Quantitative modeling of transcription factor binding specificities using DNA shape (Q35485439)

8 August 2017

Quantitative modeling of transcription factor binding specificities using DNA shape (English)

1 reference

8 August 2017

Tianyin Zhou

1

1 reference

8 August 2017

Ning Shen

2

1 reference

8 August 2017

Lin Yang

3

1 reference

8 August 2017

Namiko Abe

4

1 reference

8 August 2017

John Horton

5

1 reference

8 August 2017

Richard S Mann

6

1 reference

8 August 2017

Harmen J Bussemaker

7

1 reference

8 August 2017

Raluca Gordân

8

1 reference

8 August 2017

Remo Rohs

9

1 reference

8 August 2017

language of work or name

English

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publication date

9 March 2015

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Proceedings of the National Academy of Sciences of the United States of America

8 August 2017

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8 August 2017

112

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8 August 2017

4654-4659

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8 August 2017

15

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GBshape: a genome browser database for DNA shape annotations

8 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Absence of a simple code: how transcription factors read the genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Modeling the specificity of protein-DNA interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

In pursuit of design principles of regulatory sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Transcriptional enhancers: from properties to genome-wide predictions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Probing allostery through DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Evaluation of methods for modeling transcription factor sequence specificity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Atomistic modeling of protein-DNA interaction specificity: progress and applications

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Improved models for transcription factor binding site identification using nonindependent interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Determining the specificity of protein-DNA interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Diversity and complexity in DNA recognition by transcription factors

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

A feature-based approach to modeling protein-DNA interactions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

From "simple" DNA-protein interactions to the macromolecular machines of gene expression

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Predictive modeling of genome-wide mRNA expression: from modules to molecules

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

A systems approach to measuring the binding energy landscapes of transcription factors

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

DNA binding sites: representation and discovery

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Origins of specificity in protein-DNA recognition.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

The role of DNA shape in protein-DNA recognition

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4403198

26 September 2018

Identifiers

DOI

10.1073/PNAS.1422023112

1 reference

8 August 2017

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1 reference

8 August 2017

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