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Items: 1 to 20 of 114

1.

Web-based tools and approaches to study long-range gene regulation in Metazoa.

Fredman D, Engström PG, Lenhard B.

Brief Funct Genomic Proteomic. 2009 Jul;8(4):231-42. doi: 10.1093/bfgp/elp023. Epub 2009 Jul 15. Review.

PMID:
19605518
2.

Computational approaches to finding and analyzing cis-regulatory elements.

Brown CT.

Methods Cell Biol. 2008;87:337-65. doi: 10.1016/S0091-679X(08)00218-5. Review.

PMID:
18485306
3.

Genomic regulatory blocks underlie extensive microsynteny conservation in insects.

Engström PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B.

Genome Res. 2007 Dec;17(12):1898-908. Epub 2007 Nov 7.

4.

A guide to the integrated application of on-line data mining tools for the inference of gene functions at the systems level.

Meier S, Gehring C.

Biotechnol J. 2008 Nov;3(11):1375-87. doi: 10.1002/biot.200800142. Review.

PMID:
18830970
5.

Web-based identification of evolutionary conserved DNA cis-regulatory elements.

Benos PV, Corcoran DL, Feingold E.

Methods Mol Biol. 2007;395:425-36.

PMID:
17993689
6.
7.

A web site for the computational analysis of yeast regulatory sequences.

van Helden J, André B, Collado-Vides J.

Yeast. 2000 Jan 30;16(2):177-87.

8.

Structural relationships between highly conserved elements and genes in vertebrate genomes.

Sun H, Skogerbø G, Wang Z, Liu W, Li Y.

PLoS One. 2008;3(11):e3727. doi: 10.1371/journal.pone.0003727. Epub 2008 Nov 14.

9.

iBarcode.org: web-based molecular biodiversity analysis.

Singer GA, Hajibabaei M.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S14. doi: 10.1186/1471-2105-10-S6-S14.

10.

DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.

Sebestyén E, Nagy T, Suhai S, Barta E.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S6. doi: 10.1186/1471-2105-10-S6-S6.

11.

FactorY, a bioinformatic resource for genome-wide promoter analysis.

Guruceaga E, Segura V, Corrales FJ, Rubio A.

Comput Biol Med. 2009 Apr;39(4):385-7. doi: 10.1016/j.compbiomed.2009.01.008. Epub 2009 Mar 9.

PMID:
19272592
12.

Mapping association between long-range cis-regulatory regions and their target genes using synteny.

Mongin E, Dewar K, Blanchette M.

J Comput Biol. 2011 Sep;18(9):1115-30. doi: 10.1089/cmb.2011.0088.

PMID:
21899419
13.

Web-based tools for studying RNA structure and function.

George AD, Tenenbaum SA.

Methods Mol Biol. 2011;703:67-86. doi: 10.1007/978-1-59745-248-9_6.

PMID:
21125484
14.

dndDB: a database focused on phosphorothioation of the DNA backbone.

Ou HY, He X, Shao Y, Tai C, Rajakumar K, Deng Z.

PLoS One. 2009;4(4):e5132. doi: 10.1371/journal.pone.0005132. Epub 2009 Apr 9.

15.

UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.

Dimitrieva S, Bucher P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D101-9. doi: 10.1093/nar/gks1092. Epub 2012 Nov 27.

16.

Unravelling the world of cis-regulatory elements.

Wang Z, Wei GH, Liu DP, Liang CC.

Med Biol Eng Comput. 2007 Aug;45(8):709-18. Epub 2007 May 31. Review.

PMID:
17541666
17.

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.

Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A.

Brief Bioinform. 2009 Sep;10(5):475-89. doi: 10.1093/bib/bbp022. Epub 2009 Apr 21. Review.

PMID:
19383843
19.

Conserved non-coding sequences and transcriptional regulation.

Strähle U, Rastegar S.

Brain Res Bull. 2008 Mar 18;75(2-4):225-30. doi: 10.1016/j.brainresbull.2007.11.010. Epub 2007 Dec 18. Review.

PMID:
18331875
20.

Big genomes facilitate the comparative identification of regulatory elements.

Peterson BK, Hare EE, Iyer VN, Storage S, Conner L, Papaj DR, Kurashima R, Jang E, Eisen MB.

PLoS One. 2009;4(3):e4688. doi: 10.1371/journal.pone.0004688. Epub 2009 Mar 4.

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