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References
Alizadeh, F., Karp, R.M., Newberg, L.A., Weisser, D.K. (1992) Physical mapping of chromosomes: A combinatorial problem in molecular biology. Preprint.
Altschul, S.F., Lipman, D.J. (1989) Trees, stars, and multiple biological sequence alignment. SIAM Journal on Applied Mathematics 49:197–209.
Berger, J.O. (1985) Statistical Decision Theory and Bayesian Analysis. 2nd ed. Springer-Verlag.
Borodovsky, M. and McIninch, J. (1993a) Genmark: Parallel gene recognition for both DNA strands. Computers Chem. 17:123–133.
Borodovsky, M. and McIninch, J. (1993b) Eecognition of genes in DNA sequence with ambiguity. Biosystems 30:161–171.
Bowling, J.M., Bruner, K.L., Cmarik, J.L., Tibbets, C. (1991) Neighboring nucleotide interactions during DNA sequencing gel electrophoresis. Nucl. Acids Res. 19:3089–3097.
Branscomb, E. et al. (1990) Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries. Genomics 8:351–366.
Casella, G.C. and George, E.I. (1992) Explaining the Gibbs sampler American Statistician.
Chen, E. et al. (1991) Sequence of the human glucose-6-phosphate dehydrogenase cloned in plasmids and a yeast artificial chromosome. Genomics 10:792–800.
Chernoff H. (1992) Estimating a sequence from noisy copies. Harvard University technical report no. ONR-C-10.
Churchill, G.A. (1989) A stochastic model for heterogeneous DNA sequences. Bull. Math. Biol. 51:79–94.
Churchill, G.A., Burks, C., Eggert, M., Engle, M.L., Waterman, M.S. (1992) Assembling DNA fragments by shuffling and simulated annealing. Manuscript.
Churchill, G.A. and Thorne, J.L. (1993) The probability distribution of a molecular sequence alignment. Cornell University, Biometrics Unit technical report.
Churchill, G.A. and Waterman, M.S. (1992). The accuracy of DNA sequences: estimating sequence quality. Genomics in press.
Clark, A.G. and Whittam T.S. (1992) Sequencing errors and molecular evolutionary analysis. Mol. Biol. Evol. 9:744–752.
Clarke, L. and Carbon, J. (1976) A colony bank containing synthetic Col EI hybrid plasmids representative of the entire E. coli genome. Cell 9:91–99.
Cornish-Bowden A. (1985) Nomenclature for incompletely specified bases in DNA sequences: Recommendations 1984. Nucl. Acids Res. 13:3021–3030.
Daniels, D.L., Plunkett, G., Burland, V., Blattner, F.R. (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257: 771–778.
Dempster, A.P., Laird, N.M., Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. Royal Stat. Soc. B 39:1–38.
Edwards, A. et al. (1990) Automated DNA sequencing of the Human HPRT locus. Genomics 6:593–608.
Fu, Y.X., Timberlake, W.E., Arnold, J. (1992) On the design of genome mapping experiments using short synthetic oligonucleotides. Biometrics 48:337–359.
Gelfand A.E. and Smith, A.F.M. (1990) Sampling based approaches to calculating marginal densities. J. Amer. Statist. Assoc. 85:398–409.
Gelman, A. and Rubin, D.B. (1992) Inference from iterative simulation, with discussion. Statistical Science 7:457–511.
Geyer, C.J. (1992) Markov chain Monte Carlo maximum likelihood. Computer Science and Statistics: Proceeding of the 23rd symposium on the interface.
Golden, J.B., Torgersen, D., Tibbets, C. (1993) Pattern recognition for automated DNA sequencing: I. On-line signal conditioning and feature extraction for basecalling. In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. AAAI Press.
Hastings (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97–109.
Huang, X. (1992) A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14:18–25.
Hunkapillar, T, Kaiser, R.J., Koop, B.F., Hood, L. (1991) Large-scale automated DNA sequence determination. Science 254:59–67.
Kececioglu, J. and Myers, E. (1990). A robust automatic fragment assembly system. Preprint.
Koop, B.F., Rowan, L., Chen, W.-Q., Deshpande, P., Lee, H. and Hood, L. (1993) Sequence length and error analysis of sequenase and automated Taq cycle sequencing methods. Bio Techniques 14:442–447.
Krawetz, S.A. (1989) Sequence errors described in GenBank: A means to determine the accuracy of DNA sequence interpretation. Nucl. Acids Res. 17:3951–3957.
Krogh, A., Brown, M., Mian, I.S., Sjölander, K., Haussler, D. (1993) Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., accepted.
Lander, E.S. and Waterman, M.S. (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2:231–239.
Larson, S., Mudita, J., Myers, G. (1993) An interface for a fragment assembly kernal. University of Arizona, Department of Computer Science TR93–20.
Lawrence, C.B. and Solovyev, V.V. (1993) Assignment of position specific error probability to primary DNA sequence data, manuscript.
Lewin, B. (1992) Genes V. Wiley, New York.
Maxam, A.M. and Gilbert, W. (1977) A new method for sequencing DNA. Proc. Natl Acad. Sci. 74:5463–5467.
Oliver, S.G., et al. (1992) The complete DNA sequence of yeast chromosome III. Nature 357:38–46.
Posfai J. and Roberts, R.J. (1992) Finding errors in DNA sequences. Proc. Natl. Acad. Sci. 89: 4698–4702.
Roberts, L. (1990). Large-scale sequencing trials begin. Science, 250: 1336–1338.
Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain terminating inhibitors. Biochemistry 74:560–564.
Santner, T.J. and Duffy, D.E. (1989) The Statistical Analysis of Discrete Data. Springer-Verlag, NY.
Seto, D., Koop, B.F., Hood, L. (1993) An experimentally derived data set constructed for testing large-scale DNA sequence assembly algorithms. Genomics 15:673–676.
Staden, R. (1980). A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 8:3673–2694.
States, D.J. (1992) Molecular sequence accuracy: analysing imperfect data. Trends in Genetics 8:52–55.
States, D.J. and Botstein, D. (1991). Molecular sequence accuracy and the analysis of protein coding regions. Proc. Natl. Acad. Sci. USA 88:5518–5522.
Sulston, J. et al. (1992) The C. elegans genome sequencing project: a beginning. Nature 356:37–41.
Thorne, J.L. and Churchill, G.A. (1993) Estimation and reliability of molecular sequence alignments. Biometrics, accepted.
Thorne, J.L., Kishino, H., Felsenstein, J.F. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33:114–124.
Thorne, J.L., Kishino, H., Felsenstein, J.F. (1992) Inching toward reality: An improved likelihood model of sequence evolution. J. Mol. Evol. 34:3–16.
Tibbets, C, Bowling, J.M., Golden, J.B. (1993) Neural networks for automated base calling of gel-based DNA sequencing ladders. In Automated DNA Sequencing and Analysis Techniques Dr. J. Craig Ventner, Editor, Academic Press.
Waterman, M.S. (1984) General methods of sequence comparison. Bull. Math. Biol. 46:473–500.
Watson, J and Crick, F. (1953) Nature 171: 737–738.
Besag, J. and Mengersen, K.L. (1993) Meta-Analysis using Monte Carlo Markov Chain methods. Tech. report, Dept. of Statistics, Colorado State Univ.
Celeux, G. and Diebolt, J. (1986) The SEM algorithm: a probabilistic teacher algorithm derived from the EM algorithm for the mixture problem. Cornput. Statist. Quater. 2, 73–82.
Diebolt, J. and Robert, C.P. (1993) The Duality Principle: Discussion of Smith and Roberts, Besag and Green, and Gllks et al. J.R.S.S. (Ser. B) 55, 73–74.
Diebolt, J. and Robert, C.P. (1994) Estimation of finite mixture distributions by Bayesian sampling. J.R.S.S. (Ser. B) 56, 163–175.
Gelman, A. and Rubin, D.B. (1992) Does a single iteration suffice? In Bayesian Statistics 4 (J.O. Berger, J.M. Bernardo, A.P. Dawid and A.F.M. Smith, eds.) Oxford University Press, London.
Karlin, S., Dembo, A., and Kawabata, T. (1990). Statistical composition of high-scoring segments from molecular sequences. Ann. Statist. 18 , 571–581.
Lawrence, C.E., Atschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262, 208–214.
Muller, P. (1992) A black-box algorithm for implementing the Metropolis algorithm. Tech. Report, Dept. of Statistics, Purdue University, Lafayette.
Qian, W. and Titterington, D.M. (1991) Estimation of parameters in hidden Markov models. Phil Trans. Roy. Soc. London A 337, 407–428.
Robert, C.P. (1992) Discussion of Meng and Rubin In Bayesian Statistics 4 (J.O. Berger, J.M. Bernardo, A.P. Dawid and A.F.M. Smith, eds.) Oxford University Press, London.
Robert, C.P. (1993) Convergence assessments for Monte-Carlo Markov chain methods. Technical Report, Dept. of Math, Univ. de Rouen.
Tierney, L. (1991) Markov chains for exploring posterior distributions. Computer Sciences and Statistics: Proc. 23d Symp. Interface, 563–570.
Cleveland, W.S. (1979) Robust Locally-weighted Regression and Smoothing Scatterplots. J. Amer. Statist. Assoc. 74, 829–836.
Koop, B.F., Rowan, L., Chen, W.-Q., Deshpande, P., Lee, BL and Hood, L. (1993). Sequence Length and Error Analysis of Sequenase and Automated Taq Cycle Sequencing Methods. Biotechniques 14, 442–447.
Sanger, F., Nicklen, S. and Coulson, A.R. (1977). DNA Sequencing with Chain Terminating Inhibiters. Biochemistry 74, 560–564.
Waterman, M.S. (1984). General Methods of Sequence Comparison. Bull Math. Biol. 46, 473–500.
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Churchill, G.A. (1995). Accurate Restoration of DNA Sequences. In: Gatsonis, C., Hodges, J.S., Kass, R.E., Singpurwalla, N.D. (eds) Case Studies in Bayesian Statistics, Volume II. Lecture Notes in Statistics, vol 105. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-2546-1_3
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