Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms.

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Published in J R Soc Interface on March 18, 2009

Authors

P Gerlee1, T Lundh, B Zhang, A R A Anderson

Author Affiliations

1: Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen, Denmark. gerlee@nbi.dk

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The inducible production of nitric oxide by articular cell types. Osteoarthritis Cartilage (1994) 1.07

Prospective study of early detection for primary liver cancer. J Cancer Res Clin Oncol (1997) 1.06

Visual disturbances in man as a result of experimental and occupational exposure to dimethylethylamine. Br J Ind Med (1991) 1.06

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Droplet-based compartmentalization of chemically separated components in two-dimensional separations. Chem Commun (Camb) (2009) 1.05

[Current status and prospects of liver surgery in China]. Zhonghua Wai Ke Za Zhi (1996) 1.05

Effect of dietary protein on the liver content and subunit composition of the branched-chain alpha-ketoacid dehydrogenase complex. Arch Biochem Biophys (1994) 1.05

Treatment of P190 Bcr/Abl lymphoblastic leukemia cells with inhibitors of the serine/threonine kinase CK2. Leukemia (2006) 1.04

Upregulation of miR-27a contributes to the malignant transformation of human bronchial epithelial cells induced by SV40 small T antigen. Oncogene (2011) 1.03

Chicken ovalbumin upstream promoter transcription factor (COUP-TF) binds to a peroxisome proliferator-responsive element and antagonizes peroxisome proliferator-mediated signaling. J Biol Chem (1993) 1.03