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Results: 1 to 20 of 91

1.

Integrating sequence, evolution and functional genomics in regulatory genomics.

Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.

Genome Biol. 2009;10(1):202. doi: 10.1186/gb-2009-10-1-202. Epub 2009 Jan 30. Review.

PMID:
19226437
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Large-scale discovery and validation of functional elements in the human genome.

Bernstein BE, Kellis M.

Genome Biol. 2005;6(3):312. Epub 2005 Mar 1.

PMID:
15774039
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Discovery of regulatory elements in vertebrates through comparative genomics.

Prakash A, Tompa M.

Nat Biotechnol. 2005 Oct;23(10):1249-56.

PMID:
16211068
[PubMed - indexed for MEDLINE]
4.

Comparative genomics, cis-regulatory elements, and gene duplication.

Force A, Shashikant C, Stadler P, Amemiya CT.

Methods Cell Biol. 2004;77:545-61. No abstract available.

PMID:
15602931
[PubMed - indexed for MEDLINE]
5.

Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.

Meireles-Filho AC, Stark A.

Curr Opin Genet Dev. 2009 Dec;19(6):565-70. doi: 10.1016/j.gde.2009.10.006. Epub 2009 Nov 11. Review.

PMID:
19913403
[PubMed - indexed for MEDLINE]
6.

Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach.

Siddharthan R.

J Biosci. 2007 Aug;32(5):863-70. Review.

PMID:
17914228
[PubMed - indexed for MEDLINE]
Free Article
7.

Functional genomics: a holistic approach.

Mariani SM.

MedGenMed. 2003 Mar 6;5(1):19. No abstract available.

PMID:
12827080
[PubMed - indexed for MEDLINE]
Free Article
8.

Dissecting the transcription networks of a cell using computational genomics.

Li H, Wang W.

Curr Opin Genet Dev. 2003 Dec;13(6):611-6. Review.

PMID:
14638323
[PubMed - indexed for MEDLINE]
9.

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements.

Venkatesh B, Yap WH.

Bioessays. 2005 Jan;27(1):100-7. Review.

PMID:
15612032
[PubMed - indexed for MEDLINE]
10.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J.

Nat Protoc. 2008;3(10):1578-88. doi: 10.1038/nprot.2008.97.

PMID:
18802439
[PubMed - indexed for MEDLINE]
11.

Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.

Linhart C, Elkon R, Shiloh Y, Shamir R.

Cell Cycle. 2005 Dec;4(12):1788-97. Epub 2005 Dec 13.

PMID:
16294034
[PubMed - indexed for MEDLINE]
Free Article
12.

Computational identification of transcriptional regulatory elements in DNA sequence.

GuhaThakurta D.

Nucleic Acids Res. 2006 Jul 19;34(12):3585-98. Print 2006. Review.

PMID:
16855295
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The evolution of noncoding DNA: how much junk, how much func?

Castillo-Davis CI.

Trends Genet. 2005 Oct;21(10):533-6. Review.

PMID:
16098630
[PubMed - indexed for MEDLINE]
14.

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences.

Defrance M, Janky R, Sand O, van Helden J.

Nat Protoc. 2008;3(10):1589-603. doi: 10.1038/nprot.2008.98.

PMID:
18802440
[PubMed - indexed for MEDLINE]
15.

An introduction to bioinformatics.

Brzeski H.

Methods Mol Biol. 2002;187:193-208. No abstract available.

PMID:
12013746
[PubMed - indexed for MEDLINE]
16.

A primer on regression methods for decoding cis-regulatory logic.

Das D, Pellegrini M, Gray JW.

PLoS Comput Biol. 2009 Jan;5(1):e1000269. doi: 10.1371/journal.pcbi.1000269. Epub 2009 Jan 30. No abstract available.

PMID:
19180174
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Fruit fly family fun.

Sidow A, Lacroute P.

Cell. 2007 Dec 28;131(7):1222-3.

PMID:
18160030
[PubMed - indexed for MEDLINE]
Free Article
18.

Computational genomics of noncoding RNA genes.

Eddy SR.

Cell. 2002 Apr 19;109(2):137-40. Review.

PMID:
12007398
[PubMed - indexed for MEDLINE]
Free Article
19.

An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters.

Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C.

BMC Genomics. 2008 Jul 14;9:330. doi: 10.1186/1471-2164-9-330.

PMID:
18625071
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Recent developments in computational approaches for uncovering genomic homology.

Simillion C, Vandepoele K, Van de Peer Y.

Bioessays. 2004 Nov;26(11):1225-35. Review.

PMID:
15499578
[PubMed - indexed for MEDLINE]

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