(Q30530281)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

title

Improved predictions of transcription factor binding sites using physicochemical features of DNA (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

author name string

Mark Maienschein-Cline

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Aaron R Dinner

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Fangping Mu

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

language of work or name

English

0 references

publication date

25 August 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

volume

40

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

issue

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

page(s)

e175

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 3.0 Unported

12 February 2020

copyright license

start time

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

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Predicting target DNA sequences of DNA-binding proteins based on unbound structures

20 June 2018

1 reference

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Direct inference of protein-DNA interactions using compressed sensing methods

20 June 2018

1 reference

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A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

20 June 2018

1 reference

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Transient Hoogsteen base pairs in canonical duplex DNA.

20 June 2018

1 reference

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Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

20 June 2018

1 reference

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Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Determining the specificity of protein-DNA interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

ChIPing the cistrome of PXR in mouse liver

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Synthetic biology: applications come of age

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Origins of specificity in protein-DNA recognition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

The role of DNA shape in protein-DNA recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Insights from genomic profiling of transcription factors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

CHARMM: the biomolecular simulation program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Diversity and complexity in DNA recognition by transcription factors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Local DNA topography correlates with functional noncoding regions of the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Signatures of Protein-DNA Recognition in Free DNA Binding Sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Prediction of TF target sites based on atomistic models of protein-DNA complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Predicting transcription factor specificity with all-atom models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Species-specific transcription in mice carrying human chromosome 21

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Functional characterization of the Escherichia coli Fis-DNA binding sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

A review of feature selection techniques in bioinformatics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

A chromatin landmark and transcription initiation at most promoters in human cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Construction of a genome-scale structural map at single-nucleotide resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genome-wide mapping of in vivo protein-DNA interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

High-resolution profiling of histone methylations in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Connecting protein structure with predictions of regulatory sites.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

A genomic code for nucleosome positioning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

From genomics to chemical genomics: new developments in KEGG

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Protein-DNA binding specificity predictions with structural models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Ab initio prediction of transcription factor targets using structural knowledge

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Protein-DNA recognition patterns and predictions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

MatInspector and beyond: promoter analysis based on transcription factor binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Genomic maps and comparative analysis of histone modifications in human and mouse

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Toward an atomistic model for predicting transcription-factor binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

WebLogo: A Sequence Logo Generator

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Detection of functional DNA motifs via statistical over-representation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

A biophysical approach to transcription factor binding site discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

MATCH: A tool for searching transcription factor binding sites in DNA sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

TRANSFAC: transcriptional regulation, from patterns to profiles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Additivity in protein-DNA interactions: how good an approximation is it?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

DNA binding sites: representation and discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

RegulonDB: a database on transcriptional regulation in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Information analysis of Fis binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Sequence logos: a new way to display consensus sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

The Fis protein: it's not just for DNA inversion anymore

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Using hydroxyl radical to probe DNA structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3526315

Engineering static and dynamic control of synthetic pathways

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS771

Comparative analysis of methods for representing and searching for transcription factor binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS771

Biophysics: Flipping Watson and Crick.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS771

Probabilistic code for DNA recognition by proteins of the EGR family.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS771

21 January 2018

Identifiers

DOI

10.1093/NAR/GKS771

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22923524%20AND%20SRC:MED&resulttype=core&format=json