Unravelling the hidden DNA structural/physical code provides novel insights on promoter location (Q37122090)

18 August 2017

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location (English)

1 reference

18 August 2017

7

1 reference

18 August 2017

Roderic Guigó i Serra

6

Roderic Guigó

0 references

Sarah Djebali

Sarah Djebali

2

0 references

Josep Maria Mercader

Josep Maria Mercader

5

0 references

Modesto Orozco

9

Modesto Orozco

1 reference

18 August 2017

Elisa Durán

1

1 reference

18 August 2017

Santi González

3

1 reference

18 August 2017

Oscar Flores

4

1 reference

18 August 2017

Montserrat Soler-López

8

1 reference

18 August 2017

language of work or name

English

0 references

publication date

12 June 2013

1 reference

18 August 2017

Nucleic Acids Research

1 reference

18 August 2017

41

1 reference

18 August 2017

7220-7230

1 reference

18 August 2017

15

1 reference

Creative Commons Attribution 3.0 Unported

18 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The UCSC Genome Browser database: extensions and updates 2013.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Landscape of transcription in human cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Evidence for transcript networks composed of chimeric RNAs in human cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

A user's guide to the encyclopedia of DNA elements (ENCODE)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

ENCODE whole-genome data in the UCSC genome browser (2011 update)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

The role of epigenetic transcription repression and DNA methyltransferases in cancer.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Structure and basal transcription complex of RNA polymerase II core promoters in the mammalian genome: an overview

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Future impact of integrated high-throughput methylome analyses on human health and disease

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

A cryptic promoter in the first exon of the SPG4 gene directs the synthesis of the 60-kDa spastin isoform

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Recent advances in the study of nucleic acid flexibility by molecular dynamics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

RNA and transcriptional modulation of gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

High-resolution mapping and characterization of open chromatin across the genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Generic eukaryotic core promoter prediction using structural features of DNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Determining promoter location based on DNA structure first-principles calculations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Simple histone acetylation plays a complex role in the regulation of gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

GENCODE: producing a reference annotation for ENCODE

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Structural and functional dynamics of human centromeric chromatin

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Core promoter-selective RNA polymerase II transcription.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

CAGE: cap analysis of gene expression

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

An abundance of bidirectional promoters in the human genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

The UCSC Table Browser data retrieval tool

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

The Ensembl genome database project

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Histone methylation versus histone acetylation: new insights into epigenetic regulation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

DNA structure in human RNA polymerase II promoters

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

TRANSFAC: a database on transcription factors and their DNA binding sites

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

The relative flexibility of B-DNA and A-RNA duplexes: database analysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Exploring polymorphisms in B-DNA helical conformations.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

DNAlive: a tool for the physical analysis of DNA at the genomic scale.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Promoter prediction analysis on the whole human genome.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Nucleosomes unfold completely at a transcriptionally active promoter.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Promoter prediction in the human genome.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3753636

Computational identification of promoters and first exons in the human genome

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23761436

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23761436

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Recognition of base sequences by regulatory proteins in procaryotes and eucaryotes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23761436

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT511

1 reference

18 August 2017

1 reference

18 August 2017

1 reference