Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning (Q34487019)

2 August 2017

title

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning (English)

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2 August 2017

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Babak Alipanahi

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Brendan J. Frey

series ordinal

4

object named as

Brendan J Frey

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2 August 2017

Andrew Delong

2

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2 August 2017

Matthew T Weirauch

series ordinal

3

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2 August 2017

publication date

27 July 2015

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2 August 2017

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2 August 2017

volume

33

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2 August 2017

issue

8

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2 August 2017

page(s)

831-838

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describes a project that uses

2 August 2017

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DNA binding sites: representation and discovery

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https://api.crossref.org/works/10.1038%2FNBT.3300

Origins of specificity in protein-DNA recognition.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

Protein-DNA binding: complexities and multi-protein codes

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Design and analysis of ChIP-seq experiments for DNA-binding proteins

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Evaluation of methods for modeling transcription factor sequence specificity

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

A compendium of RNA-binding motifs for decoding gene regulation.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

RRM-RNA recognition: NMR or crystallography…and new findings

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

The role of RNA sequence and structure in RNA--protein interactions.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

MEME-ChIP: motif analysis of large DNA datasets

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

DNA-binding specificities of human transcription factors

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Transcriptional regulation and its misregulation in disease.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Functional analysis of LDLR promoter and 5' UTR mutations in subjects with clinical diagnosis of familial hypercholesterolemia

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

GATA-4 regulates Bcl-2 expression in ovarian granulosa cell tumors

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

TERT promoter mutations in familial and sporadic melanoma

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Highly recurrent TERT promoter mutations in human melanoma

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

A general framework for estimating the relative pathogenicity of human genetic variants

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development.

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

An RNA map predicting Nova-dependent splicing regulation

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

The RNA-binding protein TIA-1 is a novel mammalian splicing regulator acting through intron sequences adjacent to a 5' splice site

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNBT.3300

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

Diversity and complexity in DNA recognition by transcription factors

21 January 2018

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https://api.crossref.org/works/10.1038%2FNBT.3300

21 January 2018

Identifiers

DOI

10.1038/NBT.3300

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2 August 2017

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