Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.

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Published in Nucleic Acids Res on March 01, 2001

Authors

Y Ding1, C E Lawrence

Author Affiliations

1: Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA. yding@wadsworth.org

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Maximum likelihood estimation of subsequence conservation. J Theor Biol (1985) 0.75

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Cortisol succinate is slowly hydrolysed in organ cultures of porcine articular tissues and is not equivalent to cortisol. Cell Biochem Funct (1986) 0.75

Fertility patterns after discontinuation of use of oral contraceptives. Lancet (1976) 0.75