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Leuven, Belgium

Sanchez-Rodriguez A.,Kasteelpark Arenberg 20 | Cloots L.,Kasteelpark Arenberg 20 | Marchal K.,Kasteelpark Arenberg 20 | Marchal K.,Ghent University
Current Bioinformatics | Year: 2013

Understanding the cellular behavior from a systems perspective requires the identification of functional and physical interactions among diverse molecular entities in a cell (i.e. DNA/RNA, proteins and metabolites). Powerful and scalable technologies enabled the generation of genome-wide datasets that describe cellular systems by capturing the interactions of their building blocks under different environmental stimuli. The most straightforward way to represent such datasets is by means of molecular networks of which nodes correspond to molecular entities and edges to the interactions amongst those entities. In this review we give an overview of the different functional and physical interaction networks in bacteria that have been or potentially can be built by the integration of diverse omics datasets. © 2013 Bentham Science Publishers. Source

Meysman P.,Kasteelpark Arenberg 20 | Marchal K.,Kasteelpark Arenberg 20 | Marchal K.,Ghent University | Engelen K.,Kasteelpark Arenberg 20 | Engelen K.,Research and Innovation Center
Current Bioinformatics | Year: 2013

It is well known that transcription factors can induce deformations in their DNA-binding sites upon complex formation. However, few attempts have been made to investigate the extent to which induced structural deformations in the DNA molecule are conserved between different members of the same transcription factor family. In this article, we used the CRoSSeD methodology for describing DNA structural properties to extract common features in the binding sites of different LacI-GalR family members. The most significant feature identified in this way was located at the center of the binding sites, which is also the most likely location for an induced DNA deformation following an amino acid interdigitation. This feature was related further to specific elements present in the protein structure and was used to identify and characterize deviant family members. A general family-wide binding site model was constructed and applied to screen for unknown member binding sites. © 2013 Bentham Science Publishers. Source

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