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» Gene set analysis for longitudinal gene expression data
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BMCBI
2005
93views more  BMCBI 2005»
13 years 8 months ago
Two-part permutation tests for DNA methylation and microarray data
Background: One important application of microarray experiments is to identify differentially expressed genes. Often, small and negative expression levels were clipped-off to be e...
Markus Neuhäuser, Tanja Boes, Karl-Heinz J&ou...
BMCBI
2004
132views more  BMCBI 2004»
13 years 8 months ago
Two-stage normalization using background intensities in cDNA microarray data
Background: In the microarray experiment, many undesirable systematic variations are commonly observed. Normalization is the process of removing such variation that affects the me...
Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park
BMCBI
2007
141views more  BMCBI 2007»
13 years 8 months ago
HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing
Background: Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence...
Erik Larsson, Per Lindahl, Petter Mostad
RECOMB
2004
Springer
14 years 9 months ago
Modeling and Analysis of Heterogeneous Regulation in Biological Networks
Abstract. In this study we propose a novel model for the representation of biological networks and provide algorithms for learning model parameters from experimental data. Our appr...
Irit Gat-Viks, Amos Tanay, Ron Shamir
ACIIDS
2010
IEEE
171views Database» more  ACIIDS 2010»
13 years 11 months ago
Evolving Concurrent Petri Net Models of Epistasis
Abstract. A genetic algorithm is used to learn a non-deterministic Petri netbased model of non-linear gene interactions, or statistical epistasis. Petri nets are computational mode...
Michael Mayo, Lorenzo Beretta