Results 311 to 320 of about 345,747 (340)

Finding Feasible Pathways in Metabolic Networks

2005
Recent small-world studies of the global structure of metabolic networks have been based on the shortest-path distance. In this paper, we propose new distance measures that are based on the structure of feasible metabolic pathways between metabolites.
Juho Rousu, Ari Rantanen, Esko Ukkonen, Esa Pitkänen   +3 more
openaire   +2 more sources

Parallel extreme pathway computation for metabolic networks

Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., 2004
We parallelized the serial extreme pathways algorithm presented by Schilling et al., in J. Theor. Biol. 203 (2000) using the message passing interface (MPI). The parallel algorithm exhibits super-linear scalability because the number of independence tests performed decreases as the number of MPI nodes increases.
J. Varner, Kwok Ko, Lie-Quan Lee
openaire   +2 more sources

Gene Networks Validation based on Metabolic Pathways

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering, 2011
In the last few years, DNA microarray technology has attained a very important role in biological and biomedical research. It enables analyzing the relations among thousands of genes simultaneously, generating huge amounts of data. The gene networks represent, in a graph data structure, genes or gene products and the functional relationships between ...
Norberto Díaz-Díaz, Jesús S. Aguilar-Ruiz, Francisco Gómez-Vela   +2 more
openaire   +2 more sources

Green pathways: Metabolic network analysis of plant systems

Metabolic Engineering, 2016
Metabolic engineering of plants with enhanced crop yield and value-added compositional traits is particularly challenging as they probably exhibit the highest metabolic network complexity of all living organisms. Therefore, approaches of plant metabolic network analysis, which can provide systems-level understanding of plant physiology, appear valuable
Lisa Maria Dersch, Veronique Beckers, Christoph Wittmann   +2 more
openaire   +3 more sources

Predicting novel pathways in genome-scale metabolic networks

Biochemical Society Transactions, 2010
Elementary-modes analysis has become a well-established theoretical tool in metabolic pathway analysis. It allows one to decompose complex metabolic networks into the smallest functional entities, which can be interpreted as biochemical pathways. This analysis has, in medium-size metabolic networks, led to the successful theoretical prediction of ...
Christoph Kaleta, Luis F. de Figueiredo, Stefan Schuster   +2 more
openaire   +3 more sources

Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks

Biotechnology and Bioengineering, 2004
AbstractCentral carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast.
Kutlu O. Ulgen, Tunahan Çakır, Betul Kirdar   +2 more
openaire   +3 more sources

Analysis and visualization of metabolic pathways and networks: A hypegraph approach

IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), 2014
Metabolic pathways are series of chemical reactions occurring in a cell. Various graph-based models are used to represent metabolic data. However, diverse problems may arise from adopting these models. A more accurate modeling framework can be offered by hypergraphs.
Evaggelia M. Maniadi, Ioannis G. Tollis
openaire   +2 more sources

Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering, 2007
Network mapping is a convenient tool for comparing and exploring biological networks; it can be used for predicting unknown pathways, fast and meaningful searching of databases, and potentially establishing evolutionary relations. Unfortunately, existing tools for mapping paths into general networks (PathBlast) or trees into tree networks allowing gaps
Qiong Cheng, Alexander Zelikovsky, Robert W. Harrison   +2 more
openaire   +2 more sources

Pathway Engineering of the Plant Vitamin C Metabolic Network [PDF]

, 2007
Vitamin C (ascorbic acid, AsA) is an important primary metabolite of plants that functions as an antioxidant, an enzyme cofactor, and a cell-signalling modulator in a wide array of crucial physiological processes, including biosynthesis of the cell wall, secondary metabolites and phytohormones, stress resistance, photoprotection, cell division ...
Argelia Lorence, Craig L. Nessler
openaire   +1 more source

Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks

Science's STKE, 2005
The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources.
Christian Blaschke, Eduardo Andres, Martin Krallinger, Javier Tamames, Robert Hoffmann, Alfonso Valencia   +5 more
openaire   +3 more sources