Enhanced regulatory sequence prediction using gapped k-mer features (Q35208332)

7 August 2017

Enhanced regulatory sequence prediction using gapped k-mer features (English)

1 reference

7 August 2017

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1

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Dongwon Lee

object named as

Dongwon Lee

series ordinal

2

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author name string

Morteza Mohammad-Noori

series ordinal

3

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PubMed ID

25033408

7 August 2017

Michael A Beer

series ordinal

4

1 reference

7 August 2017

17 July 2014

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PLOS Computational Biology

7 August 2017

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7 August 2017

10

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7 August 2017

7

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7 August 2017

e1003711

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Creative Commons Attribution 4.0 International

7 August 2017

start time

17 July 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Robust k-mer frequency estimation using gapped k-mers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Evaluation of methods for modeling transcription factor sequence specificity

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Sequence and chromatin determinants of cell-type-specific transcription factor binding

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Systematic localization of common disease-associated variation in regulatory DNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Architecture of the human regulatory network derived from ENCODE data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Discriminative prediction of mammalian enhancers from DNA sequence.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

MEME-ChIP: motif analysis of large DNA datasets

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Genomewide association studies and assessment of the risk of disease

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Heritable individual-specific and allele-specific chromatin signatures in humans

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

ChIP-seq accurately predicts tissue-specific activity of enhancers

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Model-based analysis of ChIP-Seq (MACS)

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Cohesins functionally associate with CTCF on mammalian chromosome arms

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Quantifying similarity between motifs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

ROCR: visualizing classifier performance in R

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

The Ets family contains transcriptional activators and repressors involved in angiogenesis.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

DNA binding sites: representation and discovery

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Predicting gene expression from sequence.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Mismatch string kernels for discriminative protein classification

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

The spectrum kernel: a string kernel for SVM protein classification.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4102394

Accuracy and Stability of Numerical Algorithms

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003711

A training algorithm for optimal margin classifiers

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003711

A discriminative framework for detecting remote protein homologies

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25033408

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003711

1 reference

journals/ploscb/GhandiLNB14

7 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

7 August 2017

1 reference

PubMed ID

25033408