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Original Articles

Gene Pathways Discovery in Asbestos-Related Diseases using Local Causal Discovery Algorithm

, , , &
Pages 1840-1859 | Received 01 Nov 2010, Accepted 05 Sep 2011, Published online: 21 May 2012

References

  • Adamson , I. Y. , Bowden , D. H. ( 1987 ). Response of mouse lung to crocidolite asbestos. 2. Pulmonary fibrosis after long fibres . Journal of Pathology 152 : 109 – 117 .
  • Brilz , E. M. (2009). Evaluation of a local causal discovery algorithm using mixture of observational and experimental data. Dept. Computer Science, University of Montana, Master's Thesis, Missoula, MN.
  • Cooper , G. F. ( 2000 ). A Bayesian method for causal modeling and discovery under selection. Proc. Confernce on Uncertainty in Artificial Intelligence, Morgan Kaufmann, San Franciso, CA .
  • Cooper , G. F. , Herskovits , E. ( 1992 ). A Bayesian method for the induction of probabilistic networks from data . Machine Learning 9 : 309 – 347 .
  • Cooper , G. F. , Yoo , C. ( 1999 ). Causal discovery from a mixture of experimental and observational data. Proc. of the Conference on Uncertainty in Artificial Intelligence. Morgan Kaufmann, Sanfrancisco, CA .
  • Edwards , R. , Glass , L. ( 2000 ). Combinatorial explosion in model gene networks . Chaos 10 : 691 – 704 .
  • Friedman , N. , Koller , D. ( 2000 ). Being Bayesian about network structure. Proc. of Uncertainty in Artificial Intelligence.
  • Gasch , A. , Spellman , P. , Kao , C. M. , Carmel-Harel , O. , Eisen , M. B. , Storz , G. , Botstein , D. , Brown , P. O. ( 2000 ). Genomic expression programs in the response of yeast cells to environmental changes . Molecular Biology of the Cellular 11 ( 12 ): 4241 – 4257 .
  • Grzegorczyk , M. , Husmeier , D. , Edwards , K. D. , Ghazar , P. , Millar , A. J. ( 2008 ). Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler . Bioinformatics 24 : 2071 – 2078 .
  • Heckerman , D. , Geiger , D. , Chickering , D. ( 1995 ). Learning Bayesian networks: The combination of knowledge and statistical data . Machine Learning 20 : 197 – 243 .
  • Kauffman , S. ( 1993 ). Origins of Order – Self-Organization and Selection in Evolution . Oxford : Oxford University Press .
  • Lyons-Weiler , J. ( 2003 ). The Gene Expression Data Simulation Project at the University of Pittsburgh.
  • Michaud , D. , Marsh , A. , Dhurjati , P. ( 2003 ). eXPatGen: An on-line gene expression pattern generator . Bioinformatics 19 ( 9 ): 1140 – 1146 .
  • Murthy , S. , Testa , J. ( 1999 ). Asbestos, Chromosomal deletions, and tumor suppressor gene alterations in human malignant mesothelioma . Journal of Cellular Physiology 80 : 150 – 157 .
  • Nuwaysir , E. , Bittner , M. , Trent , J. , Barrett , J. C. , Afshari , C. A. ( 1999 ). Microarrays and toxicology: The advent of toxicogenomics . Molecular Carcinogenesis 24 ( 3 ): 153 – 159 .
  • Nykter , M. , Aho , T. , Ahdesmäki , M. , Ruusuvuori , P. , Lehmussola , A. , Yii-Harja , O. ( 2006 ). Simulation of microarray data with realistic characteristics. BMC Bioinformatics 7(349) .
  • Pearl , J. ( 1988 ). Probabilistic Reasoning in Intelligent Systems . San Mateo , CA : Morgan Kaufmann .
  • Spirtes , P. , Glymour , C. , Scheines , R. ( 2000 ). Causation, Prediction, and Search . Cambridge , MA : MIT Press .
  • Spirtes , P. , C. Glymour , C. , Scheines , R. ( 2008 ). The TETRAD Project: Causal Models and Statistical Data . Available at : http://www.phil.cmu.edu/projects/tetrad/ .
  • Takahashi , K. ( 2004 ). Multi-algorithm and multi-timescale cell biology simulation. Fujisawa, Keio University. Ph.D. thesis, Fujisawa, Japan .
  • Takahashi , K. ( 2006 ). Numerical Simulation and Molecular Systems Biology, International Conference on Systems Biology . Japan : Yokohama .
  • Teyssier , M. , Koller , D. ( 2005 ). Ordering-Based Search: A Simple and Effective Algorithm for Learning Bayesian Networks. Proceedings of UAI. Edinburgh, Scottland, UK. 21:584–590 .
  • Werhli , A. , Husmeier , D. ( 2007 ). Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior Knowledge. Statistical Applications in Genetics and Molecular Biology 6(1): Article 15 .
  • Yoo , C. , Blitz , E. ( 2009 ). Local causal discovery algorithm using causal bayesian networks . Annals of the NY Academy of Science 1158 : 93 – 101 .
  • Yoo , C. , Cooper , G. (2001). Causal discovery of latent-variable models from a mixture of experimental and observational data, Center for Biomedical Informatics Research Report CBMI-173. Center for Biomedical Informatics, Pittsburgh, PA.
  • Yoo , C. , Cooper , G. ( 2002 ). Discovery of Gene-Regulation Pathways Using Local Causal Search . San Antonio , TX : AMIA .
  • Yoo , C. , Cooper , G. ( 2002 ). Discovery of Gene-regulation Pathways using Local Causal Search . San Antonio , Tx : AMIA , pp. 914 – 918 .
  • Yoo , C. , Pershouse , M. , Putnam , L. ( 2004 ). Discovery of gene-regulation pathways in asbestos using background knowledge. Research in Computational Molecular Biology, San Diego, CA (poster) .
  • Yoo , C. , Thorsson , V. , Cooper , G. F. ( 2002 ). Discovery of a gene-regulation pathway from a mixture of experimental and observational DNA microarray data, Pacific Symposium on Biocomputing, World Scientific, Maui, Hawaii .
  • Yu , I. , Smith , V. A. , Wang , P. P. , Hartemink , A. J. , Jarvis , E. D. ( 2004 ). Advances to bayesian network inference for generating causal networks from observational biological data . Bioinformatics 20 : 3594 – 3603 .

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