Reconstruction of Metabolic Networks Using Incomplete Information

Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data

With the advent of the high-throughput data production, recent studies of tissue-specific metabolic networks have largely advanced our understanding of the metabolic basis of various physiological and pathological processes. However, for kidney, which plays an essential role in the body, the available kidney-specific model remains incomplete. This paper reports the reconstruction and characteri...

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

Automatic reconstruction of metabolic pathways for an organism from genomics and transcriptomics data has been a challenging and important problem in bioinformatics. Traditionally, known reference pathways can be mapped into an organism-specific ones based on its genome annotation and protein homology. However, this simple knowledge-based mapping method might produce incomplete pathways and gen...

Image Reconstruction from Incomplete Data

Image Reconstruction from Incomplete Data

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.

New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret genome data in a functional context. CARMEN supports the visualizatio...