DISCOVER: a feature-based discriminative method for motif search in complex genomes (Q30487840)

18 August 2017

DISCOVER: a feature-based discriminative method for motif search in complex genomes (English)

1 reference

18 August 2017

Pradipta Ray

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Eric P Xing

1 reference

18 August 2017

Wenjie Fu

1 reference

PMC publication ID

2687984

18 August 2017

language of work or name

English

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publication date

1 June 2009

1 reference

18 August 2017

1 reference

18 August 2017

1 reference

18 August 2017

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18 August 2017

i321-9

1 reference

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Finding sequence motifs with Bayesian models incorporating positional information: an application to 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=2687984

Systematic functional characterization of cis-regulatory motifs in human core 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=2687984

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

A nucleosome-guided map of transcription factor binding sites in yeast

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Computational analyses of eukaryotic 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=2687984

Conrad: gene prediction using conditional random fields.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

A graph-based motif detection algorithm models complex nucleotide dependencies in 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=2687984

Predicting transcription factor binding sites using local over-representation and comparative genomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

A genomic code for nucleosome positioning

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Stubb: a program for discovery and analysis of cis-regulatory modules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

A survey of motif discovery methods in an integrated framework

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

A large family of ancient repeat elements in the human genome is under strong selection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Repbase Update, a database of eukaryotic repetitive elements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous 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=2687984

Decoding human regulatory circuits

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

MSCAN: identification of functional clusters 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=2687984

Aligning multiple genomic sequences with the threaded blockset aligner

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Identification and characterization of multi-species conserved 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=2687984

Cluster-Buster: Finding dense clusters of motifs 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=2687984

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Statistical significance of clusters of motifs represented by position specific scoring matrices in 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=2687984

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

rVista for comparative sequence-based discovery of functional 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=2687984

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila 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=2687984

Deciphering genetic regulatory codes: a challenge for functional genomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

TRANSFAC: an integrated system for gene expression regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Computer methods to locate signals in nucleic acid 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=2687984

Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection.

14 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

REDfly: a Regulatory Element Database for Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

High-throughput mapping of the chromatin structure of human promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

Conformational and physicochemical DNA features specific for transcription factor binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

A Feature-Based Approach to Modeling Protein-DNA Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTP230

Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

Phylogenetic motif detection by expectation-maximization on evolutionary mixtures

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2687984

TFBScluster: a resource for the characterization of transcriptional regulatory networks

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19478006

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTP230

1 reference

journals/bioinformatics/FuRX09

18 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

2687984

18 August 2017

PubMed publication ID

19478006

1 reference

PMC publication ID

2687984