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» Near-Deterministic Inference of AS Relationships
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BMCBI
2006
166views more  BMCBI 2006»
14 years 10 months ago
Extraction of phylogenetic network modules from the metabolic network
Background: In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organis...
Takuji Yamada, Minoru Kanehisa, Susumu Goto
BMCBI
2006
122views more  BMCBI 2006»
14 years 10 months ago
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
Background: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a liv...
Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
BMCBI
2007
182views more  BMCBI 2007»
14 years 10 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
JAR
2006
236views more  JAR 2006»
14 years 10 months ago
Deciding Boolean Algebra with Presburger Arithmetic
We describe an algorithm for deciding the first-order multisorted theory BAPA, which combines 1) Boolean algebras of sets of uninterpreted elements (BA) and 2) Presburger arithmeti...
Viktor Kuncak, Huu Hai Nguyen, Martin C. Rinard
JSAT
2006
91views more  JSAT 2006»
14 years 10 months ago
Extending Existential Quantification in Conjunctions of BDDs
Abstract. We introduce new approaches intended to speed up determining the satisfiability of a given Boolean formula expressed as a conjunction of Boolean functions. A common prac...
Sean Weaver, John V. Franco, John S. Schlipf