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Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

Long Li^†, Qianqian Zhu^†, Xin He, Saurabh Sinha and Marc S Halfon^*

* Corresponding author: Marc S Halfon mshalfon@buffalo.edu
† Equal contributors

Genome Biology 2007, 8:R101 doi:10.1186/gb-2007-8-6-r101

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Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

Marc S Halfon, Qianqian Zhu, Elizabeth R Brennan, Yiyun Zhou BMC Genomics 2011, 12:578 (25 November 2011)

Abstract | Full text | PDF | PubMed

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs

Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn BMC Bioinformatics 2009, 10:82 (10 March 2009)

Abstract | Full text | PDF | PubMed

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Qianqian Zhu, Marc S Halfon BMC Genomics 2009, 10:9 (7 January 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

Andra Ivan, Marc S Halfon, Saurabh Sinha Genome Biology 2008, 9:R22 (28 January 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

Prediction of cis-regulatory modules ab initio, without any input of relevant motifs, is achieved with two novel methods.

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