Overview of computational methods for the inference of gene regulatory networks

@article{citeulike:2099432, abstract = {Increasing volumes of data about the cellular phenotype and classes of intracellular molecules have necessitated the introduction of systemic methods for the analysis of biological systems. These methods bring to focus the integrated nature and complex interactions of biological molecules and processes and, as such, define the emerging field of systems biology. Of the multitude of systems thus analyzed, we provide here an overview of foundational and current methods in the inference of gene regulatory networks (GRNs) and sequence-based pattern discovery. In GRN analysis, the reverse engineering paradigm is given particular attention, including the various types of models (discrete, continuous, hybrid) which may be utilized in reverse engineering a network's structure. Future research directions in these areas are discussed, particularly the potential for ventures that integrate GRN inference, pattern discovery, and experimental methods into a cohesive, productive methodology.}, author = {Styczynski, Mark P. and Stephanopoulos, Gregory }, booktitle = {Computational Challenges in Biology}, citeulike-article-id = {2099432}, doi = {http://dx.doi.org/10.1016/j.compchemeng.2004.08.029}, journal = {Computers \& Chemical Engineering}, keywords = {grn, network\_inference}, month = {February}, number = {3}, pages = {519--534}, posted-at = {2007-12-12 16:18:11}, priority = {2}, title = {Overview of computational methods for the inference of gene regulatory networks}, url = {http://dx.doi.org/10.1016/j.compchemeng.2004.08.029}, volume = {29}, year = {2005} }

TY - JOUR ID - citeulike:2099432 L3 - citeulike-article-id:2099432 TI - Overview of computational methods for the inference of gene regulatory networks T2 - Computational Challenges in Biology JF - Computers & Chemical Engineering VL - 29 IS - 3 SP - 519 EP - 534 N2 - Increasing volumes of data about the cellular phenotype and classes of intracellular molecules have necessitated the introduction of systemic methods for the analysis of biological systems. These methods bring to focus the integrated nature and complex interactions of biological molecules and processes and, as such, define the emerging field of systems biology. Of the multitude of systems thus analyzed, we provide here an overview of foundational and current methods in the inference of gene regulatory networks (GRNs) and sequence-based pattern discovery. In GRN analysis, the reverse engineering paradigm is given particular attention, including the various types of models (discrete, continuous, hybrid) which may be utilized in reverse engineering a network's structure. Future research directions in these areas are discussed, particularly the potential for ventures that integrate GRN inference, pattern discovery, and experimental methods into a cohesive, productive methodology. KW - grn KW - network_inference AU - Styczynski, Mark AU - Stephanopoulos, Gregory PY - 2005/02/15/ UR - http://dx.doi.org/10.1016/j.compchemeng.2004.08.029 ER -