(Q37808675)

23 August 2017

Advances in analysis of transcriptional regulatory networks (English)

1 reference

23 August 2017

Tae-Min Kim

1

1 reference

PubMed ID

21069662

23 August 2017

Peter J Park

series ordinal

2

1 reference

23 August 2017

1 January 2011

1 reference

Wiley interdisciplinary reviews. Systems biology and medicine

23 August 2017

1 reference

23 August 2017

3

1 reference

23 August 2017

1

1 reference

23 August 2017

21-35

1 reference

Transcription of eukaryotic protein-coding genes

23 August 2017

1 reference

Orchestrated response: a symphony of transcription factors for gene control

21 January 2018

1 reference

The evolutionary significance of cis-regulatory mutations

21 January 2018

1 reference

Transcriptional Regulatory Elements in the Human Genome

21 January 2018

1 reference

A census of human transcription factors: function, expression and evolution

21 January 2018

1 reference

Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins

21 January 2018

1 reference

DBD: a transcription factor prediction database

21 January 2018

1 reference

Transcriptional regulatory code of a eukaryotic genome

21 January 2018

1 reference

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

21 January 2018

1 reference

Scaling laws in the functional content of genomes

21 January 2018

1 reference

Transcription regulation and animal diversity

21 January 2018

1 reference

Functional determinants of transcription factors in Escherichia coli: protein families and binding sites

21 January 2018

1 reference

The general transcription machinery and general cofactors

21 January 2018

1 reference

Regulation of the initiation of eukaryotic transcription

21 January 2018

1 reference

Nucleosome positioning and gene regulation: advances through genomics

21 January 2018

1 reference

A chromatin insulator determines the nuclear localization of DNA.

21 January 2018

1 reference

Scanning Human Gene Deserts for Long-Range Enhancers

21 January 2018

1 reference

Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3' boundary sequence spanning 46 kilobases

21 January 2018

1 reference

Interchromosomal associations between alternatively expressed loci

21 January 2018

1 reference

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

21 January 2018

1 reference

Structure and Function in the Nucleus

21 January 2018

1 reference

Capturing chromosome conformation

21 January 2018

1 reference

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

21 January 2018

1 reference

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

21 January 2018

1 reference

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

21 January 2018

1 reference

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

21 January 2018

1 reference

Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors

21 January 2018

1 reference

DNA binding sites: representation and discovery

21 January 2018

1 reference

TRANSFAC: a database on transcription factors and their DNA binding sites

21 January 2018

1 reference

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

21 January 2018

1 reference

Enhanced position weight matrices using mixture models

21 January 2018

1 reference

Context-specific independence mixture modeling for positional weight matrices

21 January 2018

1 reference

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

21 January 2018

1 reference

A non-parametric model for transcription factor binding sites

21 January 2018

1 reference

Applied bioinformatics for the identification of regulatory elements

21 January 2018

1 reference

Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome

21 January 2018

1 reference

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

21 January 2018

1 reference

Position specific variation in the rate of evolution in transcription factor binding sites

21 January 2018

1 reference

Conserved noncoding sequences are reliable guides to regulatory elements.

21 January 2018

1 reference

Highly conserved non-coding sequences are associated with vertebrate development

21 January 2018

1 reference

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

21 January 2018

1 reference

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

21 January 2018

1 reference

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover

21 January 2018

1 reference

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

21 January 2018

1 reference

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

21 January 2018

1 reference

Cluster analysis and display of genome-wide expression patterns

21 January 2018

1 reference

Functional discovery via a compendium of expression profiles

21 January 2018

1 reference

Genomic analysis of gene expression relationships in transcriptional regulatory networks

21 January 2018

1 reference

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

21 January 2018

1 reference

Assessing computational tools for the discovery of transcription factor binding sites

21 January 2018

1 reference

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.

21 January 2018

1 reference

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells

21 January 2018

1 reference

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

21 January 2018

1 reference

Predicting gene expression from sequence.

21 January 2018

1 reference

A systems biology approach to understanding cis-regulatory module function.

21 January 2018

1 reference

Gene regulatory networks for development

21 January 2018

1 reference

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

21 January 2018

1 reference

Coordinate enhancers share common organizational features in the Drosophila genome

21 January 2018

1 reference

Transcriptional control in the segmentation gene network of Drosophila

21 January 2018

1 reference

Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network

21 January 2018

1 reference

Computational methods for the detection of cis-regulatory modules

21 January 2018

1 reference

Transcriptional regulatory networks in Saccharomyces cerevisiae

21 January 2018

1 reference

Core transcriptional regulatory circuitry in human embryonic stem cells

21 January 2018

1 reference

Serial regulation of transcriptional regulators in the yeast cell cycle

21 January 2018

1 reference

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

21 January 2018

1 reference

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

21 January 2018

1 reference

The challenges of sequencing by synthesis

21 January 2018

1 reference

Next-generation DNA sequencing

21 January 2018

1 reference

ChIP-seq: advantages and challenges of a maturing technology

21 January 2018

1 reference

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

Genomic location analysis by ChIP-Seq

21 January 2018

1 reference

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

21 January 2018

1 reference

Design and analysis of ChIP-seq experiments for DNA-binding proteins

21 January 2018

1 reference

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

21 January 2018

1 reference

A large genome center's improvements to the Illumina sequencing system

21 January 2018

1 reference

Network biology: understanding the cell's functional organization

21 January 2018

1 reference

Hierarchical organization of modularity in metabolic networks

21 January 2018

1 reference

Lethality and centrality in protein networks

21 January 2018

1 reference

The large-scale organization of metabolic networks

21 January 2018

1 reference

Error and attack tolerance of complex networks

21 January 2018

1 reference

Genomic analysis of essentiality within protein networks

21 January 2018

1 reference

Scale-Free Networks Are Ultrasmall

21 January 2018

1 reference

Network motifs: simple building blocks of complex networks

21 January 2018

1 reference

Network motifs in the transcriptional regulation network of Escherichia coli

21 January 2018

1 reference

Gene regulatory network growth by duplication

21 January 2018

1 reference

Convergent evolution of gene circuits

21 January 2018

1 reference

Genomic analysis of regulatory network dynamics reveals large topological changes

21 January 2018

1 reference

Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks

21 January 2018

1 reference

A protein interaction map of Drosophila melanogaster

21 January 2018

1 reference

Network-based prediction of protein function

21 January 2018

1 reference

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

1 reference

Reconstruction of microbial transcriptional regulatory networks

21 January 2018

1 reference

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

21 January 2018

1 reference

Transcriptional regulation in constraints-based metabolic models of Escherichia coli

21 January 2018

1 reference

Modeling and simulation of genetic regulatory systems: a literature review

21 January 2018

1 reference

Insights from genomic profiling of transcription factors

21 January 2018

1 reference

MIPS: a database for genomes and protein sequences

21 January 2018

1 reference

Human Protein Reference Database--2009 update

21 January 2018

1 reference

Protein networks in disease

21 January 2018

1 reference

A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease

21 January 2018

1 reference

A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration

21 January 2018

1 reference

A gene-centered C. elegans protein-DNA interaction network

21 January 2018

1 reference

Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.

21 January 2018

1 reference

Gene co-expression network topology provides a framework for molecular characterization of cellular state

21 January 2018

1 reference

Predicting gene function by conserved co-expression

21 January 2018

1 reference

A gene-coexpression network for global discovery of conserved genetic modules

21 January 2018

1 reference

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

21 January 2018

1 reference

Information-theoretic inference of large transcriptional regulatory networks.

21 January 2018

1 reference

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

21 January 2018

1 reference

On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information.

21 January 2018

1 reference

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information

21 January 2018

1 reference

Reverse engineering of regulatory networks in human B cells

21 January 2018

1 reference

The transcriptional network for mesenchymal transformation of brain tumours.

21 January 2018

1 reference

cis-Regulatory networks during development: a view of Drosophila.

21 January 2018

1 reference

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

21 January 2018

1 reference

Evolution of cis-regulatory elements in duplicated genes of yeast

21 January 2018

1 reference

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/WSBM.105

1 reference

23 August 2017

1 reference

PubMed ID

21069662