A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

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Published in BMC Genomics on November 04, 2005

Authors

N Balandraud1, P Gouret, E G J Danchin, M Blanc, D Zinn, J Roudier, P Pontarotti

Author Affiliations

1: EA 3781, Evolution Biologique, Université de Provence, 3 pl. V. Hugo, 13331 Marseille Cedex 03, France. npbalandraud@yahoo.fr

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Molecular analysis of the human MHC class I region using yeast artificial chromosome clones. Immunogenetics (1990) 0.80

Site-specific epithelial-mesenchymal interactions in digestive neuroendocrine tumors. An experimental in vivo and in vitro study. Am J Pathol (2000) 0.80

Oxygen dissociation at Pt steps. Phys Rev Lett (2001) 0.80

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HLA DRB1, DMA, and DMB gene polymorphisms in rheumatoid arthritis. Hum Immunol (1999) 0.79

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[Final height in 69 patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency]. Arch Pediatr (1994) 0.79

The diversity and idiotypic patterns of human rheumatoid factors in disease. Concepts Immunopathol (1988) 0.79

On the etiology of rheumatoid arthritis. Scand J Rheumatol Suppl (1988) 0.79

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Long term outcome of patients with hairy cell leukemia treated with pentostatin. Cancer (1999) 0.79

Effects of six beta-blockers on the isolated guinea-pig trachea. J Pharmacol (1986) 0.78