@article{Beer12005,
  author = {Beerenwinkel, N and Rahnenf\"uhrer, J and D\"aumer, M and Hoffmann, D and
  Kaiser, R and Selbig, J and Lengauer, T },
  title = {Learning multiple evolutionary pathways from cross-sectional data},
  journal = {Journal of Computational Biology},
  year = {2005},
  volume = {12},
  pages = {584-598},
  number = {6},
  publisher = {Mary Ann Liebert, Inc.},
  address = {New Rochelle, NY, USA},
}

@article{Beer22005,
  author = {Beerenwinkel, N and Rahnenf\"uhrer, J and Kaiser, R and
    Hoffmann, D and Selbig, J and Lengauer, T },
  title = {Mtreemix: a software package for learning and using mixture models
    of mutagenetic trees},
  journal = {Bioinformatics},
  year = {2005},
  volume = {21},
  pages = {2106-2107},
  number = {9},
  month = {May},
  publisher = {Oxford University Press},
  address = {Oxford, UK},
}

@article{Bogo2008,
  author = {Bogojeska, J and Rahnenf\"uhrer, J and Lengauer, T},
  title = {Stability analysis of mixtures of mutagenetic trees},
  journal = {BMC Bioinformatics},
  year = {2008},
  volume = {9},
  number = {1},
}

@article{Demp1977,
    author = {Dempster, A P and Laird, N M and Rubin, D B },
    title = {Maximum Likelihood from Incomplete Data via the EM Algorithm},
    journal = {Journal of the Royal Statistical Society, Series B},
    volume = {39},
    year = {1977},
    pages = {1-38},
    publisher = {Blackwell Publishing},
    address = {Oxford, UK},
}

@article{Desp1999,
    author = {Desper, R and Jiang, F and Kallioniemi, O P and Moch, H and Papadimitriou, C H and Schaffer, A A },
    title = {Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data},
    journal = {Journal of Computational Biology},
    volume = {6},
    number = {1},
    year = {1999},
    pages = {37-52},
    publisher = {Mary Ann Liebert, Inc.},
    address = {New Rochelle, NY, USA},
}


@incollection{SL2001,
    author = {Hastie, T and Tibshirani, R and Friedman, J },
    booktitle = {The Elements of Statistical Learning},
    month = {August},
    publisher = {Springer-Verlag},
    series = {Springer Series in Statistics},
    title = {The Elements of Statistical Learning: Data Mining, Inference, and Prediction},
    year = {2001},
    pages = {193-222},
    address = {New York, NY, USA},
    edition = {1st},
}

@article{Rahn2005,
 author = {Rahnenf\"uhrer, J and Beerenwinkel, N and Schulz, W A and Hartmann, C and Deimling, A V and Wullich, B and Lengauer, T },
 title = {Estimating cancer survival and clinical outcome based on genetic tumor progression scores},
 journal = {Bioinformatics},
 volume = {21},
 number = {10},
 year = {2005},
 pages = {2438-2446},
 publisher = {Oxford University Press},
 address = {Oxford, UK},
 }

@article{Edm1967,
 author = {Edmonds, J },
 title = {Optimum Branchings},
 journal = {Journal of Research of the National Bureau of Standards},
 volume = {71B},
 year = {1967},
 pages = {233-240},
 address = {Washington, DC, USA},
 }

@article{Yin2006,
  author = {Yin, J and Beerenwinkel, N and Rahnenf\"uhrer, J and Lengauer, T },
  title = {Model selection for mixtures of mutagenetic trees},
  journal = {Statistical applications in genetics and molecular biology},
  year = {2006},
  number = {1},
  volume = {5},
  pages = {Article17},
  address  = {Berkeley, USA},
}

@inproceedings{Allen2000,
    author = {Allen, T V and Greiner, R },
    title = {Model Selection Criteria for Learning Belief Nets: An Empirical
    Comparison},
    booktitle = {Proceedings 17th International Conference on Machine Learning},
    publisher = {Morgan Kaufmann},
    pages = {1047-1054},
    year = {2000},
    address = {San Francisco, CA, USA},
}

@article{Prufer1918,
  author = {Pr\"ufer, H },
  title = {Beweis eines Satzes \"uber Permutationen},
  journal = {Arch. Math. Phys.},
  year = {1918},
  volume = {27},
  pages = {742-744},
}

@article{Cayle1989,
  author = {Cayley, A },
  title = {A theorem on trees},
  journal = {Quarterly Journal of Mathematics},
  year = {1889},
  volume = {23},
  pages = {376-378},
  publisher = {Oxford University Press},
  address = {Oxford, UK},
}

@book{Bootstrap1993,
    author = {Efron, B and Tibshirani, R J },
    publisher = {Chapman and Hall/CRC},
    series = {Monographs on Statistics and Applied Probability},
    title = {An introduction to the Bootstrap.},
    volume = {57},
    year = {1993},
}

@article{Jiang2000,
  author = {Jiang, F and Desper, R and Papadimitriou, C H and
  Schäffer, A A and Kallioniemi, O P and Richter, J and Schraml, P and
  Sauter, G and Mihatsch, M J and Moch, H },
  title = {Construction of evolutionary tree models for renal cell carcinoma
    from comparative genomic hybridization data},
  journal = {Cancer Research},
  year = {2000},
  volume = {60},
  pages = {6503-6509},
  number = {22},
}

@article{Ludwig2005,
    author = {Ludwig, J A and Weinstein, J N },
    title = {Biomarkers in Cancer Staging, Prognosis and Treatment Selection},
    journal = {Nat Rev Cancer},
    number = {11},
    pages = {845-856},
    volume = {5},
    year = {2005},
}

@article{Kalli1999,
  author = {Kallioniemi, A and Kallioniemi, O P and Sudar, D and
  Rutovitz, D and Gray, J W and Waldman, F and Pinkel, D },
  title = {Comparative genomic hybridization for molecular cytogenetic analysis
    of solid tumors},
  journal = {Science},
  year = {1992},
  volume = {258},
  pages = {818-821},
  number = {5083},
}

@inpress{Ketter2007,
  author = {Ketter, R and Kim, Y and Storck, S and Rahnenf\"uhrer, J
    and Romeike, R and Steudel, W and Zang, K and Henn, W },
  title = {Hyperdiploidy defines a distinct cytogenetic entity of meningiomas},
  journal = {Journal of neuro-oncology},
  year = {2007},
  note = {in press},
}

@article{Larder1989,
  author = {B. A. Larder and G. Darby and D. D. Richman},
  title = {HIV with reduced sensitivity to zidovudine (AZT) isolated during
    prolonged therapy},
  journal = {Science},
  year = {1989},
  volume = {243},
  pages = {1731-1734},
  number = {4899},
}

@article{LarKem1989,
  author = {B. A. Larder and S. D. Kemp},
  title = {Multiple mutations in HIV-1 reverse transcriptase confer high-level
    resistance to zidovudine (AZT)},
  journal = {Science},
  year = {1989},
  volume = {246},
  pages = {1155-1158},
  number = {4934},
}

@article{Boucher1992,
  author = {Boucher, C A and O'Sullivan, E and Mulder, J W and Ramautarsing, C
    and Kellam, P and Darby, G and Lange, J M and Goudsmit, J and
    Larder, B A},
  title = {Ordered appearance of zidovudine resistance mutations during treatment
    of 18 human immunodeficiency virus-positive subjects},
  journal = {J Infect Dis},
  year = {1992},
  volume = {165},
  pages = {105-110},
  number = {1},
}

@article{Rhee2003,
  author = {Rhee, S and Gonzales, M J and Kantor, R and
    Betts, B J and Ravela, J and Shafer, R W },
  title = {Human immunodeficiency virus reverse transcriptase and protease sequence
    database},
  journal = {Nucleic Acids Res},
  year = {2003},
  volume = {31},
  pages = {298-303},
  number = {1},
}

@article{Kuhn1955,
  author = {Kuhn, H W},
  title = {The Hungarian Method for the assignment problem},
  journal = {Naval Research Logistic Quarterly},
  year = {1955},
  volume = {2},
  pages = {83-97},
}
