Phys-Rev-E: Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. [clip]

Fig. 3 of this paper looks a lot like the "C-runs" artifact on Affy chips.
Other Naef & Magnasco and Magnasco lab papers are also quite interesting in
relation to Affy analysis -- see http://asterion.rockefeller.edu/felix/CV .

[SCIENCE]

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Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906. Epub 2003
Jul 16.
Solving the riddle of the bright mismatches: labeling and effective binding
in oligonucleotide arrays.

Naef F, Magnasco MO.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12935175&query_hl=7

http://asterion.rockefeller.edu/felix/CV/PDFs/riddle.pdf

RNA binding to high-density oligonucleotide arrays has shown tantalizing
differences with solution experiments. We analyze here its sequence specificity,
fitting binding affinities to sequence composition in large datasets. Our
results suggest that the fluorescent labels interfere with binding.....
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