Alin G. Voina, Petre G. Pop, Mircea F. Vaida Technical University of Cluj Napoca,


  1. [1] Mathieu Blanchette, Martin Tompa, Discovery ofRegulatory Elements by a Computational Method forPhylogenetic Footprinting, Genome Res, 2002
  2. [2] Modan K Das, Ho-Kwok Dai, A survey of DNA motiffinding algorithms, BMC Bioinformatics, 2007
  3. [3] Jonathan M. Carlson, Arijit Chakravarty, Charles e. DeZiel,Robert H. Gross, SCOPE: a web server for practical denovo motif discovery, Nucl. Acids Res, (2007)
  4. [4] Patrik D'haeseleer, What are DNA motifs?, NatureBiotechnology 24, 423 - 425 (2006)
  5. [5] Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, GishWR, Waterston RH, Johnston M, SurveyingSaccharomyces genomes to identify functional elements bycomparative DNA sequence analysis, Genome Res 2001,11:1175-1186.
  6. [6] Hon LS, Jain AN, A deterministic motif finding algorithmwith application to the human genome, Bioinformatics2006, 22:1047-1054.
  7. [7] van Helden J, Andre B, Collado-Vides J, Extractingregulatory sites from the upstream region of yeast genes bycomputational analysis of oligonucleotide frequencies,Journal of Molecular Biology 1998, 281:827-842.
  8. [8] Tompa M, An exact method for finding short motifsinsequences, with application to the ribosome binding siteproblem, Proceedings of the Seventh InternationalConference on Intelligent Systems on Molecular Biology1999:262-271.
  9. [9] Sinha S, Tompa M, A statistical method for findingtranscription factor binding site”, Proceedings of the EighthInternational Conference on Intelligent Systems onMolecular Biology, San Diego, CA 2000:344-354.
  10. [10] Bailey TL, Elkan C, Unsupervised learning of multiplemotifs in biopolymers using expectation maximization,Machine Learning 1995, 21:51-80.
  11. [11] Roth FP, Hughes JD, Estep PW, Church GM, FindingDNA regulatory motifs within unaligned noncodingsequences clustered by whole-genome mRNA quantization,Nature Biotechnology 1998, 16:939-945.
  12. [12] Hertz GZ, Hartzell GW, Stormo GD, Identification ofconsensus patterns in unaligned DNA sequences known tobe functionally related, Comput Appl Biosci 1990, 6:81-92.
  13. [13] Down TA, Hubbard TJ., NestedMICA: sensitive inferenceof over-represented motifs in nucleic acid sequence,Nucleic Acids Res. 2005 Mar 10;33(5):1445-53.
  14. [14] Ao, W., Gaudet, J., Kent, W.J., Muttumu, S. & Mango S.E,Environmentally Induced foregut remodelling by PHA-4/FoxA and DAF-12/NHR, Science 305, 1743-1746 (2004)
  15. [15] Pavesi, G., Mereghetti, P., Mauri, G. & Pesole, G., WeederWeb: discovery of transcription factor binding sites bystatistical overrepresentation, Nucleic Acid Res. 31, 3586-3588 (2003).

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