Bieda M - Search Results

1

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.

Cormier N, Kolisnik T, Bieda M. Cormier N, et al. Among authors: bieda m. BMC Bioinformatics. 2016 Jul 5;17(1):270. doi: 10.1186/s12859-016-1125-3. BMC Bioinformatics. 2016. PMID: 27377783 Free PMC article.

2

Workflows for microarray data processing in the Kepler environment.

Stropp T, McPhillips T, Ludäscher B, Bieda M. Stropp T, et al. Among authors: bieda m. BMC Bioinformatics. 2012 May 17;13:102. doi: 10.1186/1471-2105-13-102. BMC Bioinformatics. 2012. PMID: 22594911 Free PMC article.

3

An inhaled dose of budesonide induces genes involved in transcription and signaling in the human airways: enhancement of anti- and proinflammatory effector genes.

Leigh R, Mostafa MM, King EM, Rider CF, Shah S, Dumonceaux C, Traves SL, McWhae A, Kolisnik T, Kooi C, Slater DM, Kelly MM, Bieda M, Miller-Larsson A, Newton R. Leigh R, et al. Among authors: bieda m. Pharmacol Res Perspect. 2016 Jul 12;4(4):e00243. doi: 10.1002/prp2.243. eCollection 2016 Aug. Pharmacol Res Perspect. 2016. PMID: 28116096 Free PMC article.

4

Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters.

Yoo S, Bieda MC. Yoo S, et al. BMC Genomics. 2014 Aug 27;15(1):724. doi: 10.1186/1471-2164-15-724. BMC Genomics. 2014. PMID: 25163646 Free PMC article.

5

Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes.

Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, Lasalle JM. Yasui DH, et al. Among authors: bieda mc. Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19416-21. doi: 10.1073/pnas.0707442104. Epub 2007 Nov 27. Proc Natl Acad Sci U S A. 2007. PMID: 18042715 Free PMC article.

6

A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members.

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. Xu X, et al. Among authors: bieda m. Genome Res. 2007 Nov;17(11):1550-61. doi: 10.1101/gr.6783507. Epub 2007 Oct 1. Genome Res. 2007. PMID: 17908821 Free PMC article.

7

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.

Bieda M, Xu X, Singer MA, Green R, Farnham PJ. Bieda M, et al. Genome Res. 2006 May;16(5):595-605. doi: 10.1101/gr.4887606. Epub 2006 Apr 10. Genome Res. 2006. PMID: 16606705 Free PMC article.

8

Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors.

Acevedo LG, Bieda M, Green R, Farnham PJ. Acevedo LG, et al. Among authors: bieda m. Cancer Res. 2008 Apr 15;68(8):2641-51. doi: 10.1158/0008-5472.CAN-07-5590. Cancer Res. 2008. PMID: 18413731 Free PMC article.

9

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays.

Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ. Krig SR, et al. J Biol Chem. 2007 Mar 30;282(13):9703-9712. doi: 10.1074/jbc.M611752200. Epub 2007 Jan 26. J Biol Chem. 2007. PMID: 17259635 Free PMC article.

10

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. Johnson DS, et al. Among authors: bieda m. Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7. Genome Res. 2008. PMID: 18258921 Free PMC article.

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