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- ArticleSeptember 2021
Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study
AbstractMany techniques have been developed to infer Boolean regulations from a prior knowledge network and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling networks, but they fail to ...
- research-articleOctober 2012
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks
- Vicente Acuña,
- Paulo Vieira Milreu,
- Ludovic Cottret,
- Alberto Marchetti-Spaccamela,
- Leen Stougie,
- Marie-France Sagot
Bioinformatics (BIOI), Volume 28, Issue 19Pages 2474–2483https://doi.org/10.1093/bioinformatics/bts423Motivation: In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal ...
- articleOctober 2012
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets
- Vicente Acuña,
- Etienne Birmelé,
- Ludovic Cottret,
- Pierluigi Crescenzi,
- Fabien Jourdan,
- Vincent Lacroix,
- Alberto Marchetti-Spaccamela,
- Andrea Marino,
- Paulo Vieira Milreu,
- Marie-France Sagot,
- Leen Stougie
We present a constrained version of the problem of enumerating all maximal directed acyclic subgraphs (DAG) of a graph G. In this version, we enumerate maximal DAGs whose sources and targets belong to a predefined subset of the nodes. We call such DAGs ...
- ArticleJuly 2012
Systrip: A Visual Environment for the Investigation of Time-series Data in the Context of Metabolic Networks
IV '12: Proceedings of the 2012 16th International Conference on Information VisualisationPages 204–213https://doi.org/10.1109/IV.2012.43Technological advances in biology lead to a profusion of quantitative data, raising analytical challenges. Visual analytics is particularly well suited to address these difficulties. It helps to interactively move through the different levels of ...
- introductionOctober 2008
An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 5, Issue 4Pages 594–617https://doi.org/10.1109/TCBB.2008.79There has been a renewed interest for metabolism in the computational biology community, leading to an avalanche of papers coming from methodological network analysis as well as experimental and theoretical biology. This paper is meant to serve as an ...
- ArticleSeptember 2008
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network
- Ludovic Cottret,
- Paulo Vieira Milreu,
- Vicente Acuña,
- Alberto Marchetti-Spaccamela,
- Fábio Viduani Martinez,
- Marie-France Sagot,
- Leen Stougie
WABI '08: Proceedings of the 8th international workshop on Algorithms in BioinformaticsPages 233–244https://doi.org/10.1007/978-3-540-87361-7_20We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account ...