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Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.


PRE-1, a cis element sufficient to enhance cone- and rod- specific expression in differentiating zebrafish photoreceptors.

Morrissey ME, Shelton S, Brockerhoff SE, Hurley JB, Kennedy BN.

BMC Dev Biol. 2011 Jan 24;11:3. doi: 10.1186/1471-213X-11-3.


Development of a novel data mining tool to find cis-elements in rice gene promoter regions.

Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S.

BMC Plant Biol. 2008 Feb 27;8:20. doi: 10.1186/1471-2229-8-20.


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. doi: 10.1186/1471-2105-9-455.


Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.

Liseron-Monfils C, Lewis T, Ashlock D, McNicholas PD, Fauteux F, Strömvik M, Raizada MN.

BMC Plant Biol. 2013 Mar 15;13:42. doi: 10.1186/1471-2229-13-42.


Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.


PRECISE: software for prediction of cis-acting regulatory elements.

Trindade LM, van Berloo R, Fiers M, Visser RG.

J Hered. 2005 Sep-Oct;96(5):618-22. Epub 2005 Aug 31.


Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.

Fauteux F, Strömvik MV.

BMC Plant Biol. 2009 Oct 20;9:126. doi: 10.1186/1471-2229-9-126.


CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.

Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T.

Genome Res. 2010 Nov;20(11):1512-25. doi: 10.1101/gr.109405.110. Epub 2010 Aug 6.


Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription.

Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Dröge-Laser W.

BMC Plant Biol. 2012 Aug 1;12:125. doi: 10.1186/1471-2229-12-125.


Bounded search for de novo identification of degenerate cis-regulatory elements.

Carlson JM, Chakravarty A, Khetani RS, Gross RH.

BMC Bioinformatics. 2006 May 15;7:254.


Isolation of a zebrafish rod opsin promoter to generate a transgenic zebrafish line expressing enhanced green fluorescent protein in rod photoreceptors.

Kennedy BN, Vihtelic TS, Checkley L, Vaughan KT, Hyde DR.

J Biol Chem. 2001 Apr 27;276(17):14037-43. Epub 2001 Jan 18.


In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70.


OSCAR: one-class SVM for accurate recognition of cis-elements.

Jiang B, Zhang MQ, Zhang X.

Bioinformatics. 2007 Nov 1;23(21):2823-8. Epub 2007 Oct 5.


Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M.

BMC Bioinformatics. 2005 May 2;6:110.


Deciphering the contribution of known cis-elements in the mouse cone arrestin gene to its cone-specific expression.

Pickrell SW, Zhu X, Wang X, Craft CM.

Invest Ophthalmol Vis Sci. 2004 Nov;45(11):3877-84.


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