Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice.

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Published in Plant Physiol on June 07, 2007

Authors

Randall W Shultz1, Vinaya M Tatineni, Linda Hanley-Bowdoin, William F Thompson

Author Affiliations

1: Department of Plant Biology , North Carolina State University, Raleigh, North Carolina 27695, USA.

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Predicting coiled coils from protein sequences. Science (1991) 38.18

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