(Q41228232)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28898266%20AND%20SRC:MED&resulttype=core&format=json

29 March 2020

title

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28898266%20AND%20SRC:MED&resulttype=core&format=json

29 March 2020

0 references

1 reference

1 reference

1

1 reference

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29 March 2020

David S Lawrie

6

1 reference

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29 March 2020

author name string

Konstantin N Kozlov

2

1 reference

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29 March 2020

Ivan V Kulakovskiy

3

1 reference

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29 March 2020

Asif Zubair

4

1 reference

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29 March 2020

Paul Marjoram

5

1 reference

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29 March 2020

Sergey V Nuzhdin

7

1 reference

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29 March 2020

Maria G Samsonova

8

1 reference

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29 March 2020

language of work or name

English

0 references

publication date

12 September 2017

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29 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28898266%20AND%20SRC:MED&resulttype=core&format=json

29 March 2020

volume

12

1 reference

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29 March 2020

issue

9

1 reference

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29 March 2020

page(s)

e0184657

1 reference

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Creative Commons Attribution 4.0 International

29 March 2020

copyright license

start time

12 September 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Integrative approaches for large-scale transcriptome-wide association studies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Gap Gene Regulatory Dynamics Evolve along a Genotype Network.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Methods of integrating data to uncover genotype-phenotype interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Sequence-based model of gap gene regulatory network.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Evidence for deep regulatory similarities in early developmental programs across highly diverged insects

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Precise developmental gene expression arises from globally stochastic transcriptional activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Post-GWAS: where next? More samples, more SNPs or more biology?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Genome-wide inference of natural selection on human transcription factor binding sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Strong purifying selection at synonymous sites in D. melanogaster

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

A primer on thermodynamic-based models for deciphering transcriptional regulatory logic

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Bridging the genotype-phenotype gap: what does it take?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Drosophila blastoderm patterning

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Complex effects of nucleotide variants in a mammalian cis-regulatory element.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Unconstrained evolution in short introns? - an analysis of genome-wide polymorphism and divergence data from Drosophila

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Computational models for large-scale simulations of facilitated diffusion

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Methods to detect selection on noncoding DNA

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Massively parallel functional dissection of mammalian enhancers in vivo

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

The Drosophila melanogaster Genetic Reference Panel

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Evolutionary origins of transcription factor binding site clusters

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

The Drosophila gap gene network is composed of two parallel toggle switches

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

28 September 2017

The gap gene network.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Artificial selection on egg size perturbs early pattern formation in Drosophila melanogaster.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Modelling the Drosophila embryo

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Motif discovery and motif finding from genome-mapped DNase footprint data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Positive and negative selection on noncoding DNA in Drosophila simulans

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Data and theory point to mainly additive genetic variance for complex traits

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Characterization of the Drosophila segment determination morphome.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Evolution of genes and genomes on the Drosophila phylogeny

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Canalization of segmentation and its evolution in Drosophila.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Transcriptional control in the segmentation gene network of Drosophila

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

On schemes of combinatorial transcription logic

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Abundant raw material for cis-regulatory evolution in humans

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Specificity, free energy and information content in protein-DNA interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Effects of single P-element insertions on bristle number and viability in Drosophila melanogaster

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Adaptive evolution of non-coding DNA in Drosophila

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

Dynamic control of positional information in the early Drosophila embryo.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5595321

10.1371/JOURNAL.PONE.0184657

19 August 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28898266%20AND%20SRC:MED&resulttype=core&format=json

29 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28898266%20AND%20SRC:MED&resulttype=core&format=json

29 March 2020

PubMed publication ID

28898266

1 reference