(Q42048196)

15 October 2017

Statistical detection of cooperative transcription factors with similarity adjustment (English)

1 reference

15 October 2017

0 references

3

Martin Vingron

1 reference

15 October 2017

Utz J Pape

1

1 reference

15 October 2017

Holger Klein

series ordinal

2

1 reference

15 October 2017

language of work or name

English

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publication date

13 March 2009

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15 October 2017

7

1 reference

inferred from page(s)

published in

Bioinformatics

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15 October 2017

25

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15 October 2017

16

1 reference

15 October 2017

2103-2109

1 reference

Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

A distance difference matrix approach to identifying transcription factors that regulate differential gene expression

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Computational identification of transcriptional regulatory elements in DNA sequence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

De novo cis-regulatory module elicitation for eukaryotic genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Transcriptional regulatory code of a eukaryotic genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

WebLogo: A Sequence Logo Generator

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Detection of functional DNA motifs via statistical over-representation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

The composition of the deoxyribonucleic acid of salmon sperm.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Computational detection of cis -regulatory modules.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Homotypic regulatory clusters in Drosophila.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

TRANSFAC: transcriptional regulation, from patterns to profiles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Predicting transcription factor synergism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Detection of cis-element clusters in higher eukaryotic DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Identifying regulatory networks by combinatorial analysis of promoter elements

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

DNA binding sites: representation and discovery

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Identification of regulatory regions which confer muscle-specific gene expression.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

A computational genomics approach to the identification of gene networks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

The hardwiring of development: organization and function of genomic regulatory systems.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

A statistical model for locating regulatory regions in genomic DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Coordinate positioning of MEF2 and myogenin binding sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

A new statistical model to select target sequences bound by transcription factors.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Searching for transcription factor binding site clusters: how true are true positives?

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

A self-organizing system of repressor gradients establishes segmental complexity in Drosophila.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Searching for statistically significant regulatory modules.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

New computational approaches for analysis of cis-regulatory networks.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2722994

Identifying target sites for cooperatively binding factors

17 August 2018

1 reference

12 December 2020

Using transcription factor binding site co-occurrence to predict regulatory regions

1 reference

12 December 2020

Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes

1 reference

12 December 2020

Long range interaction of cis-DNA elements mediated by architectural transcription factor Bach1

1 reference

12 December 2020

Poisson Approximation for Dependent Trials

1 reference

20 June 2022

https://opencitations.net/index/coci/api/v1/citations/10.1214/AOP/1176996359

Identifiers

DOI

10.1093/BIOINFORMATICS/BTP143

1 reference

journals/bioinformatics/PapeKV09

15 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 October 2017

PubMed publication ID

19286833

1 reference