Allex, C.F., Baldwin, S.F., Shavlik, J.W., and Blattner, F.R. (1996). Improving the quality of automatic DNA sequence assembly using fluorescent trace-data classifications. Proceedings, Fourth International Conference on Intelligent Systems for Molecular Biology, 3-14. St. Louis, MO. Menlo Park, CA. ISMB-96 Proceedings, AAAI Press.
Allex, C.F., Baldwin, S.F., Shavlik, J.W., and Blattner, F.R. (1997). Increasing consensus accuracy in DNA fragment assemblies by incorporating fluorescent trace representations. Proceedings, Fifth International Conference on Intelligent Systems for Molecular Biology, 3-14. Halkidiki, Greece. Menlo Park, CA. ISMB-97 Proceedings, AAAI Press.
Allex CF (1999). Computational Methods for Fast and Accurate DNA Fragment Assembly (Doctoral thesis). Department of Computer Sciences, University of Wisconsin-Madison.
Allex, C.F., Shavlik, J.W., and Blattner, F.R. (1999). Neural network input representations that produce accurate consensus sequences from DNA fragment assemblies. BioInformatics 15(9):723-728.
Altshuler et al. (2000). A SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-516.
Anson E and Myers E (1997). "ReAligner: A program for refining DNA sequence multi-alignments." Journal of Computational Biology 4(3):369-383.
Blattner FR et al. (1997). The Complete Genome Sequence of Escherichia coli K-12. Science 05 Sep 1997: Vol. 277, Issue 5331, pp. 1453-1462. DOI: 10.1126/ science.277.5331.1453. [View on PubMed]
Davydov et al. (2010). “Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++.” PLoS Comput. Biol. 6: e1001025.
Ewing B, Hillier L, Wendl MC and Green P (1998). "Base-calling of automated sequencer traces using Phred. I. Accuracy assessment." Genome Research, 8:175-185.
Ewing B and Green P (1998). "Base-calling of automated sequencer traces using Phred. II. Error probabilities." Genome Research, 8:186-194.
Martinez HM (1983). "An efficient method for finding repeats in molecular sequences." Nucleic Acids Res. 11: 4629-4634.
Needleman SB and Wunsch CD (1970). "A general method applicable to the search for similarities in the amino acid sequence of two proteins." J. Mol. Biol. 48: 443-453.