Aligning Metabolic Pathways Exploiting Binary Relation of Reactions

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasi...

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

We consider the problem of aligning two metabolic pathways. Unlike traditional approaches, we do not restrict the alignment to one-to-one mappings between the molecules (nodes) of the input pathways (graphs). We follow the observation that, in nature, different organisms can perform the same or similar functions through different sets of reactions and molecules. The number and the topology of t...

Comparing Metabolic Pathways through Reactions and Potential Fluxes

Aligning Projection Images from Binary Volumes

In tomography, slight differences between the geometry of the scanner hardware and the geometric model used in the reconstruction lead to alignment artifacts. To exploit high-resolution detectors used in many applications of tomography, alignment of the projection data is essential. Markerless alignment algorithms are the preferred choice over alignment with markers, in case a fully automatic t...

Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping.

Comparison of metabolic pathways provides a systematic way for understanding the evolutionary and phylogenetic relationships in systems biology. Although a number of phylogenetic methods have been developed, few efforts have been made to provide a unified phylogenetic framework that sufficiently reflects the metabolic features of organisms. In this paper, we propose a phylogenetic framework tha...