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Items: 1 to 20 of 46

1.

Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs.

Sartor MA, Schnekenburger M, Marlowe JL, Reichard JF, Wang Y, Fan Y, Ma C, Karyala S, Halbleib D, Liu X, Medvedovic M, Puga A.

Environ Health Perspect. 2009 Jul;117(7):1139-46. doi: 10.1289/ehp.0800485. Epub 2009 Mar 24.

2.

Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression.

Fu Z, Malureanu L, Huang J, Wang W, Li H, van Deursen JM, Tindall DJ, Chen J.

Nat Cell Biol. 2008 Sep;10(9):1076-82. doi: 10.1038/ncb1767.

3.

LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data.

Sartor MA, Leikauf GD, Medvedovic M.

Bioinformatics. 2009 Jan 15;25(2):211-7. doi: 10.1093/bioinformatics/btn592. Epub 2008 Nov 27.

4.

The humoral immune system has a key prognostic impact in node-negative breast cancer.

Schmidt M, Böhm D, von Törne C, Steiner E, Puhl A, Pilch H, Lehr HA, Hengstler JG, Kölbl H, Gehrmann M.

Cancer Res. 2008 Jul 1;68(13):5405-13. doi: 10.1158/0008-5472.CAN-07-5206.

5.

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.

Genome Res. 2008 Sep;18(9):1518-29. doi: 10.1101/gr.077479.108. Epub 2008 Jun 24.

6.

Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures.

Tan MP, Smith EN, Broach JR, Floudas CA.

BMC Bioinformatics. 2008 Jun 6;9:268. doi: 10.1186/1471-2105-9-268.

7.

Global considerations in hierarchical clustering reveal meaningful patterns in data.

Varshavsky R, Horn D, Linial M.

PLoS One. 2008 May 21;3(5):e2247. doi: 10.1371/journal.pone.0002247.

8.

Clustering approaches to identifying gene expression patterns from DNA microarray data.

Do JH, Choi DK.

Mol Cells. 2008 Apr 30;25(2):279-88. Epub 2008 Mar 31. Review.

9.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

10.

KEGG for linking genomes to life and the environment.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y.

Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4. Epub 2007 Dec 12.

11.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21. Epub 2007 Nov 27.

12.

FOXM1, a typical proliferation-associated transcription factor.

Wierstra I, Alves J.

Biol Chem. 2007 Dec;388(12):1257-74. Review.

PMID:
18020943
13.

Hierarchical tree snipping: clustering guided by prior knowledge.

Dotan-Cohen D, Melkman AA, Kasif S.

Bioinformatics. 2007 Dec 15;23(24):3335-42. Epub 2007 Nov 7.

PMID:
17989094
14.

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.

15.

Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series.

Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris AL, Klijn JG, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C; TRANSBIG Consortium.

Clin Cancer Res. 2007 Jun 1;13(11):3207-14.

16.

Integrative molecular concept modeling of prostate cancer progression.

Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, Dhanasekaran SM, Kalyana-Sundaram S, Wei JT, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM.

Nat Genet. 2007 Jan;39(1):41-51. Epub 2006 Dec 17.

PMID:
17173048
17.

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Pruitt KD, Tatusova T, Maglott DR.

Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5. Epub 2006 Nov 27.

19.

Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset.

Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M.

Bioinformatics. 2006 Jul 15;22(14):1737-44. Epub 2006 May 18.

20.

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