhang P, Li J, Chen Z.

BMC Bioinformatics. 2006 Jan 11;7:13.

PMID:
16403238
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The impact of new technologies on human population studies.

Waters MD, Selkirk JK, Olden K.

Mutat Res. 2003 Nov;544(2-3):349-60. Review.

PMID:
14644337
[PubMed - indexed for MEDLINE]
11.

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

Barrett T, Edgar R.

Methods Enzymol. 2006;411:352-69. Review.

PMID:
16939800
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

CanGEM: mining gene copy number changes in cancer.

Scheinin I, Myllykangas S, Borze I, Böhling T, Knuutila S, Saharinen J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D830-5. Epub 2007 Oct 11.

PMID:
17932056
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

Yi M, Mudunuri U, Che A, Stephens RM.

BMC Bioinformatics. 2009 Jun 29;10:200. doi: 10.1186/1471-2105-10-200.

PMID:
19563622
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Safety and nutritional assessment of GM plants and derived food and feed: the role of animal feeding trials.

EFSA GMO Panel Working Group on Animal Feeding Trials.

Food Chem Toxicol. 2008 Mar;46 Suppl 1:S2-70. doi: 10.1016/j.fct.2008.02.008. Epub 2008 Feb 13. Review.

PMID:
18328408
[PubMed - indexed for MEDLINE]
15.

EzArray: a web-based highly automated Affymetrix expression array data management and analysis system.

Zhu Y, Zhu Y, Xu W.

BMC Bioinformatics. 2008 Jan 24;9:46. doi: 10.1186/1471-2105-9-46.

PMID:
18218103
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Gene Aging Nexus: a web database and data mining platform for microarray data on aging.

Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D756-9. Epub 2006 Nov 7.

PMID:
17090592
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Internet-based Profiler system as integrative framework to support translational research.

Kim R, Demichelis F, Tang J, Riva A, Shen R, Gibbs DF, Mahavishno V, Chinnaiyan AM, Rubin MA.

BMC Bioinformatics. 2005 Dec 19;6:304.

PMID:
16364175
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

[Toxicogenomics as a tool for evaluation of chemical effects].

Watanabe H.

Yakugaku Zasshi. 2007 Dec;127(12):1967-74. Review. Japanese.

PMID:
18057786
[PubMed - indexed for MEDLINE]
Free Article
19.

4DXpress: a database for cross-species expression pattern comparisons.

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4.

PMID:
17916571
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.

Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, Thompson KL.

BMC Genomics. 2008 Jun 12;9:285. doi: 10.1186/1471-2164-9-285.

PMID:
18549499
[PubMed - indexed for MEDLINE]
Free PMC Article
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