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CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting

Henry R Bigelow^†, Adam S Wenick^†, Allan Wong and Oliver Hobert^*

* Corresponding author: Oliver Hobert or38@columbia.edu
† Equal contributors

BMC Bioinformatics 2004, 5:27 doi:10.1186/1471-2105-5-27

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A Caenorhabditis motif compendium for studying transcriptional gene regulation

Christoph Dieterich, Ralf J Sommer BMC Genomics 2008, 9:30 (23 January 2008)

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NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae

Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata BMC Bioinformatics 2005, 6(Suppl 4):S22 (1 December 2005)

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

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

Voichita D Marinescu, Isaac S Kohane, Alberto Riva BMC Bioinformatics 2005, 6:79 (30 March 2005)

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

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004)

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

MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.

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