This file was created with JabRef 1.3.1.

@ARTICLE{bairoch00swiss-prot,
  author = {Bairoch A., and Apweiler R},
  title = {The SWISS-PROT protein sequence database and its supplement TrEMBL},
  journal = {Nucleic Acids Res.},
  year = {2000},
  number = {28},
  pages = {45-48},
  owner = {adyssoft},
  url = {http://www.expasy.ch/sprot/sprot-top.html},
}

@INPROCEEDINGS{andorf02discovering,
  author = {Andorf, C., Dobbs, D., and Honavar, V.},
  title = {Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences},
  booktitle = {Proceedings of the Conference on Computational Biology and Genome Informatics. Durham, North Carolina},
  year = {2002},
  owner = {adyssoft},
}

@ARTICLE{bach02kernel,
  author = {Bach, Francis and Jordan, Michael I.},
  title = {Latent Dirichlet Allocation},
  journal = {JMLR},
  year = {2002},
  volume = {3},
  pages = {1--48},
  month = {Jul},
  url = {xxx},
}

@ARTICLE{blei03latent,
  author = {Blei, David M. and Ng, Andrew Y. and Jordan, Michael I.},
  title = {Latent Dirichlet Allocation},
  journal = {JMLR},
  year = {2003},
  volume = {3},
  pages = {993--1022},
  month = {Jan},
  url = {xxx},
}

@INPROCEEDINGS{blei01latent,
  author = {David M. Blei and Andrew Y. Ng and Michael I. Jordan},
  title = {Latent Dirichlet Allocation},
  booktitle = {Neural Information Processing Systems 14, NIPS2001},
  year = {2001},
  url = {citeseer.nj.nec.com/article/blei02latent.html},
}

@INPROCEEDINGS{boutilier96contextspecific,
  author = {Craig Boutilier and Nir Friedman and Moises Goldszmidt and Daphne Koller},
  title = {Context-Specific Independence in {Bayesian} Networks},
  booktitle = {Uncertainty in Artificial Intelligence},
  year = {1996},
  pages = {115--123},
  url = {citeseer.nj.nec.com/article/boutilier96contextspecific.html},
}

@BOOK{charniak93statistical,
  title = {Statistical Language Learning, Cambridge: 1993 },
  publisher = {MIT Press},
  year = {1993},
  author = {Eugene Charniak},
  owner = {adyssoft},
}

@ARTICLE{gene00gene,
  author = {Consortium, The Gene Ontology},
  title = {Gene Ontology: tool for the unification of biology},
  journal = {Nature Genet.},
  year = {2000},
  number = {25},
  pages = {25-29},
  owner = {adyssoft},
}

@BOOK{cowell99probabilistic,
  title = {Probabilistic Networks and Expert Systems },
  publisher = {Springer},
  year = {1999},
  author = {Cowell, R.G., Dawid, A.P., Lauritzen, S.L., Spiegelhalter, D.J. },
  owner = {adyssoft},
}

@BOOK{durbin98biological,
  title = {Biological sequence  analysis},
  publisher = {Cambridge University Press},
  year = {1998},
  author = {Durbin, R. and Eddy, S. and Krogh, A. and Mitchison G.  },
  owner = {adyssoft},
}

@INPROCEEDINGS{hofmann99probabilistic,
  author = {Thomas Hofmann},
  title = {Probabilistic Latent Semantic Analysis},
  booktitle = {Proc. of Uncertainty in Artificial Intelligence, UAI'99},
  year = {1999},
  address = {Stockholm},
  url = {citeseer.nj.nec.com/hofmann99probabilistic.html},
}

@BOOK{manning99foundations,
  title = {Foundations of Statistical Natural Language Processing},
  publisher = {MIT Press},
  year = {1999},
  author = {Christopher D. Manning and Hinrich Schütze},
  address = {Cambridge, MA},
  month = {May},
  url = {xxx},
}

@INPROCEEDINGS{mccallum98comparison,
  author = {Andrew McCallum and Kamal Nigam},
  title = {A Comparison of Event Models for Naive Bayes Text Classification},
  booktitle = {AAAI-98 Workshop on "Learning for Text Categorization" },
  year = {1998},
  owner = {adyssoft},
}

@TECHREPORT{silvescu04inter-element,
  author = {Adrian Silvescu and Carson Andorf and Drena Dobbs and Vasant Honavar},
  title = {Inter-element dependency models for sequence classification, www.cs.iastate.edu/~silvescu/papers/nbktr/nbktr.ps},
  institution = {Department of Computer Science, Iowa State University },
  year = {2004},
  owner = {adyssoft},
}

@BOOK{ewens01statistical,
  title = {Statistical Methods in Bioinformatics},
  publisher = {Springer},
  year = {2001},
  author = {Warren J. Ewens, Gregory R. Grant },
  owner = {adyssoft},
}

@INPROCEEDINGS{xing03hierachical,
  author = {Xing, E.P. and Jordan, M.I. and Karp, R.M. and Russell, S.},
  title = {A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Sequences},
  booktitle = {Neural Information Processing Systems 15, NIPS2002},
  year = {2002},
  url = {xxx},
}

@INPROCEEDINGS{xing02logos,
  author = {E.P. Xing and W. Wu and M.I. Jordan and R.M. Karp},
  title = {LOGOS: A modular Bayesian model for de novo motif detection},
  booktitle = {IEEE Computer Society Bioinformatics Conference, CSB2003},
  year = {2003},
  url = {xxx},
}

@MANUAL{andorf04pcdatasets,
  title = {www.cs.iastate.edu/~andorfc/pcdatasets.html},
  owner = {adyssoft},
  url = {www.cs.iastate.edu/~andorfc/pcdatasets.html},
}

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