Systems biology

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

J. Schneider, Vorhölter, F. - J., Trost, E., Blom, J., Musa, Y. R., Neuweger, H., Niehaus, K., Schatschneider, S., Tauch, A., and Goesmann, A., CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks, vol. 9, pp. 1660-1672, 2010.

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.

Correlation between liver cancer occurrence and gene expression profiles in rat liver tissue

C. S. Xu, Wang, G. P., Zhang, L. X., Chang, C. F., Zhi, J., and Hao, Y. P., Correlation between liver cancer occurrence and gene expression profiles in rat liver tissue, vol. 10, pp. 3480-3513, 2011.

Liver cancer (LC) is generally characterized by malignant cell proliferation and growth; it normally develops in stages that progress from non-specific injury of the liver to liver fibrosis, liver cirrhosis, dysplasia nodules, and liver carcinoma. We used a rat model of diethylnitrosamine (DENA)-induced LC; a Rat Genome 230 2.0 Array was used to detect gene expression profile of liver tissues from male rats 5, 8, 12, 16, and 18 weeks following the beginning of DENA-induced LC.

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