ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? (Q37100332)

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scientific article published on 07 April 2008

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English	ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?	scientific article published on 07 April 2008

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scholarly article

1 reference

Europe PubMed Central

18 August 2017

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? (English)

1 reference

Europe PubMed Central

18 August 2017

Bernard Thienpont

object named as

Bernard Thienpont

3

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object named as

Peter Van Loo

1

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object named as

Stein Aerts

2

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5

object named as

Yves Moreau

1 reference

Europe PubMed Central

18 August 2017

4

object named as

Bart De Moor

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Europe PubMed Central

18 August 2017

author name string

Peter Marynen

6

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Europe PubMed Central

18 August 2017

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publication date

7 April 2008

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Europe PubMed Central

18 August 2017

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Europe PubMed Central

18 August 2017

9

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Europe PubMed Central

18 August 2017

4

1 reference

Europe PubMed Central

18 August 2017

R66

1 reference

Europe PubMed Central

18 August 2017

https://scigraph.springernature.com/pub.10.1186/gb-2008-9-4-r66

0 references

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes

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14 September 2017

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Anecdotes, data and regulatory modules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

In vivo enhancer analysis of human conserved non-coding sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

DeltaEF1 mediates TGF-beta signaling in vascular smooth muscle cell differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Gene prioritization through genomic data fusion

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14 September 2017

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.

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14 September 2017

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

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14 September 2017

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

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14 September 2017

Building the mammalian heart from two sources of myocardial cells

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14 September 2017

Cardiac neural crest

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14 September 2017

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

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14 September 2017

De novo cis-regulatory module elicitation for eukaryotic genomes

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Assessing computational tools for the discovery of transcription factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Highly conserved non-coding sequences are associated with vertebrate development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Transcriptional control in the segmentation gene network of Drosophila

1 reference

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14 September 2017

CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Applied bioinformatics for the identification of regulatory elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

A gene atlas of the mouse and human protein-encoding transcriptomes

1 reference

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14 September 2017

Detection of functional DNA motifs via statistical over-representation

1 reference

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14 September 2017

The genetic and molecular basis of congenital eye defects

1 reference

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14 September 2017

Scanning Human Gene Deserts for Long-Range Enhancers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Computational detection of cis -regulatory modules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Prediction of cell type-specific gene modules: identification and initial characterization of a core set of smooth muscle-specific genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Combinatorial Control of Smooth Muscle–Specific Gene Expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Toucan: deciphering the cis-regulatory logic of coregulated genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

TRANSFAC: transcriptional regulation, from patterns to profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

A predictive model for regulatory sequences directing liver-specific transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Coordinate positioning of MEF2 and myogenin binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

14 September 2017

Decoding human regulatory circuits

1 reference

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29 September 2017

Whole-genome discovery of transcription factor binding sites by network-level conservation

1 reference

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29 September 2017

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

1 reference

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29 September 2017

Distinguishing regulatory DNA from neutral sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

29 September 2017

Identification of regulatory regions which confer muscle-specific gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

27 June 2018

A rationale for the enhanceosome and other evolutionarily constrained enhancers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

Predicting gene expression from sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

A probabilistic method to detect regulatory modules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

3 September 2018

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2643937

4 December 2018

Identifiers

10.1186/GB-2008-9-4-R66

1 reference

Europe PubMed Central

18 August 2017

1 reference

Europe PubMed Central

18 August 2017

1 reference

Europe PubMed Central

18 August 2017

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