Gene Regulatory NetworksGene Expression ProfilingModels, GeneticComputational BiologyTranscription FactorsAlgorithmsSystems BiologyGene Expression Regulation, DevelopmentalGene Expression RegulationComputer SimulationOligonucleotide Array Sequence AnalysisModels, BiologicalSea UrchinsSignal TransductionStrongylocentrotus purpuratusEvolution, MolecularEmbryo, NonmammalianTranscription, GeneticNeural Networks (Computer)Bayes TheoremDatabases, GeneticEchinodermataMetabolic Networks and PathwaysStochastic ProcessesSoftwareGenomicsHomeodomain ProteinsMicroRNAsTranscriptomeMolecular Sequence DataCell Physiological PhenomenaBase SequenceNucleotide MotifsEndodermCluster AnalysisFeedback, PhysiologicalPromoter Regions, GeneticGenes, RegulatorGene Expression Regulation, BacterialSaccharomyces cerevisiaeModels, StatisticalMajor Histocompatibility ComplexGenes, MHC Class IIBinding SitesMutationDrosophilaGene Expression Regulation, PlantRegulatory Elements, TranscriptionalProtein Interaction MappingDrosophila ProteinsProteomeHLA-DP alpha-ChainsPhylogenyArabidopsisBody PatterningMesodermCell DifferentiationPhenotypeGenomeImmune System PhenomenaRNA, MessengerMarkov ChainsChromatin ImmunoprecipitationGenes, InsectRepressor ProteinsMultigene FamilyEctodermBiological EvolutionGastrulationClostridium butyricumCell LineageDrosophila melanogasterGene Expression Regulation, FungalDNA-Binding ProteinsNonlinear DynamicsEscherichia coliReproducibility of ResultsCiona intestinalisConserved SequencePosition-Specific Scoring MatricesVertebratesSkeletonBlastulaStarfishEmbryonic Stem CellsRegulonModels, TheoreticalGene ExpressionAmino Acid SequenceWork SimplificationLytechinusGenes, MHC Class IGenes, PlantSequence Analysis, DNASpecies SpecificityEpistasis, GeneticProtein Interaction MapsCaenorhabditis elegansNeural CrestArabidopsis Proteins