(Q40431723)

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CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting

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scholarly article

1 reference

Europe PubMed Central

20 September 2017

CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting (English)

1 reference

Europe PubMed Central

20 September 2017

1 reference

based on heuristic

inferred from title

Eugène Berezikov

1

1 reference

Europe PubMed Central

20 September 2017

object named as

Victor Guryev

2

0 references

author name string

Ronald H A Plasterk

3

1 reference

Europe PubMed Central

20 September 2017

Edwin Cuppen

4

1 reference

Europe PubMed Central

20 September 2017

publication date

12 December 2003

1 reference

Europe PubMed Central

20 September 2017

Genome Research

1 reference

Europe PubMed Central

20 September 2017

14

1 reference

Europe PubMed Central

20 September 2017

170-178

1 reference

Europe PubMed Central

20 September 2017

1

1 reference

Europe PubMed Central

20 September 2017

Comparative genomics: genome-wide analysis in metazoan eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 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=314294

22 September 2017

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Human-mouse alignments with BLASTZ

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

AVID: A global alignment program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 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=314294

22 September 2017

Ensembl 2002: accommodating comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

The Bioperl toolkit: Perl modules for the life sciences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

TFBS: Computational framework for transcription factor binding site analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

ChIP-chip: a genomic approach for identifying 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=314294

22 September 2017

rVista for comparative sequence-based discovery of functional 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=314294

22 September 2017

Discovery of regulatory elements by a computational method for phylogenetic footprinting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Active conservation of noncoding sequences revealed by three-way species comparisons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

PipMaker--a web server for aligning two genomic DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Affinity purification of sequence-specific DNA binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Nuclease hypersensitive sites in chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Multiple sequence alignment with hierarchical clustering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

22 September 2017

Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

15 June 2018

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

15 June 2018

Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

20 August 2018

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

20 August 2018

Human-mouse genome comparisons to locate regulatory sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

20 August 2018

DIALIGN: finding local similarities by multiple sequence alignment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

20 August 2018

Bayesian adaptive sequence alignment algorithms.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=314294

20 August 2018

Identification of essential sequence motifs in the node/notochord enhancer of Foxa2 (Hnf3beta) gene that are conserved across vertebrate species

1 reference

https://pubmed.ncbi.nlm.nih.gov/14672977

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifying functional elements by comparative DNA sequence analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/14672977

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/14672977

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.1642804

1 reference

Europe PubMed Central

20 September 2017

1 reference

Europe PubMed Central

20 September 2017

1 reference

Europe PubMed Central

20 September 2017

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