| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/ploscb/MosesPNILBE06 |
| P356 | DOI | 10.1371/JOURNAL.PCBI.0020130 |
| P932 | PMC publication ID | 1599766 |
| P698 | PubMed publication ID | 17040121 |
| P5875 | ResearchGate publication ID | 6755684 |
| P50 | author | Michael B. Eisen | Q3308179 |
| P2093 | author name string | Alan M Moses | |
| Daniel A Pollard | |||
| David A Nix | |||
| Mark D Biggin | |||
| Venky N Iyer | |||
| Xiao-Yong Li | |||
| P2860 | cites work | Ancient and recent positive selection transformed opioid cis-regulation in humans | Q21146079 |
| Functional evolution of a cis-regulatory module | Q21563626 | ||
| Gapped BLAST and PSI-BLAST: a new generation of protein database search programs | Q24545170 | ||
| MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model | Q24557460 | ||
| Sequence logos: a new way to display consensus sequences | Q24598387 | ||
| Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70 | Q24612004 | ||
| Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae | Q24791620 | ||
| A neutral model of transcriptome evolution | Q24796827 | ||
| Position specific variation in the rate of evolution in transcription factor binding sites | Q24803388 | ||
| Evolutionary trees from DNA sequences: A maximum likelihood approach | Q27860898 | ||
| Dating of the human-ape splitting by a molecular clock of mitochondrial DNA | Q27860908 | ||
| PAML: a program package for phylogenetic analysis by maximum likelihood | Q27861096 | ||
| Genome-wide location and function of DNA binding proteins | Q28131765 | ||
| DNA binding sites: representation and discovery | Q28144459 | ||
| Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene | Q28235451 | ||
| Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila | Q28305701 | ||
| Molecular phylogeny and divergence times of drosophilid species. | Q49195852 | ||
| Positive Selection on a Human-Specific Transcription Factor Binding Site Regulating IL4 Expression | Q57309676 | ||
| Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes | Q57818465 | ||
| LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA | Q28775786 | ||
| Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting | Q29037546 | ||
| Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli | Q29540586 | ||
| Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF | Q29547783 | ||
| Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks | Q29618476 | ||
| Transcription regulation and animal diversity | Q29618752 | ||
| Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments | Q33253683 | ||
| Evidence for stabilizing selection in a eukaryotic enhancer element. | Q33890254 | ||
| The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces. | Q33924285 | ||
| Evolution of transcriptional regulation | Q34026971 | ||
| Enrichment of regulatory signals in conserved non-coding genomic sequence | Q34098915 | ||
| Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. | Q34115908 | ||
| Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover | Q34135129 | ||
| Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. | Q34454534 | ||
| Methods for calculating the probabilities of finding patterns in sequences | Q34527638 | ||
| Evidence for redundancy but not trans factor-cis element coevolution in the regulation of Drosophila Yp genes | Q34607100 | ||
| Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans | Q34645182 | ||
| Transcriptional regulation and the evolution of development. | Q35645793 | ||
| Natural selection on gene expression | Q36522213 | ||
| The initiation of pair-rule stripes in the Drosophila blastoderm | Q37068318 | ||
| Two types of molecular evolution. Evidence from studies of interspecific hybridization | Q37453108 | ||
| Positive selection on MMP3 regulation has shaped heart disease risk | Q38337161 | ||
| A method for the rapid sequence-independent amplification of microdissected chromosomal material | Q38513770 | ||
| Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes | Q38668650 | ||
| The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos | Q39542144 | ||
| GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response element | Q39798461 | ||
| Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. | Q40464226 | ||
| Computer methods to locate signals in nucleic acid sequences | Q40466746 | ||
| The Drosophila zeste protein binds cooperatively to sites in many gene regulatory regions: implications for transvection and gene regulation | Q41095085 | ||
| Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro | Q41388831 | ||
| Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos. | Q41454917 | ||
| Searching for regulatory elements in human noncoding sequences. | Q41515830 | ||
| Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks | Q42607317 | ||
| Human-mouse genome comparisons to locate regulatory sites | Q45161206 | ||
| Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes | Q45327718 | ||
| Computational models for neurogenic gene expression in the Drosophila embryo. | Q46006127 | ||
| Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts | Q46523598 | ||
| Adaptive evolution of non-coding DNA in Drosophila | Q46601551 | ||
| Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies | Q47873575 | ||
| Expected rates and modes of evolution of enhancer sequences | Q47968467 | ||
| Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites | Q47990156 | ||
| Turnover of binding sites for transcription factors involved in early Drosophila development | Q48241765 | ||
| Rapid evolution of cis-regulatory sequences via local point mutations. | Q48347837 | ||
| P275 | copyright license | Creative Commons CC0 License | Q6938433 |
| P6216 | copyright status | copyrighted, dedicated to the public domain by copyright holder | Q88088423 |
| P4510 | describes a project that uses | Bayes' theorem | Q182505 |
| P433 | issue | 10 | |
| P921 | main subject | Drosophila | Q312154 |
| P304 | page(s) | e130 | |
| P577 | publication date | 2006-08-21 | |
| P1433 | published in | PLOS Computational Biology | Q2635829 |
| P1476 | title | Large-scale turnover of functional transcription factor binding sites in Drosophila | |
| P478 | volume | 2 |
| Q21144867 | 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage |
| Q30000980 | A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data |
| Q33388238 | A closer look at the eve stripe 2 enhancers of Drosophila and Themira |
| Q34700119 | A comparative encyclopedia of DNA elements in the mouse genome |
| Q41505408 | A functional selection model explains evolutionary robustness despite plasticity in regulatory networks |
| Q41950902 | A new systematic computational approach to predicting target genes of transcription factors |
| Q30485562 | A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2 |
| Q33419102 | Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution |
| Q28755362 | Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences |
| Q37112503 | Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes |
| Q37194766 | Architectural and functional diversity of polycomb group response elements in Drosophila |
| Q43121061 | Assessing phylogenetic motif models for predicting transcription factor binding sites |
| Q38507419 | Assigning roles to DNA regulatory motifs using comparative genomics |
| Q52685589 | Association between levels of coding sequence divergence and gene misregulation in Drosophila male hybrids. |
| Q28473313 | Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species |
| Q33303488 | Bioinformatic identification of novel putative photoreceptor specific cis-elements |
| Q36061946 | CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. |
| Q33340982 | CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing |
| Q42955158 | Cancer cell line specific co-factors modulate the FOXM1 cistrome |
| Q37215185 | Candida glabrata PHO4 is necessary and sufficient for Pho2-independent transcription of phosphate starvation genes |
| Q34537612 | Changes in selective effects over time facilitate turnover of enhancer sequences |
| Q46249001 | Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny |
| Q37607823 | Characterizing natural variation using next-generation sequencing technologies. |
| Q38248919 | Cis-regulatory elements and human evolution |
| Q92886346 | Co-opted transposons help perpetuate conserved higher-order chromosomal structures |
| Q61442417 | Comparative Genomics of Transcription Factor Binding in Drosophila |
| Q34239260 | Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution |
| Q33400098 | Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes |
| Q21092422 | Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness |
| Q30978725 | Conservation and divergence of known apicomplexan transcriptional regulons |
| Q35198311 | Conservation of transcription factor binding events predicts gene expression across species |
| Q57250268 | Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants |
| Q34695037 | De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets |
| Q22066251 | Defining functional DNA elements in the human genome |
| Q29346719 | Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria |
| Q42323461 | Dissecting sources of quantitative gene expression pattern divergence between Drosophila species |
| Q37326818 | Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis |
| Q36820801 | Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression |
| Q21563386 | Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules |
| Q35167874 | Drosophila 3' UTRs are more complex than protein-coding sequences |
| Q36287733 | Drosophila biology in the genomic age. |
| Q35834497 | Dynamics of Transcription Factor Binding Site Evolution. |
| Q34590894 | Eukaryotic transcription factor binding sites--modeling and integrative search methods |
| Q57026949 | Evidence for Stabilizing Selection Driving Mutational Turnover of Short Motifs in the Eukaryotic Complementary Sex Determiner (Csd) Protein |
| Q35542045 | Evidence that purifying selection acts on promoter sequences |
| Q21145863 | Evolution acts on enhancer organization to fine-tune gradient threshold readouts |
| Q33314598 | Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites |
| Q34790876 | Evolution of insect dorsoventral patterning mechanisms |
| Q36969577 | Evolution of primate gene expression: drift and corrective sweeps? |
| Q51636584 | Evolution of prokaryotic genes by shift of stop codons. |
| Q33398518 | Evolution of regulatory sequences in 12 Drosophila species |
| Q41955907 | Evolution of the mammalian transcription factor binding repertoire via transposable elements |
| Q45402652 | Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. |
| Q41902514 | Evolution of transcriptional regulatory circuits in bacteria |
| Q33526988 | Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers |
| Q33540999 | Evolutionary tinkering with conserved components of a transcriptional regulatory network |
| Q21284311 | Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites |
| Q61453665 | Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy |
| Q21090201 | Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression |
| Q46064782 | Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids |
| Q33417844 | Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs |
| Q33304533 | Fine-tuning enhancer models to predict transcriptional targets across multiple genomes |
| Q31036385 | Formation of regulatory modules by local sequence duplication |
| Q33285869 | Frequent gain and loss of functional transcription factor binding sites |
| Q33399874 | Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos |
| Q56985332 | Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals |
| Q42620155 | G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis |
| Q38610460 | Genetics. It's the sequence, stupid! |
| Q51416565 | Genome-wide determinants of sequence-specific DNA binding of general regulatory factors. |
| Q28756629 | Genome-wide nucleotide-level mammalian ancestor reconstruction |
| Q34629124 | Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans |
| Q37142037 | Genome-wide profiling of salt fractions maps physical properties of chromatin |
| Q27489067 | Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase |
| Q37611219 | Genotype-phenotype mapping developmental biology confronts the toolkit paradox |
| Q34637938 | H2A.Z nucleosomes enriched over active genes are homotypic |
| Q42636810 | Histone H1 binding is inhibited by histone variant H3.3. |
| Q46051331 | How transcription circuits explore alternative architectures while maintaining overall circuit output |
| Q30039538 | Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite |
| Q40972113 | Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models |
| Q37201438 | Identification of direct T-box target genes in the developing zebrafish mesoderm |
| Q37467333 | Impact of DNA-binding position variants on yeast gene expression |
| Q36971902 | Inference of natural selection from interspersed genomic elements based on polymorphism and divergence |
| Q46284251 | Insights into Epigenome Evolution from Animal and Plant Methylomes |
| Q28301622 | Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project |
| Q34382839 | Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? |
| Q91895296 | K-mer-Based Motif Analysis in Insect Species across Anopheles, Drosophila, and Glossina Genera and Its Application to Species Classification |
| Q30837902 | MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules |
| Q35935229 | Making sense of transcription networks |
| Q28749162 | Massive turnover of functional sequence in human and other mammalian genomes |
| Q33799118 | Measuring the evolutionary rewiring of biological networks |
| Q28082759 | Mechanisms of mutational robustness in transcriptional regulation |
| Q33780964 | Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs |
| Q43067706 | Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome |
| Q36779247 | Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation |
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| Q38268538 | New insights in the clockwork mechanism regulating lineage specification: Lessons from the Drosophila nervous system. |
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