A novel Bayesian DNA motif comparison method for clustering and retrieval (Q33332464)

25 July 2017

A novel Bayesian DNA motif comparison method for clustering and retrieval (English)

1 reference

25 July 2017

4

1 reference

25 July 2017

3

Hanah Margalit

0 references

Tommy Kaplan

object named as

Tommy Kaplan

series ordinal

2

0 references

author name string

Naomi Habib

series ordinal

1

1 reference

25 July 2017

29 February 2008

1 reference

PLOS Computational Biology

25 July 2017

1 reference

25 July 2017

4

1 reference

25 July 2017

2

1 reference

25 July 2017

e1000010

1 reference

Creative Commons Attribution 4.0 International

25 July 2017

start time

29 February 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

STAMP: a web tool for exploring DNA-binding motif similarities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Quantifying similarity between motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Practical strategies for discovering regulatory DNA sequence motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Protein-DNA binding specificity predictions with structural models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Ab initio prediction of transcription factor targets using structural knowledge

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Direct activation of genes involved in intracellular iron use by the yeast iron-responsive transcription factor Aft2 without its paralog Aft1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

T-Reg Comparator: an analysis tool for the comparison of position weight matrices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Transcriptional regulatory code of a eukaryotic genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Local feature frequency profile: a method to measure structural similarity in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

The Gene Ontology (GO) database and informatics resource

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Toucan: deciphering the cis-regulatory logic of coregulated genes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

TRANSFAC: transcriptional regulation, from patterns to profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

The UCSC Genome Browser Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Additivity in protein-DNA interactions: how good an approximation is it?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

A second iron-regulatory system in yeast independent of Aft1p

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Genomic expression programs in the response of yeast cells to environmental changes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

DNA binding sites: representation and discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Cluster analysis and display of genome-wide expression patterns

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Methods and statistics for combining motif match scores

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Exploring the metabolic and genetic control of gene expression on a genomic scale

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Combinatorial control required for the specificity of yeast MAPK signaling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Searching databases of conserved sequence regions by aligning protein multiple-alignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

The value of prior knowledge in discovering motifs with MEME

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Critical comparison of consensus methods for molecular sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2265534

Comparative analysis of methods for representing and searching for transcription factor binding sites.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

Fus3-regulated Tec1 degradation through SCFCdc4 determines MAPK signaling specificity during mating in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

Rst1 and Rst2 are required for the a/alpha diploid cell type in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

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/10.1371%2FJOURNAL.PCBI.1000010

CIS: compound importance sampling method for protein-DNA binding site p-value estimation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

Three yeast proteome databases: YPD, PombePD, and Ca1PD (MycoPathPD)

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000010

BEST: binding-site estimation suite of tools

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18463706

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Pheromone-regulated sumoylation of transcription factors that mediate the invasive to mating developmental switch in yeast

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18463706

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000010

1 reference

journals/ploscb/HabibKMF08

25 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

25 July 2017

1 reference

PubMed ID

18463706