Signal processing for DNA sequencing

by Petros T. Boufounos Submitted to the Department of Electrical Engineering and Computer Science in partial fulfillment of the requirements for the degrees of Bachelor of Science in Electrical Engineering and Computer Science and Master of Engineering in Electrical Engineering and Computer Science at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY June, 2002  Massachusetts Institute of Technology, 2002. All Rights Reserved.

[1]  V. Solovyev,et al.  Assignment of position-specific error probability to primary DNA sequence data. , 1994, Nucleic acids research.

[2]  C. Yanisch-Perron,et al.  Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. , 1985, Gene.

[3]  Michael S. Waterman,et al.  Genetic mapping and DNA sequencing , 1996 .

[4]  Athanasios Papoulis,et al.  Probability, Random Variables and Stochastic Processes , 1965 .

[5]  C. Tibbetts,et al.  Neighboring nucleotide interactions during DNA sequencing gel electrophoresis. , 1991, Nucleic acids research.

[6]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[7]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[8]  Maria Huhtala,et al.  Random Variables and Stochastic Processes , 2021, Matrix and Tensor Decompositions in Signal Processing.

[9]  Lawrence R. Rabiner,et al.  A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[10]  I. Miller.  Probability, Random Variables, and Stochastic Processes , 1966 .

[11]  G. Hartzell,et al.  DNA sequence confidence estimation. , 1994, Genomics.

[12]  Simon Haykin,et al.  Neural Networks: A Comprehensive Foundation , 1998 .

[13]  W. Huse,et al.  Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. , 1988, Nucleic acids research.

[14]  D. Nelson,et al.  IMPROVING DNA SEQUENCING ACCURACY AND THROUGHPUT , 1996 .

[15]  Robert G. Gallager,et al.  Discrete Stochastic Processes , 1995 .

[16]  Richard O. Duda,et al.  Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.

[17]  Yoshua Bengio,et al.  Global optimization of a neural network-hidden Markov model hybrid , 1992, IEEE Trans. Neural Networks.

[18]  Lawrence R. Rabiner,et al.  On the relations between modeling approaches for speech recognition , 1990, IEEE Trans. Inf. Theory.

[19]  A. Berno.  A graph theoretic approach to the analysis of DNA sequencing data. , 1996, Genome research.

[20]  Yariv Ephraim,et al.  On the relations between modeling approaches for information sources (speech recognition) , 1988, ICASSP-88., International Conference on Acoustics, Speech, and Signal Processing.

[21]  L. M. Smith,et al.  An adaptive, object oriented strategy for base calling in DNA sequence analysis. , 1993, Nucleic acids research.

[22]  M. Westphall,et al.  A software system for data analysis in automated DNA sequencing. , 1998, Genome research.

[23]  T. Minka.  Expectation-Maximization as lower bound maximization , 1998 .

[24]  C Y Ou,et al.  Polymerase chain reaction. , 1988, The Journal of infectious diseases.