PubMed

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. Epub 2008 Feb 15.PMID: 18279518 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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. Epub 2009 Aug 21.PMID: 19698106 [PubMed - indexed for MEDLINE]Related articlesFree article

Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements.

Doh ST, Zhang Y, Temple MH, Cai L.

BMC Bioinformatics. 2007 Mar 15;8:94.PMID: 17362514 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18366802 [PubMed - indexed for MEDLINE]Related articlesFree article

Organization of conserved elements near key developmental regulators in vertebrate genomes.

Woolfe A, Elgar G.

Adv Genet. 2008;61:307-38. Review.PMID: 18282512 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

A web based resource characterizing the zebrafish developmental profile of over 16,000 transcripts.

Ouyang M, Garnett AT, Han TM, Hama K, Lee A, Deng Y, Lee N, Liu HY, Amacher SL, Farber SA, Ho SY.

Gene Expr Patterns. 2008 Feb;8(3):171-80. Epub 2007 Nov 7.PMID: 18068546 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.

Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard B.

BMC Genomics. 2004 Dec 21;5(1):99.PMID: 15613238 [PubMed - indexed for MEDLINE]Related articlesFree article

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7.PMID: 18321385 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Nov 12.PMID: 19073165 [PubMed - indexed for MEDLINE]Related articles

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articles

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS.

Genome Res. 2007 May;17(5):545-55. Epub 2007 Mar 26.PMID: 17387144 [PubMed - indexed for MEDLINE]Related articlesFree article

A universal framework for regulatory element discovery across all genomes and data types.

Elemento O, Slonim N, Tavazoie S.

Mol Cell. 2007 Oct 26;28(2):337-50.PMID: 17964271 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 19549339 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2009 Oct 21.PMID: 19846439 [PubMed - indexed for MEDLINE]Related articlesFree article

RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements.

Abreu-Goodger C, Merino E.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W690-2.PMID: 15980564 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article