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Xie","year":"2005","journal-title":"Nature"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1101\/gr.6902","article-title":"Discovery of regulatory elements by a computational method for phylogenetic footprinting.","volume":"12","author":"M Blanchette","year":"2002","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-540-78839-3_9","article-title":"A Fast, Alignment-free, Conservation-based Method for Transcription Factor Binding Site Discovery.","volume":"2008(RECOMB08)","author":"R Gord\u00e2n","year":"2008","journal-title":"Research in Computational Molecular Biology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4108","DOI":"10.1093\/nar\/gkn374","article-title":"Associating transcription factor-binding site motifs with target GO terms and target genes.","volume":"36","author":"M Boden","year":"2008","journal-title":"Nucleic Acids 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Nelson","year":"2003","journal-title":"Trends Cell Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2580","DOI":"10.1073\/pnas.0438000100","article-title":"Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding.","volume":"100","author":"B van Steensel","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1093\/icb\/icj054","article-title":"The divergent roles of the segmentation gene hunchback.","volume":"46","author":"J Pinnell","year":"2006","journal-title":"Integr Comp Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1101\/gad.1.10.1268","article-title":"Molecular characterization of the zerknullt region of the Antennapedia gene complex in Drosophila.","volume":"1","author":"C Rushlow","year":"1987","journal-title":"Genes 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apoptosis of differentiated motoneurons in the Drosophila embryonic central nervous system.","volume":"135","author":"A Rogulja-Ortmann","year":"2008","journal-title":"Development"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/0092-8674(91)90452-5","article-title":"Heat shock factor and the heat shock response.","volume":"65","author":"PK Sorger","year":"1991","journal-title":"Cell"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1016\/0896-6273(95)90314-3","article-title":"Defective glia induce neuronal apoptosis in the repo visual system of Drosophila.","volume":"14","author":"WC Xiong","year":"1995","journal-title":"Neuron"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1242\/dev.125.19.3753","article-title":"Signals transmitted along retinal axons in Drosophila: Hedgehog signal reception and the cell circuitry of lamina cartridge assembly.","volume":"125","author":"Z Huang","year":"1998","journal-title":"Development"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1242\/dev.125.6.1037","article-title":"Dorsotonals\/homothorax, the Drosophila homologue of meis1, interacts with extradenticle in patterning of the embryonic PNS.","volume":"125","author":"E Kurant","year":"1998","journal-title":"Development"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1242\/dev.122.4.1113","article-title":"The GAGA factor is required in the early Drosophila embryo not only for transcriptional regulation but also for nuclear division.","volume":"122","author":"KM Bhat","year":"1996","journal-title":"Development"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1093\/genetics\/139.2.781","article-title":"Characterization of the cis-regulatory region of the Drosophila homeotic gene Sex combs reduced.","volume":"139","author":"JG Gindhart Jr","year":"1995","journal-title":"Genetics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"4959","DOI":"10.1242\/dev.127.22.4959","article-title":"Characterization of a novel subset of cardiac cells and their progenitors in the Drosophila embryo.","volume":"127","author":"EJ Ward","year":"2000","journal-title":"Development"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/S0960-9822(06)00117-5","article-title":"Muscles in the Drosophila second thoracic segment are patterned independently of autonomous homeotic gene function.","volume":"7","author":"S Roy","year":"1997","journal-title":"Curr Biol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1749","DOI":"10.1002\/j.1460-2075.1988.tb03004.x","article-title":"The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo.","volume":"7","author":"T Berleth","year":"1988","journal-title":"Embo J"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nature04445","article-title":"Localized maternal orthodenticle patterns anterior and posterior in the long germ wasp Nasonia.","volume":"439","author":"JA Lynch","year":"2006","journal-title":"Nature"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1126\/science.1086807","article-title":"Gene expression profiles in the brain predict behavior in individual honey bees.","volume":"302","author":"CW Whitfield","year":"2003","journal-title":"Science"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1006\/dbio.2002.0594","article-title":"The expression of the let-7 small regulatory RNA is controlled by ecdysone during metamorphosis in Drosophila melanogaster.","volume":"244","author":"LF Sempere","year":"2002","journal-title":"Dev Biol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S0896-6273(00)00016-7","article-title":"nalyot, a mutation of the Drosophila myb-related Adf1 transcription factor, disrupts synapse formation and olfactory memory.","volume":"27","author":"J DeZazzo","year":"2000","journal-title":"Neuron"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"e154","DOI":"10.1371\/journal.pgen.0020154","article-title":"Quantitative genomics of aggressive behavior in Drosophila melanogaster.","volume":"2","author":"AC Edwards","year":"2006","journal-title":"PLoS Genet"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.1242\/dev.129.9.2259","article-title":"Broad specifies pupal development and mediates the \u2018status quo\u2019 action of juvenile hormone on the pupal-adult transformation in Drosophila and Manduca.","volume":"129","author":"X Zhou","year":"2002","journal-title":"Development"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"16068","DOI":"10.1073\/pnas.0606909103","article-title":"Genomic dissection of behavioral maturation in the honey bee.","volume":"103","author":"CW Whitfield","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/S0896-6273(04)00073-X","article-title":"Highwire regulates presynaptic BMP signaling essential for synaptic growth.","volume":"41","author":"BD McCabe","year":"2004","journal-title":"Neuron"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1101\/gad.1391006","article-title":"Genome-wide analyses identify transcription factors required for proper morphogenesis of Drosophila sensory neuron dendrites.","volume":"20","author":"JZ Parrish","year":"2006","journal-title":"Genes Dev"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/1471-2148-7-215","article-title":"The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates.","volume":"7","author":"D Porcelli","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref70","article-title":"Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia.","author":"JD Gibson","year":"2010","journal-title":"Heredity"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1080\/15216540500215572","article-title":"A Drosophila model of mitochondrial DNA replication: proteins, genes and regulation.","volume":"57","author":"R Garesse","year":"2005","journal-title":"IUBMB 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OXBOX\/REBOX in the ATPsyn beta promoter.","volume":"269","author":"Y Haraguchi","year":"1994","journal-title":"J Biol Chem"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0167-4781(02)00343-3","article-title":"Nuclear activators and coactivators in mammalian mitochondrial biogenesis.","volume":"1576","author":"RC Scarpulla","year":"2002","journal-title":"Biochim Biophys Acta"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1471-2164-9-18","article-title":"Transcriptional co-expression and co-regulation of genes coding for components of the oxidative phosphorylation system.","volume":"9","author":"C van Waveren","year":"2008","journal-title":"BMC Genomics"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"W238","DOI":"10.1093\/nar\/gkm308","article-title":"PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis.","volume":"35","author":"LW Chang","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1093\/bioinformatics\/btl565","article-title":"Predicting transcription factor affinities to DNA from a biophysical model.","volume":"23","author":"HG Roider","year":"2007","journal-title":"Bioinformatics"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1093\/bioinformatics\/17.10.878","article-title":"Detection of cis-element clusters in higher eukaryotic DNA.","volume":"17","author":"MC Frith","year":"2001","journal-title":"Bioinformatics"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1471-2105-3-30","article-title":"Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.","volume":"3","author":"N Rajewsky","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1186\/1471-2105-9-372","article-title":"Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast.","volume":"9","author":"U Keich","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/1471-2105-8-84","article-title":"Statistical tests to compare motif count exceptionalities.","volume":"8","author":"S Robin","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.","volume":"37","author":"W Huang da","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1016\/j.cell.2008.05.023","article-title":"Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.","volume":"133","author":"MB Noyes","year":"2008","journal-title":"Cell"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"D486","DOI":"10.1093\/nar\/gkl827","article-title":"FlyBase: genomes by the dozen.","volume":"35","author":"MA Crosby","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"D773","DOI":"10.1093\/nar\/gkm966","article-title":"The UCSC Genome Browser Database: 2008 update.","volume":"36","author":"D Karolchik","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.","volume":"21","author":"CM Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkm960","article-title":"The Pfam protein families database.","volume":"36","author":"RD Finn","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref88","article-title":"Proteins: Structures and Molecular Properties W. H. Freeman.","author":"TE Creighton","year":"1992"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"e27","DOI":"10.1371\/journal.pbio.0060027","article-title":"Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.","volume":"6","author":"XY Li","year":"2008","journal-title":"PLoS Biol"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1101\/gad.1509607","article-title":"Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.","volume":"21","author":"J Zeitlinger","year":"2007","journal-title":"Genes Dev"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"e1000178","DOI":"10.1371\/journal.pgen.1000178","article-title":"Stability and dynamics of polycomb target sites in Drosophila development.","volume":"4","author":"C Kwong","year":"2008","journal-title":"PLoS Genet"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000652","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T02:25:15Z","timestamp":1634783115000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000652"}},"subtitle":[],"editor":[{"given":"Wyeth W.","family":"Wasserman","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2010,1,29]]},"references-count":91,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2010,1,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000652","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,29]]}}}