TFBSshape: a motif database for DNA shape features of transcription factor binding sites (Q37661734)

21 August 2017

TFBSshape: a motif database for DNA shape features of transcription factor binding sites (English)

1 reference

21 August 2017

0 references

Anthony Mathelier

4

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Wyeth Wasserman

object named as

Wyeth W Wasserman

5

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author name string

Lin Yang

1

1 reference

21 August 2017

Tianyin Zhou

2

1 reference

21 August 2017

Iris Dror

3

1 reference

21 August 2017

Raluca Gordân

6

1 reference

21 August 2017

Remo Rohs

7

1 reference

21 August 2017

language of work or name

English

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publication date

7 November 2013

1 reference

21 August 2017

Nucleic Acids Research

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21 August 2017

42

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21 August 2017

D148-55

1 reference

21 August 2017

Database issue

1 reference

Creative Commons Attribution 3.0 Unported

21 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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1 reference

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Covariation between homeodomain transcription factors and the shape of their DNA binding sites

23 August 2017

1 reference

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Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions

23 August 2017

1 reference

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Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

23 August 2017

1 reference

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The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals

23 August 2017

1 reference

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Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

23 August 2017

1 reference

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Probing DNA shape and methylation state on a genomic scale with DNase I.

23 August 2017

1 reference

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Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

23 August 2017

1 reference

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Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

23 August 2017

1 reference

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Probing allostery through DNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Evaluation of methods for modeling transcription factor sequence specificity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Improved predictions of transcription factor binding sites using physicochemical features of DNA.

23 August 2017

1 reference

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Improved models for transcription factor binding site identification using nonindependent interactions

23 August 2017

1 reference

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YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

23 August 2017

1 reference

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DNA shape, genetic codes, and evolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

FIMO: scanning for occurrences of a given motif

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

23 August 2017

1 reference

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UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

23 August 2017

1 reference

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

23 August 2017

1 reference

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Origins of specificity in protein-DNA recognition.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

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

23 August 2017

1 reference

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The role of DNA shape in protein-DNA recognition

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

MEME SUITE: tools for motif discovery and searching

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

A feature-based approach to modeling protein-DNA interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

DNA binding sites: representation and discovery

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Sequence logos: a new way to display consensus sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Lineages, cell types and functional states: a genomic view

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Modeling the specificity of protein-DNA interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Stability selection for regression-based models of transcription factor-DNA binding specificity.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964943

1 September 2018

Identifiers

DOI

10.1093/NAR/GKT1087

1 reference

journals/nar/YangZDMWGR14

21 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

21 August 2017

1 reference