title: A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.
abstract: 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.
authors.affiliation: Center for Advanced Genomic Technology, Bioinformatics Program and Biomedical Engineering Department, Boston University, Boston, MA 02215, USA. kasif@bu.edu
authors.forename: Simon
authors.initials: S
authors.lastname: Kasif
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Adnan
authors.initials: A
authors.lastname: Derti
authors.forename: Richard
authors.initials: R
authors.lastname: Beigel
authors.forename: Charles
authors.initials: C
authors.lastname: DeLisi
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000138:chemical synthesis*; D012333:RNA, Messenger / Q000032:analysis; D016415:Sequence Alignment
chemical_list: D009841:Oligonucleotides; D012333:RNA, Messenger