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BMCBI
2010
151views more  BMCBI 2010»
14 years 12 months ago
TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and e
Background: Identification of transcription factors (TFs) involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms...
Xiaoqi Cui, Tong Wang, Huann-Sheng Chen, Victor Bu...
BIBM
2009
IEEE
118views Bioinformatics» more  BIBM 2009»
15 years 3 months ago
Inexact Local Alignment Search over Suffix Arrays
We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may conta...
Mohammadreza Ghodsi, Mihai Pop
83
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RECOMB
2004
Springer
16 years 1 days ago
The Statistical Significance of Max-Gap Clusters
Identifying gene clusters, genomic regions that share local similarities in gene organization, is a prerequisite for many different types of genomic analyses, including operon pred...
Rose Hoberman, David Sankoff, Dannie Durand
BMCBI
2007
182views more  BMCBI 2007»
14 years 11 months ago
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
Background: ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct transcriptional regulatory networks. Howev...
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
BMCBI
2008
126views more  BMCBI 2008»
14 years 12 months ago
Relating gene expression data on two-component systems to functional annotations in Escherichia coli
Background: Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionall...
Anne M. Denton, Jianfei Wu, Megan K. Townsend, Pre...