title: A pattern-oriented specification of gene network inference processes.
abstract: Patterns have been widely used in Computer Science. A pattern describes a generic solution to an existing problem in a more readable and accessible form. A pattern-oriented process specification consists of a generic and abstract description of a process. This paper presents a pattern-oriented specification of a genetic regulatory network inference process performed from microarray data and prior biological knowledge. The proposed specification was conceived based on prior work on gene inference networks. The adequacy of the proposed solution was then evaluated with respect to modern tendencies of the genes network inference literature.
authors.affiliation: Department of Computer Science and Mathematics (DCM), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto 14040-901, SP, Brazil. Electronic address: walter@usp.br.
authors.forename: Nestor W
authors.initials: NW
authors.lastname: Trepode
authors.forename: Cléver R G
authors.initials: CR
authors.lastname: de Farias
authors.forename: Junior
authors.initials: J
authors.lastname: Barrera
mesh_terms: D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated / Q000379:methods*
keywords: Dynamical system identification; Gene network inference; Genetic regulatory networks; Microarray data analysis; Patterns; Process modeling