@article{ forney1973viterbi,
  title={The viterbi algorithm},
  author={Forney Jr, G.D.},
  journal={Proceedings of the IEEE},
  volume={61},
  number={3},
  pages={268--278},
  year={1973},
  publisher={IEEE}
}

@article{ flusberg2010direct,
  title={Direct detection of DNA methylation during single-molecule, real-time sequencing},
  author={Flusberg, B.A. and Webster, D.R. and Lee, J.H. and Travers, K.J. and Olivares, E.C. and Clark, T.A. and Korlach, J. and Turner, S.W.},
  journal={Nature methods},
  volume={7},
  number={6},
  pages={461--465},
  year={2010},
  publisher={Nature Publishing Group}
}

@article{ eid2009real,
  title={Real-time DNA sequencing from single polymerase molecules},
  author={Eid, J. and Fehr, A. and Gray, J. and Luong, K. and Lyle, J. and Otto, G. and Peluso, P. and Rank, D. and Baybayan, P. and Bettman, B. and others},
  journal={Science},
  volume={323},
  number={5910},
  pages={133--138},
  year={2009},
  publisher={American Association for the Advancement of Science}
}

@article{ clark2012characterization,
  title={Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing},
  author={Clark, T.A. and Murray, I.A. and Morgan, R.D. and Kislyuk, A.O. and Spittle, K.E. and Boitano, M. and Fomenkov, A. and Roberts, R.J. and Korlach, J.},
  journal={Nucleic Acids Research},
  volume={40},
  number={4},
  pages={e29--e29},
  year={2012},
  publisher={Oxford Univ Press}
}

@Article{ blasr, 
AUTHOR = {Chaisson, Mark and Tesler, Glenn},
TITLE = {Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application},
JOURNAL = {BMC Bioinformatics},
VOLUME = {13},
YEAR = {2012},
NUMBER = {1},
PAGES = {238},
URL = {http://www.biomedcentral.com/1471-2105/13/238},
DOI = {10.1186/1471-2105-13-238},
ISSN = {1471-2105},
ABSTRACT = {We describe the method BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error. We also present a combinatorial model of sequencing error that motivates why our approach is effective. The results indicate that mapping SMS reads is both highly specific and rapid.},
}


@book{ cart,
author = "L. Breiman and J. H. Friedman and R. Olshen and C. J. Stone",
title = "Classification and Regression Trees",
publisher = "Wadsworth",
address = "Belmont, California",
year = "1984"
}

@article{ gradientboost,
   AUTHOR="Jerome H. Friedman",
   TITLE="Greedy Function Approximation: A Gradient Boosting Machine",
   JOURNAL="The Annals of Statistics",
   YEAR="2001",
  VOLUME="29",
  PAGES="1189-1232"
}

@article{ crf-boost,
  AUTHOR= "Thomas G. Dietterich, Adam Ashenfelter, and Yaroslav Bulatov",
  TITLE="Training Conditional Random Fields via Gradient Tree Boosting",
  JOURNAL="International Conference on Machine Learning",
  YEAR="2004",
  VOLUME="1",
  PAGES="1-2"
}

@Manual{ gbm,
  title = {gbm: Generalized Boosted Regression Models},
  author = {Greg Ridgeway},
  year = {2010},
  note = {R package version 1.6-3.1},
  url = {http://CRAN.R-project.org/package=gbm},
}
