Creating Regular Expressions as mRNA Motifs with GP to Predict Human Exon Splitting

Created by W.Langdon from gp-bibliography.bib Revision:1.2031

@InProceedings{langdon:2009:gecco,
  author =       "William B. Langdon and J. Rowsell and A. P. Harrison",
  title =        "Creating Regular Expressions as m{RNA} Motifs with
                 {GP} to Predict Human Exon Splitting",
  booktitle =    "GECCO '09: Proceedings of the 11th Annual conference
                 on Genetic and evolutionary computation",
  year =         "2009",
  editor =       "Guenther Raidl and Franz Rothlauf and 
                 Giovanni Squillero and Rolf Drechsler and Thomas Stuetzle and 
                 Mauro Birattari and Clare Bates Congdon and 
                 Martin Middendorf and Christian Blum and Carlos Cotta and 
                 Peter Bosman and Joern Grahl and Joshua Knowles and 
                 David Corne and Hans-Georg Beyer and Ken Stanley and 
                 Julian F. Miller and Jano {van Hemert} and 
                 Tom Lenaerts and Marc Ebner and Jaume Bacardit and 
                 Michael O'Neill and Massimiliano {Di Penta} and Benjamin Doerr and 
                 Thomas Jansen and Riccardo Poli and Enrique Alba",
  pages =        "1789--1790",
  address =      "Montreal",
  month =        "8-12 " # jul,
  organisation = "SIGEVO",
  publisher =    "ACM",
  publisher_address = "New York, NY, USA",
  keywords =     "genetic algorithms, genetic programming, Poster, Gene
                 expression and regulation, alternative splicing,
                 Microarray analysis, Integration of genetic programming
                 into bioinformatics, Biological interpretation of
                 computer generated motifs, Bioinformatics, Affymetrix
                 GeneChip, strongly typed genetic programming, grammar,
                 regular expression, Alternative splicing of Homosapiens
                 exons, HDONA",
  isbn13 =       "978-1-60558-325-9",
  URL =          "http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/papers/langdon_2009_gecco.pdf",
  doi =          "doi:10.1145/1569901.1570162",
  size =         "2 pages",
  abstract =     "RNAnet \cite{CES-486}
                 http://bioinformatics.essex.ac.uk/users/wlangdon/rnanet/
                 allows the user to calculate correlations of gene
                 expression, both between genes and between components
                 within genes. We investigate all of Ensembl
                 http://www.ensembl.org and find all the Homo Sapiens
                 exons for which there are sufficient robust Affymetrix
                 HG-U133 Plus 2 GeneChip probes. Calculating correlation
                 between mRNA probe measurements for the same exon shows
                 many exons whose components are consistently up
                 regulated and down regulated. However we identify other
                 Ensembl exons where sub-regions within them are self
                 consistent but these transcript blocks are not well
                 correlated with other blocks in the same exon. We
                 suggest many current Ensembl exon definitions are
                 incomplete.

                 Secondly, having identified exon with substructure we
                 use machine learning to try and identify patterns in
                 the DNA sequence lying between blocks of high
                 correlation which might yield biological or
                 technological explanations. A Backus-Naur form (BNF)
                 context-free grammar constrains strongly typed genetic
                 programming (STGP) to evolve biological motifs in the
                 form of regular expressions (RE) (e.g. TCTTT) which
                 classify gene exons with potential alternative mRNA
                 expression from those without. We show biological
                 patterns can be data mined by a GP written in gawk and
                 using egrep from NCBI's GEO
                 http://www.ncbi.nlm.nih.gov/geo/ database. The
                 automatically produced DNA motifs suggest that
                 alternative polyadenylation is not responsible. (Full
                 version in TR-09-02
                 \cite{langdon:2009:TR-09-02}.)

                 Blocky exons can be found in
                 http://bioinformatics.essex.ac.uk/users/wlangdon/tr-09-02.tar.gz",
  notes =        "t03p220. Longer version in
                 \cite{langdon:2009:TR-09-02}.

                 GECCO-2009 A joint meeting of the eighteenth
                 international conference on genetic algorithms
                 (ICGA-2009) and the fourteenth annual genetic
                 programming conference (GP-2009).

                 ACM Order Number 910092. Also known as
                 \cite{DBLP:conf/gecco/LangdonRH09}",
}

Genetic Programming entries for William B Langdon J Rowsell A P Harrison