(Q33302687)

25 July 2017

title

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm (English)

1 reference

25 July 2017

2

1 reference

15 November 2018

Emma Redhead

1

1 reference

25 July 2017

publication date

15 October 2007

1 reference

25 July 2017

1 reference

25 July 2017

volume

8

1 reference

25 July 2017

page(s)

385

1 reference

Creative Commons Attribution 2.0 Generic

25 July 2017

copyright license

start time

15 October 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

Quantifying similarity between motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

On counting position weight matrix matches in a sequence, with application to discriminative motif finding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

In silico identification of putative promoter motifs of White Spot Syndrome Virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Conservation and diversity of HMW1 and HMW2 adhesin binding domains among invasive nontypeable Haemophilus influenzae isolates.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

A regularized discriminative model for the prediction of protein-peptide interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Discover protein sequence signatures from protein-protein interaction data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Limitations and potentials of current motif discovery algorithms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

A motif-based framework for recognizing sequence families

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

DIP-chip: rapid and accurate determination of DNA-binding specificity.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Identifying tissue-selective transcription factor binding sites in vertebrate promoters

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Assessing computational tools for the discovery of transcription factor binding sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Transcriptional regulatory code of a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

WebLogo: A Sequence Logo Generator

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Finding functional sequence elements by multiple local alignment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Finding subtle motifs by branching from sample strings

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Finding motifs using random projections

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Combinatorial approaches to finding subtle signals in DNA sequences.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

DNA binding sites: representation and discovery

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Methods and statistics for combining motif match scores

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Specificity, free energy and information content in protein-DNA interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

The value of prior knowledge in discovering motifs with MEME

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Using Dirichlet mixture priors to derive hidden Markov models for protein families

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Information content of binding sites on nucleotide sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Finding motifs from all sequences with and without binding sites

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

31 October 2018

Discriminative motifs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2194741

Information content and free energy in DNA--protein interactions

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17937785

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Novel motifs in amino acid permease genes from Leishmania

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17937785

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-8-385

1 reference

journals/bmcbi/RedheadB07

25 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1004490779

0 references

Fatcat ID

release_ufcthyqi4rg5bjz4vlvuukflr4

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ufcthyqi4rg5bjz4vlvuukflr4

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

2194741

1 reference

25 July 2017

1 reference