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Results: 1 to 20 of 84

1.

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes.

Engström PG, Fredman D, Lenhard B.

Genome Biol. 2008;9(2):R34. doi: 10.1186/gb-2008-9-2-r34. Epub 2008 Feb 15.

PMID:
18279518
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
17989259
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes.

Dong X, Fredman D, Lenhard B.

Genome Biol. 2009;10(8):R86. doi: 10.1186/gb-2009-10-8-r86. Epub 2009 Aug 21.

PMID:
19698106
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

PMID:
18366802
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The identification and functional characterisation of conserved regulatory elements in developmental genes.

Dickmeis T, Müller F.

Brief Funct Genomic Proteomic. 2005 Feb;3(4):332-50. Review.

PMID:
15814024
[PubMed - indexed for MEDLINE]
Free Article
6.

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Ovcharenko I, Nobrega MA, Loots GG, Stubbs L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6.

PMID:
15215395
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.

Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS.

Dev Biol. 2009 Mar 15;327(2):526-40. doi: 10.1016/j.ydbio.2008.10.044. Epub 2008 Nov 12.

PMID:
19073165
[PubMed - indexed for MEDLINE]
Free Article
8.

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout.

Moghadam HK, Ferguson MM, Danzmann RG.

BMC Genomics. 2009 Jun 23;10:278. doi: 10.1186/1471-2164-10-278.

PMID:
19549339
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.

Lavigne R, Sun WD, Volckaert G.

Bioinformatics. 2004 Mar 22;20(5):629-35. Epub 2004 Jan 22.

PMID:
15033869
[PubMed - indexed for MEDLINE]
Free Article
10.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.

Genomics. 2008 Jul;92(1):65-74. doi: 10.1016/j.ygeno.2008.04.003. Epub 2008 Jun 3.

PMID:
18511233
[PubMed - indexed for MEDLINE]
Free Article
11.

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
[PubMed - indexed for MEDLINE]
Free Article
12.

G-compass: a web-based comparative genome browser between human and other vertebrate genomes.

Kawahara Y, Sakate R, Matsuya A, Murakami K, Sato Y, Zhang H, Gojobori T, Itoh T, Imanishi T.

Bioinformatics. 2009 Dec 15;25(24):3321-2. doi: 10.1093/bioinformatics/btp594. Epub 2009 Oct 21.

PMID:
19846439
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
14.

Using the Ensembl genome server to browse genomic sequence data.

Fernández-Suárez XM, Schuster MK.

Curr Protoc Bioinformatics. 2007 Jan;Chapter 1:Unit 1.15. doi: 10.1002/0471250953.bi0115s16.

PMID:
18428779
[PubMed - indexed for MEDLINE]
15.

cis-regulatory region analysis using BEARR.

Vega VB.

Methods Mol Biol. 2006;338:119-27.

PMID:
16888354
[PubMed - indexed for MEDLINE]
16.

RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

Thongjuea S, Ruanjaichon V, Bruskiewich R, Vanavichit A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D996-1000. doi: 10.1093/nar/gkn638. Epub 2008 Sep 27.

PMID:
18820292
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.

Qu Y, Brown P, Barbe JF, Puljic M, Merino E, Adkins RM, Lovley DR, Krushkal J.

OMICS. 2009 Oct;13(5):439-49. doi: 10.1089/omi.2009.0081.

PMID:
19792871
[PubMed - indexed for MEDLINE]
18.

Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.

Elnitski L, King D, Hardison RC.

Methods Mol Biol. 2006;338:91-103.

PMID:
16888352
[PubMed - indexed for MEDLINE]
19.

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A.

Genome Res. 2007 Jun;17(6):960-4.

PMID:
17568012
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes.

Mrázek J, Xie S, Guo X, Srivastava A.

Bioinformatics. 2008 Apr 15;24(8):1041-8. doi: 10.1093/bioinformatics/btn077. Epub 2008 Feb 26.

PMID:
18304933
[PubMed - indexed for MEDLINE]
Free Article

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