@Book{biolog:seq,
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title = 	 {{Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids}},
publisher = 	 {Cambridge University Press},
year = 	 {1998},
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}


@Book{cox:miller,
author = 	 {Cox, D. R. and Miller, H. D.},
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title = 	 {{The Theory of Stochastic Processes}},
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year = 	 {1965},
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}




@Article{klotz:est,
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volume = 43,
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pages = {431--436}
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@Article{sharp:gibbs,
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volume = 12,
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@Article{kay:mark,
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year = 1986,
volume = 42,
pages = {855--865}
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@Article{gruger:valid,
author = 	 {Gr\"uger, J. and Kay, R. and Schumacher, M.},
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journal = 	 {Biometrics},
year = 	 {1991},
OPTkey = 	 {},
volume = 	 {47},

OPTnumber = 	 {},
pages = 	 {595--605},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
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@Article{long1,
author = 	 {Longini, I. M. and Clark, W. S. and Byers, R. H. and Ward, J. W. and Darrow, W. W. and Lemp, G. F. and Hethcote, H. W.},
title = 	 {Statistical analysis of the stages of {HIV}
infection using a {M}arkov model},
journal = 	 {Statistics in Medicine},
year = 	 {1989},
OPTkey = 	 {},
volume = 	 {8},
OPTnumber = 	 {},
pages = 	 {851--843},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {Original HIV Markov paper, four states}
}



@Article{long2,
author = 	 {Longini, I. M. and Clark, W. S. and Gardner, L. I. and Brundage, J. F.},
title = 	 {The dynamics of {CD4}+ {T}-lymphocyte decline in {HIV}-infected individuals: a {M}arkov modelling approach},
journal = 	 {Journal of Acquired Immune Deficiency Syndromes},
year = 	 {1991},
OPTkey = 	 {},
volume = 	 {4},
OPTnumber = 	 {4},
pages = 	 {1141--1147},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {original paper defining CD4 ranges as disease states}
}

@Article{sattlong,
author = 	 {Satten, G. A. and Longini, I. M.},
title = 	 {Markov chains with measurement error: {E}stimating
the `true' course of a marker of the progression of human
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journal = 	 {Applied Statistics - Journal of the Royal
Statistical Society Series C},
year = 	 {1996},
OPTkey = 	 {},
volume = 	 {45},
number = 	 {3},
pages = 	 {275--295},
month = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{retino2,
author = 	 {Marshall, G. and Jones, R. H.},
title = 	 {Multi-state {M}arkov models and diabetic retinopathy},
journal = 	 {Statistics in Medicine},
year = 	 {1995},
OPTkey = 	 {},
volume = 	 {14},
OPTnumber = 	 {},
OPTpages = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {This is the paper that includes covariates in
multistate models.}
}


@Article{duffy95,
author = 	 {Duffy, S. W. and Chen, H. H.},
title = 	 {Estimation of mean sojourn time in breast cancer screening
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detectable phase},
journal = 	 {Statistics in Medicine},
year = 	 {1995},
OPTkey = 	 {},
volume = 	 {14},
OPTnumber = 	 {},
pages = 	 {1531--1543},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {3 states, no death or recovery. Fitted with NLIN}
}



@Article{duffy96,
author = 	 {Chen, H. H. and Duffy, S. W. and Tabar, L.},
title = 	 {A {M}arkov chain method to estimate the tumour progression rate from preclinical to clinical phase, sensitivity and positive predictive value for mammography in breast cancer screening},
journal = 	 {The Statistician},
year = 	 {1996},
OPTkey = 	 {},
volume = 	 {45},
number = 	 {3},
pages = 	 {307--317},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {Measurement error introduction}
}

@Article{duffy:mover,
author = 	 {Chen, H. H. and Duffy, S. W. and Tabar, L.},
title = 	 {A mover-stayer mixture of {M}arkov chain models for the assessment of dedifferentiation and tumour progression in breast cancer},
journal = 	 {Journal of Applied Statistics},
year = 	 {1997},
OPTkey = 	 {},
volume =	 {24},
number =	 {3},
pages =	 {265--278},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}


@InCollection{kirby:spiegelhalter,
author = 	 {Kirby, A. J. and Spiegelhalter, D. J.},
title = 	 {Statistical modelling for the precursors of cervical cancer},
booktitle = 	 {Case Studies in Biometry},
OPTcrossref =  {},
OPTkey = 	 {},
OPTpages = 	 {},
publisher =	 {Wiley},
year =	 {1994},
OPTeditor = 	 {},
OPTvolume = 	 {},
OPTnumber = 	 {},
OPTseries = 	 {},
OPTtype = 	 {},
OPTchapter = 	 {},
address =	 {New York},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{ander:proth,
author = 	 {Andersen, P. K. and Hansen, L. S. and Keiding, N.},
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journal = 	 {Statistics in Medicine},
year = 	 {1991},
OPTkey = 	 {},
volume = 	 {10},
OPTnumber = 	 {},
pages = 	 {1061--1067},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{kalb:agg,
author = 	 {Kalbfleisch, J. D. and Lawless, J. F. and Vollmer, W. M.},
title = 	 {Estimation in {M}arkov models from aggregate data},
journal = 	 {Biometrics},
year = 	 {1983},
OPTkey = 	 {},
volume = 	 {39},
OPTnumber = 	 {},
pages = 	 {907--919},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{klein:marker,
author = 	 {Klein, J. P. and Klotz, J. H. and Grever, M. R.},
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journal = 	 {Biometrics},
year = 	 {1984},
OPTkey = 	 {},
volume = 	 {40},
OPTnumber = 	 {},
pages = 	 {927--936},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {Only transitions 1->2->3, with covariates included
as in a Cox model}
}


@Article{gail,
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year = 	 {1981},
OPTkey = 	 {},
volume = 	 {37},
OPTnumber = 	 {},
pages = 	 {67--78},
OPTmonth = 	 {},
OPTnote = 	 {},
annote = 	 {Interpolation to reduce to common monitoring times}
}



@Article{gentlaw,
author = 	 {Gentleman, R. C. and Lawless, J. F. and Lindsey, J. C. and Yan, P.},
title = 	 {Multi-state {M}arkov models for analysing incomplete disease history data with illustrations for {HIV} disease},
journal = 	 {Statistics in Medicine},
year = 	 {1994},
key = 	 {},
volume = 	 {13},
number = 	 {3},
pages = 	 {805--821},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{rich,
author = 	 {Guihenneuc-Jouyaux, C. and Richardson, S. and Longini, I. M.},
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year = 	 {2000},
OPTkey = 	 {},
volume =	 {56},
OPTnumber = 	 {},
pages =	 {733--741},
OPTmonth =	 {September},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Book{andersen,
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ALTeditor = 	 {},
title = 	 {Statistical Models based on Counting Processes},
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year = 	 {1993},
OPTkey = 	 {},
OPTvolume = 	 {},
OPTnumber = 	 {},
OPTseries = 	 {},
address =	 {New York},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Book{macdonald:zucchini,
author =	 {Macdonald, I. L. and Zucchini, W.},
ALTeditor = 	 {},
title = 	 {Hidden Markov and Other Models for Discrete-Valued Time Series},
publisher = 	 {Chapman and Hall},
year = 	 {1997},
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OPTvolume = 	 {},
OPTnumber = 	 {},
OPTseries = 	 {},
address =	 {London},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Book{guttorp,
author =	 {Guttorp, P.},
ALTeditor = 	 {},
title = 	 {Stochastic Modeling of Scientific Data},
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year = 	 {1995},
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OPTvolume = 	 {},
OPTnumber = 	 {},
OPTseries = 	 {},
address =	 {London},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{juang:rabiner,
author = 	 {Juang, B. H. and Rabiner, L. R.},
title = 	 {Hidden {M}arkov models for speech recognition},
journal = 	 {Technometrics},
year = 	 {1991},
OPTkey = 	 {},
volume =	 {33},
OPTnumber = 	 {},
pages =	 {251--272},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{baum:petrie66,
author = 	 {Baum, L. E. and Petrie, T.},
title = 	 {Statistical inference for probabilistic functions of finite state {M}arkov chains},
journal = 	 {Annals of Mathematical Statistics},
year = 	 {1966},
OPTkey = 	 {},
volume =	 {37},
OPTnumber = 	 {},
pages =	 {1554--1563},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{baum:petrie70,
author = 	 {Baum, L. E. and Petrie, T. and Soules, G. and Weiss, N.},
title = 	 {A maximisation technique occurring in the statistical analysis of probabilistic functions of {M}arkov chains},
journal = 	 {Annals of Mathematical Statistics},
year = 	 {1970},
OPTkey = 	 {},
volume =	 {41},
OPTnumber = 	 {},
pages =	 {164--171},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{rabiner,
author = 	 {Rabiner, L. R.},
title = 	 {A tutorial on hidden {M}arkov models and selected applications in speech recognition},
journal = 	 {Proceedings of the {IEEE}},
year = 	 {1989},
OPTkey = 	 {},
volume =	 {77},
OPTnumber = 	 {},
pages =	 {257--286},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Book{rabiner:juang,
author =	 {Rabiner, L. R. and Juang, B. H.},
ALTeditor = 	 {},
title = 	 {Fundamentals of speech recognition},
publisher = 	 {Prentice-Hall},
year = 	 {1993},
OPTkey = 	 {},
OPTvolume = 	 {},
OPTnumber = 	 {},
OPTseries = 	 {},
OPTaddress = 	 {},
OPTedition = 	 {},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{albert99,
author = 	 {Albert, P. S.},
title = 	 {A mover-stayer model for longitudinal marker data},
journal = 	 {Biometrics},
year = 	 {1999},
OPTkey = 	 {},
volume =	 {55},
number =	 {4},
pages =	 {1252--1257},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{albert:wac,
author = 	 {Albert, P. S. and Waclawiw, M. A.},
title = 	 {A two-state {M}arkov chain for heterogeneous transitional data: A quasi-likelihood approach},
journal = 	 {Statistics in Medicine},
year = 	 {1998},
OPTkey = 	 {},
volume =	 {17},
number =	 {13},
pages =	 {1481--1493},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{albert94,
author = 	 {Albert, P. S.},
title = 	 {A {Ma}rkov model for sequences of ordinal data from a relapsing-remitting disease},
journal = 	 {Biometrics},
year = 	 {1994},
OPTkey = 	 {},
volume =	 {50},
number =	 {1},
pages =	 {51--60},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{viterbi,
author = 	 {Viterbi, J.},
title = 	 {Error bounds for convolutional codes and an asymptotically optimal decoding algorithm},
journal = 	 {IEEE Transactions on Information Theory},
year = 	 {1967},
OPTkey = 	 {},
volume =	 {13},
OPTnumber = 	 {},
pages =	 {260--269},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{albert:2000,
author = 	 {Albert, P. S.},
title = 	 {A transitional model for longitudinal binary data subject to nonignorable missing data},
journal = 	 {Biometrics},
year = 	 {2000},
OPTkey = 	 {},
volume =	 {56},
number =	 {2},
pages =	 {602--608},
month =	 {June},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{aalen:deangelis,
author = 	 {Aalen, O. O. and Farewell, V. T. and DeAngelis, D. and Day, N. E. and Gill, O. N.},
title = 	 {A {M}arkov model for {HIV} disease progression including the effect of {HIV} diagnosis and treatment: Application to {AIDS} prediction},
journal = 	 {Statistics in Medicine},
year = 	 {1997},
OPTkey = 	 {},
volume =	 {16},
number =	 {19},
pages =	 {2191--2210},
OPTmonth =	 {October},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{destavola,
author = 	 {de Stavola, B. L.},
title = 	 {Testing departures from homogeneity in multistate {M}arkov processes},
journal = 	 {Applied Statistics - Journal of the Royal Statistical Society, Series C},
year = 	 {1988},
OPTkey = 	 {},
volume =	 {37},
OPTnumber = 	 {},
pages =	 {242--250},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
}

@Article{andersen88,
author = 	 {Andersen, P. K.},
title = 	 {Multistate models in survival analysis: a study of nephropathy and mortality in diabetes},
journal = 	 {Statistics in Medicine},
year = 	 {1988},
OPTkey = 	 {},
volume =	 {7},
number =	 {6},
pages =	 {661--670},
OPTmonth =	 {June},
OPTnote = 	 {},
OPTannote = 	 {}
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@Article{leroux:consist,
author = 	 {Leroux, B. G.},
title = 	 {Maximum-likelihood estimation for hidden {M}arkov models},
journal = 	 {Stochastic Processes and their Applications},
year = 	 {1992},
OPTkey = 	 {},
volume =	 {40},
OPTnumber = 	 {},
pages =	 {127--143},
OPTmonth = 	 {},
OPTnote = 	 {},
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@Article{bickel:ritov:ryden,
author = 	 {Bickel,  P. J. and Ritov, Y. and Ryd\'en, T.},
title = 	 {Asymptotic normality of the maximum likelihood estimator for general hidden {M}arkov models},
journal = 	 {Annals of Statistics},
year = 	 {1998},
OPTkey = 	 {},
volume =	 {26},
OPTnumber = 	 {},
pages =	 {1614--1635},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
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@Article{perez,
author = 	 {P\'erez-Oc\'on, R. and Ruiz-Castro, J. E. and G\'amiz-P\'erez, M.Luz},
title = 	 {Non-homogeneous {M}arkov models in the analysis of survival after breast cancer},
journal = 	 {Applied Statistics - Journal of the Royal Statistical Society, Series C},
year = 	 {2001},
OPTkey = 	 {},
volume =	 {50},
number =	 {1},
pages =	 {111--124},
OPTmonth = 	 {},
OPTnote = 	 {},
OPTannote = 	 {}
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@ARTICLE{bureau:hughes:shiboski:00,
author	    = {Bureau, A. and Hughes, J. P. and Shiboski, S. C.},
title	    = {An {S-Plus} implementation of hidden {M}arkov models in
continuous time},
journal     = {Journal of Computational and Graphical Statistics},
year	    = {2000},
volume	    = {9},
pages	    = {621--632},
abstract    = {}
}

@Article{oehlert,
author = 	 {Oehlert, G. W.},
title = 	 {A note on the delta method},
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number =	 1,
month =	 {February}
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@Book{lindsey:rm,
  author =	 {Lindsey, J. K.},
  ALTeditor = 	 {},
  title = 	 {Models for Repeated Measurements},
  publisher = 	 {Oxford University Press},
  year = 	 {1999},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  series =	 {Oxford Statistical Science Series},
  OPTaddress = 	 {},
  edition =	 {second},
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  OPTnote = 	 {},
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@Article{jackson:sharples:2002,
  author = 	 {Jackson, C. H. and Sharples,L. D.},
  title = 	 {Hidden {M}arkov models for the onset and progression of bronchiolitis
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  journal = 	 {Statistics in Medicine},
  year = 	 {2002},
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  OPTannote = 	 {}
}


@Article{jackson:sharples:2003,
  author = 	 {Jackson, C. H. and Sharples, L. D. and Thompson, S. G. and Duffy, S. W. and Couto, E.},
  title = 	 {Multistate {M}arkov models for disease progression with classification error},
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  year = 	 {2003},
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  volume =	 {52},
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  note =	 {},
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@PhdThesis{my:phd,
  author = 	 {Jackson, C. H.},
  title = 	 {Statistical models for the latent progression of chronic diseases using serial biomarkers},
  school = 	 {University of Cambridge},
  year = 	 {2002},
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  OPTnote = 	 {},
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@Article{kalbfleisch:lawless,
  author = 	 {Kalbfleisch, J.D. and Lawless, J.F.},
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  year = 	 {1985},
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  volume =	 {80},
  number =	 {392},
  pages =	 {863--871},
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@Article{my:cav,
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@Article{matrixexp,
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  title = 	 {Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later},
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@Article{ahf,
  author = 	 {Aguirre-Hernandez, R. and Farewell, V.},
  title = 	 {{A Pearson-type goodness-of-fit test for stationary and time-continuous Markov regression models}},
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  pages =	 {1899-1911},
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  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{titman:sharples,
  author = 	 {Titman, A. and Sharples, L. D.},
  title = 	 {{A general goodness-of-fit test for Markov and hidden Markov models}},
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  OPTkey = 	 {},
  volume =	 {27},
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  pages =	 {2177--95},
  OPTmonth = 	 {},
  OPTannote = 	 {}
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@PhdThesis{titman:phd,
  author = 	 {Titman, A.},
  title = 	 {Model diagnostics in multi-state models of biological systems},
  school = 	 {University of Cambridge},
  year = 	 {2008},
  OPTkey = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{titman:asympnull,
  title={Computation of the asymptotic null distribution of goodness-of-fit tests for multi-state models},
  author={Titman, A.C.},
  journal={Lifetime Data Analysis},
  volume={15},
  number={4},
  pages={519--533},
  year={2009},
}

@Article{putter:mstate,
  author = 	 {Putter, H. and Fiocco, M. and Geskus, R. B.},
  title = 	 {{Tutorial in biostatistics: competing risks and multi-state models}},
  journal = 	 {Statistics in Medicine},
  year = 	 {2007},
  OPTkey = 	 {},
  volume =	 {26},
  OPTnumber = 	 {},
  pages =	 {2389--2430},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{sweeting:inform:msm,
  author = 	 {Sweeting, M. J. and Farewell, V. and De Angelis, D.},
  title = 	 {{Multi-State Markov Models for Disease Progression in the Presence of Informative Examination Times: an Application to Hepatitis C}},
  journal = 	 {Statistics in Medicine},
  year = 	 {2010},
  OPTkey = 	 {},
  volume =	 {29},
  number =	 {11},
  pages =	 {1161-1174},
  OPTmonth = 	 {},
  OPTannote = 	 {}
}
