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Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling)

  • Published:2012-09-14 Issue:1 Volume:13 Page:
  • ISSN:1471-2105
  • Container-title:BMC Bioinformatics
  • language:en
  • Short-container-title:BMC Bioinformatics

Author:

Beuf Kristof De,Pipelers Peter,Andriankaja Megan,Thas Olivier,Inzé Dirk,Crainiceanu Ciprian,Clement Lieven

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Reference41 articles.

1. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MMH, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, et al: Empirical analysis of transcriptional activity in the arabidopsis genome. Science. 2003, 302 (5646): 842-846.

2. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR: Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 2004, 14: 331-342.

3. Schadt E, Edwards S, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart K, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres R, Johnson J, Armour C, Garrett-Engele P, Tsinoremas N, Shoemaker D: A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol. 2004, 5 (10): R73.

4. Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC, Hegeman A, Nelson C, Rancour D, Bednarek S, Ulrich EL, Zhao Q, Wrobel RL, Newman CS, Fox BG, Phillips GN, Markley JL, Sussman MR: Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Nat Acad Sci U S A. 2005, 102 (12): 4453-4458.

5. Toyoda T, Shinozaki K: Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. Plant J. 2005, 43 (4): 611-621.
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