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» A factor analysis model for functional genomics
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BMCBI
2005
145views more  BMCBI 2005»
13 years 8 months ago
CAGER: classification analysis of gene expression regulation using multiple information sources
Background: Many classification approaches have been applied to analyzing transcriptional regulation of gene expressions. These methods build models that can explain a gene's...
Jianhua Ruan, Weixiong Zhang
BMCBI
2005
152views more  BMCBI 2005»
13 years 8 months ago
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Background: Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling ar...
Markus Wistrand, Erik L. L. Sonnhammer
BMCBI
2006
123views more  BMCBI 2006»
13 years 8 months ago
Computational models with thermodynamic and composition features improve siRNA design
Background: Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large fun...
Svetlana A. Shabalina, Alexey N. Spiridonov, Aleks...
BMCBI
2006
127views more  BMCBI 2006»
13 years 8 months ago
Using local gene expression similarities to discover regulatory binding site modules
Background: We present an approach designed to identify gene regulation patterns using sequence and expression data collected for Saccharomyces cerevisae. Our main goal is to rela...
Bartek Wilczynski, Torgeir R. Hvidsten, Andriy Kry...
BMCBI
2007
167views more  BMCBI 2007»
13 years 8 months ago
A stochastic differential equation model for transcriptional regulatory networks
Background: This work explores the quantitative characteristics of the local transcriptional regulatory network based on the availability of time dependent gene expression data se...
Adriana Climescu-Haulica, Michelle D. Quirk