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Items: 15

1.

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M.

Bioinformatics. 2006 Dec 15;22(24):3016-24. Epub 2006 Oct 12.

PMID:
17038339
2.

In-depth query of large genomes using tiling arrays.

Samanta MP, Tongprasit W, Stolc V.

Methods Mol Biol. 2007;377:163-74. Review.

PMID:
17634616
3.

Hidden Markov model and its applications in motif findings.

Wu J, Xie J.

Methods Mol Biol. 2010;620:405-16. doi: 10.1007/978-1-60761-580-4_13. Review.

PMID:
20652513
4.

Effects of functional bias on supervised learning of a gene network model.

Lee I, Marcotte EM.

Methods Mol Biol. 2009;541:463-75. doi: 10.1007/978-1-59745-243-4_20. Review.

PMID:
19381535
5.

Computational cluster validation in post-genomic data analysis.

Handl J, Knowles J, Kell DB.

Bioinformatics. 2005 Aug 1;21(15):3201-12. Epub 2005 May 24. Review.

PMID:
15914541
6.

Whole-genome microarrays: applications and technical issues.

Gregory BD, Belostotsky DA.

Methods Mol Biol. 2009;553:39-56. doi: 10.1007/978-1-60327-563-7_3. Review.

PMID:
19588100
7.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.

Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M.

Trends Genet. 2005 Aug;21(8):466-75. Review.

8.

Genomic location analysis by ChIP-Seq.

Barski A, Zhao K.

J Cell Biochem. 2009 May 1;107(1):11-8. doi: 10.1002/jcb.22077. Review.

9.

Mapping the genome landscape using tiling array technology.

Yazaki J, Gregory BD, Ecker JR.

Curr Opin Plant Biol. 2007 Oct;10(5):534-42. Epub 2007 Aug 20. Review.

10.

Insights from genomic profiling of transcription factors.

Farnham PJ.

Nat Rev Genet. 2009 Sep;10(9):605-16. doi: 10.1038/nrg2636. Epub 2009 Aug 11. Review.

11.

Ontology application and use at the ENCODE DCC.

Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL.

Database (Oxford). 2015 Mar 16;2015. pii: bav010. doi: 10.1093/database/bav010. Print 2015. Review.

12.

The incredible shrinking world of DNA microarrays.

Wheelan SJ, Martínez Murillo F, Boeke JD.

Mol Biosyst. 2008 Jul;4(7):726-32. doi: 10.1039/b706237k. Epub 2008 Apr 17. Review.

13.

A review of three different studies on hidden markov models for epigenetic problems: a computational perspective.

Lee KE, Park HS.

Genomics Inform. 2014 Dec;12(4):145-50. doi: 10.5808/GI.2014.12.4.145. Epub 2014 Dec 31. Review.

14.

Progress in DNA chip technology.

Li L, Ma W, Zheng W, Xu Q.

Chin Med Sci J. 2001 Mar;16(1):59-62. Review.

PMID:
12899353
15.

[Recent advances in the gene chip and its role in the post-genome era].

Uchida K.

Seikagaku. 1999 Feb;71(2):119-24. Review. Japanese. No abstract available.

PMID:
10200604

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