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BMCBI
2008
83views more  BMCBI 2008»
8 years 9 months ago
Prioritization of gene regulatory interactions from large-scale modules in yeast
Background: The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological s...
Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin...
BMCBI
2008
90views more  BMCBI 2008»
8 years 9 months ago
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Background: The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent res...
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne,...
BMCBI
2010
154views more  BMCBI 2010»
8 years 9 months ago
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
Background: A major goal of molecular biology is determining the mechanisms that control the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine which DNA-b...
Robert C. McLeay, Timothy L. Bailey
BMCBI
2010
106views more  BMCBI 2010»
8 years 9 months ago
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes
Background: Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that pr...
Guofeng Meng, Axel Mosig, Martin Vingron
APBC
2004
116views Bioinformatics» more  APBC 2004»
8 years 10 months ago
Structure-Function Relationship in DNA Sequence Recognition by Transcription Factors
Transcription factors play essential role in the gene regulation in higher organisms, binding to multiple target sequences and regulating multiple genes in a complex manner. In or...
Akinori Sarai, Samuel Selvaraj, M. Michael Gromiha...
ICMLA
2007
8 years 10 months ago
SVMotif: A Machine Learning Motif Algorithm
We describe SVMotif, a support vector machine-based learning algorithm for identification of cellular DNA transcription factor (TF) motifs extrapolated from known TF-gene interact...
Mark A. Kon, Yue Fan, Dustin T. Holloway, Charles ...
GECCO
2007
Springer
258views Optimization» more  GECCO 2007»
9 years 1 months ago
TFBS identification by position- and consensus-led genetic algorithm with local filtering
Identification of Transcription Factor Binding Site (TFBS) motifs in multiple DNA upstream sequences is important in understanding the mechanism of gene regulation. This identific...
Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee
CSB
2003
IEEE
124views Bioinformatics» more  CSB 2003»
9 years 2 months ago
SMASHing regulatory sites in DNA by human
Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, t...
Mihaela Zavolan, Nicholas D. Socci, Nikolaus Rajew...
RECOMB
2007
Springer
9 years 3 months ago
Nucleosome Occupancy Information Improves de novo Motif Discovery
A complete understanding of transcriptional regulatory processes in the cell requires identification of transcription factor binding sites on a genomewide scale. Unfortunately, th...
Leelavati Narlikar, Raluca Gordân, Alexander...
BIOWIRE
2007
Springer
9 years 3 months ago
Evolutionary and Temporal Dynamics of Transcriptional Regulatory Networks
Transcriptional regulation is a key mechanism that allows cells to make the appropriate amount of proteins at the right time. This is mediated by transcription factors that respond...
M. Madan Babu
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