Pavlovic, M., Cavallo, M., Kats, A., Kotlarchyk, A., Zhuang, H. and Shoenfels, Y. (2011) From Pauling’s Abzyme concept to the new era of hydrolytic anti-DNA autoantobodies: A link to rational vaccine desin? – A review. International Journal of Bioinformatics Research and Applications (accepted for publication).

has been cited by the following article:

• TITLE: Fuzzy splicing in precursor-mRNA sequences: prediction of aberrant splice-junctions in viral DNA context

  AUTHORS: Perambur S. Neelakanta, Sharmistha Chatterjee, Mirjana Pavlovic, Abijit Pandya, Dolores de Groff

  KEYWORDS: DNA; Exon/intron; Aberrant/Cryptic Splice–Junction; MRNA Sequence; Fuzzy Subspace; Spatial SNR

  JOURNAL NAME: Journal of Biomedical Science and Engineering, Vol.4 No.4, April 22, 2011

  ABSTRACT: RNA splicing normally generates stable splice- junction sequences in viruses that are important in the context of virus mimicry. Potential variability in envelop proteins may occur with point-mutations inducing cryptic splice-junctions, which would remain unrecognized by T-memory cells of higher organisms in vaccine trials. Such aberrant splice- junctions result from evolution-specific non-conser- vation of actual splice-junction sites due to mutations; as such, locations of splice-junctions in a test DNA sequence could only be imprecisely specified. Such impreciseness of splice-junction locations (or cryptic sites) in a sequence is evaluated in this study via “noisy” attributes (with associated stochastics) to the mutated subspace; and, relevant fuzzy considerations are invoked with membership attributes expressed in terms of a spatial signal-to-noise ratio (SSNR). That is, SSNR adopted as a membership function expresses the belongingness of a site-region to exon/intron subspaces. An illustrative example with actual (Dengue 1 viral) DNA data is furnished demonstrating the pursuit developed in predicting aberrant splice-junctions at cryptic sites in the test sequence.