(Q35113491)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

title

Quantitative modeling of a gene's expression from its intergenic sequence (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

publication date

6 March 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

9 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

page(s)

e1003467

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

9 March 2020

copyright license

start time

6 March 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

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A regulatory archipelago controls Hox genes transcription in digits

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Mapping and analysis of chromatin state dynamics in nine human cell types

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

A cis-regulatory map of the Drosophila genome.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Mathematical modeling of gene expression: a guide for the perplexed biologist

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Shadow enhancers foster robustness of Drosophila gastrulation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Discovery and characterization of chromatin states for systematic annotation of the human genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Graded dorsal and differential gene regulation in the Drosophila embryo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Combinatorial binding predicts spatio-temporal cis-regulatory activity

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Genomic views of distant-acting enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Cis-regulatory mutations in human disease

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

ChIP-seq accurately predicts tissue-specific activity of enhancers

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Shadow enhancers as a source of evolutionary novelty

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Global analysis of patterns of gene expression during Drosophila embryogenesis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Developmental mechanisms and cis-regulatory codes.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Transcriptional regulation by the numbers: models.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Logic functions of the genomic cis-regulatory code

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Modulefinder: a tool for computational discovery of cis regulatory modules

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Transcriptional control in the segmentation gene network of Drosophila

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

A global control region defines a chromosomal regulatory landscape containing the HoxD cluster

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

On schemes of combinatorial transcription logic

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Homotypic regulatory clusters in Drosophila.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Analysis and function of transcriptional regulatory elements: insights from Drosophila

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

DNA binding sites: representation and discovery

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

hairy mediates dominant repression in the Drosophila embryo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Cross-talk between different enhancer elements during mitogenic induction of the human stromelysin-1 gene

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Repression of Drosophila pair-rule segmentation genes by ectopic expression of tramtrack.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Mechanism of eve stripe formation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Cross-regulatory interactions among pair-rule genes in Drosophila

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Region-specific alleles of the Drosophila segmentation gene hairy.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Autoregulatory and gap gene response elements of the even-skipped promoter of Drosophila

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Segmental determination in Drosophila conferred by hunchback (hb), a repressor of the homeotic gene Ultrabithorax (Ubx)

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Regulation of even-skipped stripe 2 in the Drosophila embryo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.

9 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Computational models for neurogenic gene expression in the Drosophila embryo.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Going the distance: a current view of enhancer action

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

A probabilistic method to detect regulatory modules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Multiple evolutionarily conserved enhancers control expression of Eya1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

TWO-LAYER MATHEMATICAL MODELING OF GENE EXPRESSION: INCORPORATING DNA-LEVEL INFORMATION AND SYSTEM DYNAMICS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Transgenic analysis of Hoxd gene regulation during digit development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003467

Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

Decoding positional information: regulation of the pair-rule gene hairy

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945089

TFBScluster: a resource for the characterization of transcriptional regulatory networks

27 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24604095

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24604095

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003467

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

DBLP publication ID

journals/ploscb/SameeS14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

PubMed publication ID

24604095

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24604095%20AND%20SRC:MED&resulttype=core&format=json