What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation (Q28647431)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

EVOLUTION IN MENDELIAN POPULATIONS

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Adaptive evolution of transcription factor binding sites

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Rates of spontaneous mutation

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Quantitative modeling of a gene's expression from its intergenic sequence.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Deep conservation of cis-regulatory elements in metazoans

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Genome-wide quantitative enhancer activity maps identified by STARR-seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Pattern formation by graded and uniform signals in the early Drosophila embryo

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evolutionary origins of transcription factor binding site clusters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Temporal coordination of gene networks by Zelda in the early Drosophila embryo.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Formation of regulatory modules by local sequence duplication

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

STAT is an essential activator of the zygotic genome in the early Drosophila embryo.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Modeling the evolution of a classic genetic switch

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Shadow enhancers foster robustness of Drosophila gastrulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Emergence of mammals by emergency: exaptation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evolution of regulatory sequences in 12 Drosophila species

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Dual regulation by the Hunchback gradient in the Drosophila embryo

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Deriving structure from evolution: metazoan segmentation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Sequence-level population simulations over large genomic regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Emerging principles of regulatory evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Mitotic recombination accelerates adaptation in the fungus Aspergillus nidulans

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Large-scale turnover of functional transcription factor binding sites in Drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Genetics, development and evolution of adaptive pigmentation in vertebrates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

JAK/STAT signalling in Drosophila: insights into conserved regulatory and cellular functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Sequence turnover and tandem repeats in cis-regulatory modules in drosophila

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Functional analyses of natural variation in Sp1 binding sites of a TATA-less promoter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Does diploidy increase the rate of adaptation?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evolution of Drosophila mitochondrial DNA and the history of the melanogaster subgroup

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4494070

Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Regulation of SPARC expression during early Xenopus development: evolutionary divergence and conservation of DNA regulatory elements between amphibians and mammals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

On the selection and evolution of regulatory DNA motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Different combinations of gap repressors for common stripes in Anopheles and Drosophila embryos

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Expected rates and modes of evolution of enhancer sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Rapid evolution of cis-regulatory sequences via local point mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Perspective: Complex Adaptations and the Evolution of Evolvability

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

Computational models for neurogenic gene expression in the Drosophila embryo.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVV080

An evolutionary advantage of haploidy in large yeast populations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25956793

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sex-dependent gene expression and evolution of the Drosophila transcriptome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25956793

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25956793

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/GBE/EVV080

1 reference

1 reference

1 reference

PubMed publication ID

25956793

1 reference