(Q34318696)

1 August 2017

title

Towards a theoretical understanding of false positives in DNA motif finding (English)

1 reference

1 August 2017

Amin Zia

1

1 reference

1 August 2017

Alan M Moses

series ordinal

2

1 reference

1 August 2017

publication date

27 June 2012

1 reference

1 August 2017

1 reference

1 August 2017

volume

13

1 reference

1 August 2017

page(s)

151

1 reference

Creative Commons Attribution 2.0 Generic

1 August 2017

copyright license

start time

27 June 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

Factoring local sequence composition in motif significance analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

A survey of DNA motif finding algorithms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Improved benchmarks for computational motif discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Connecting protein structure with predictions of regulatory sites.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Discovering motifs in ranked lists of DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Informative priors based on transcription factor structural class improve de novo motif discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

MEME: discovering and analyzing DNA and protein sequence motifs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Extensive low-affinity transcriptional interactions in the yeast genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Limitations and potentials of current motif discovery algorithms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Assessing computational tools for the discovery of transcription factor binding sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Transcriptional regulatory code of a eukaryotic genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Applied bioinformatics for the identification of regulatory elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Finding functional sequence elements by multiple local alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Combining phylogenetic data with co-regulated genes to identify regulatory motifs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Sequencing and comparison of yeast species to identify genes and regulatory elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Subtle motifs: defining the limits of motif finding algorithms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Regulatory element detection using correlation with expression.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

DNA binding sites: representation and discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Methods for calculating the probabilities of finding patterns in sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR.

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

Computing exact P-values for DNA motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

GIMSAN: a Gibbs motif finder with significance analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

Information content of individual genetic sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-151

A conservative parametric approach to motif significance analysis.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

Computing the P-value of the information content from an alignment of multiple sequences

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436861

An algorithm for finding signals of unknown length in DNA sequences

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22738169

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-13-151

1 reference

1 August 2017

DBLP publication ID

journals/bmcbi/ZiaM12

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1027479259

0 references

Fatcat ID

release_f4yqh2lnmfb7hdq4ai7b4jtk4e

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/f4yqh2lnmfb7hdq4ai7b4jtk4e

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3436861

1 reference

1 August 2017

1 reference