Assessing computational methods of cis-regulatory module prediction (Q33769725)

29 July 2017

Assessing computational methods of cis-regulatory module prediction (English)

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29 July 2017

2

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29 July 2017

Jing Su

1

1 reference

PubMed ID

21152003

29 July 2017

Thomas A Down

series ordinal

3

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29 July 2017

2 December 2010

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PLOS Computational Biology

29 July 2017

1 reference

29 July 2017

6

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29 July 2017

12

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29 July 2017

e1001020

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Creative Commons Attribution 4.0 International

29 July 2017

start time

2 December 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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

28 July 2018

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Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies

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Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

28 July 2018

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Statistical significance of cis-regulatory modules

28 July 2018

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Experimental validation of predicted mammalian erythroid cis-regulatory modules

28 July 2018

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Long-range downstream enhancers are essential for Pax6 expression

28 July 2018

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28 July 2018

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Comparative genomics of Drosophila and human core promoters

28 July 2018

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A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

28 July 2018

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A distal enhancer and an ultraconserved exon are derived from a novel retroposon

28 July 2018

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Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

28 July 2018

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28 July 2018

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De novo discovery of a tissue-specific gene regulatory module in a chordate

28 July 2018

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Functional evolution of a cis-regulatory module

28 July 2018

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Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

28 July 2018

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Transcriptional control in the segmentation gene network of Drosophila

28 July 2018

1 reference

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

28 July 2018

1 reference

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Combining phylogenetic and hidden Markov models in biosequence analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Applied bioinformatics for the identification of regulatory elements

28 July 2018

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Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

28 July 2018

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MAVID: constrained ancestral alignment of multiple sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Conservation of regulatory elements between two species of Drosophila

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Computational detection of cis -regulatory modules.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

A computational analysis of sequence features involved in recognition of short introns

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

TRANSFAC: an integrated system for gene expression regulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Compositional differences within and between eukaryotic genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Multiple regulatory elements in the intergenic region between the alpha-fetoprotein and albumin genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Regulatory elements in the first intron contribute to transcriptional regulation of the beta 3 tubulin gene by 20-hydroxyecdysone in Drosophila Kc cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Chromosomal subunits in active genes have an altered conformation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

28 July 2018

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Searching for statistically significant regulatory modules.

21 January 2018

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A probabilistic method to detect regulatory modules.

21 January 2018

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MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

21 January 2018

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Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

21 January 2018

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REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

21 January 2018

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Using hexamers to predict cis-regulatory motifs in Drosophila.

21 January 2018

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Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

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

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors

21 January 2018

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DiRE: identifying distant regulatory elements of co-expressed genes

21 January 2018

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Identification and characterization of a conserved erythroid-specific enhancer located in intron 8 of the human 5-aminolevulinate synthase 2 gene.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

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

21 January 2018

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PReMod: a database of genome-wide mammalian cis-regulatory module predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Human and mouse gene structure: comparative analysis and application to exon prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

21 January 2018

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

21 January 2018

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Unlocking the secrets of the genome

21 January 2018

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Predicting expression patterns from regulatory sequence in Drosophila segmentation.

21 January 2018

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Expected rates and modes of evolution of enhancer sequences.

21 January 2018

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Rapid evolution of cis-regulatory sequences via local point mutations.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001020

Automatic annotation of genomic regulatory sequences by searching for composite clusters.

21 January 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2996316

10.1371/JOURNAL.PCBI.1001020

30 October 2018

Identifiers

DOI

1 reference

29 July 2017

journals/ploscb/SuTD10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

29 July 2017

1 reference

PubMed ID

21152003