Research references

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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.

Taylor WR (1997). “Residual colours: a proposal for aminochromography.” Protein Engineering vol.10 no.7 pp.743 – 746. (See the PDF file.) [“Taylor” color scheme]

Waterhouse AM, Procter JB, Martin DMA, Clamp M and Barton GJ (2009). “JalView version 2: a multiple sequence alignment and analysis workbench.” Bioinformatics 25:1189 – 1191. (See on PMC.) [Discusses methodology later used to create the “Taylor” and “Zappo” color schemes]