Cluster analysis and display of genome-wide expression patterns.

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🔗 View Article (PMC 24541)

Published in Proc Natl Acad Sci U S A on December 08, 1998

Authors

M B Eisen1, P T Spellman, P O Brown, D Botstein

Author Affiliations

1: Department of Genetics, Stanford University School of Medicine, 300 Pasteur Avenue, Stanford, CA 94305, USA.

Associated clinical trials:

Gene Expression Profiles in Healing and Non-Healing Wounds (WHGS1) | NCT01101854

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Secretion of beta-lactamase requires the carboxy end of the protein. Cell (1980) 5.03

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Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast. Proc Natl Acad Sci U S A (1977) 4.86

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