Nucleic Acids Research, 2002, Vol. 30, No. 20 e106
© 2002 Oxford University Press
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays
1 Center for Advanced Genomic Technology (CAGT), Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA, USA, 2 MIT Genome Center, Whitehead Institute, MIT, Cambridge, MA, USA and 3 Institute for Advanced Studies, Princeton, NJ, USA and 4 Temple University, Philadelphia, PA, USA
*To whom correspondence should be addressed at 44 Cummington Street, Boston University, Boston, MA 02215, USA. Tel: +1 617 358 1845; Fax: +1 617 353 6766; Email: kasif{at}bu.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
High-throughput genomic technologies are revolutionizing modern biology. In particular, DNA microarrays have become one of the most powerful tools for profiling global mRNA expression in different tissues and environmental conditions, and for detecting single nucleotide polymorphisms. The broad applicability of gene expression profiling to the biological and medical realms has generated expanding demand for mass production of microarrays, which in turn has created considerable interest in improving the cost effectiveness of microarray fabrication techniques. We have developed the computational framework for an optimal synthesis strategy for oligonucleotide microarrays. The problem was introduced by Hubbell et al. Here, we formalize the problem, obtain precise bounds on its complexity and devise several computational solutions.
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