Papers

Refereed publications

2010

  • J.P. Baudry, A.E. Raftery, G. Celeux, K. Lo and R. Gottardo (2010). Combining Mixture Components for Clustering.  Journal of Graphical and Computational Statistics, 19: 332:353. [link]
  • X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo (2010). PICS: Probabilistic Inference for ChIP-seq. Biometrics, 66: xx-xx. [link]
  • B. Luke, A. Doucet and R. Gottardo (2010). An Efficient Computational Approach for Prior Sensitivity Analysis and Cross-Validation. Canadian Journal of Statistics, 38: 47 - 64. [link]
  • A. Droit, C. Cheung, and R. Gottardo (2010). rMAT – an R/Bioconductor package for analyzing ChIP-chip experiments, Bioinformatics, 26:678-679. [link]

2009

  • Gottardo, R., Brinkman, R.R., Luta, G. and Wand, M.P. (2009). Recent bioinformatics advances in the analysis of high throughput flow cytometry data. Editorial article. Advances In Bioinformatics, doi:10.1155/2009/461763 [link].
  • G. Finak, A. Bashashati, R. Brinkman, R. Gottardo (2009). Merging Mixture Components for Cell Population Identification in Flow Cytometry. Advances in Bioinformatics, doi:10.1155/2009/247646 [link].
  • K. Lo, F. Hahne, R. Brinkman and R. Gottardo (2009). flowClust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinformatics, 10: R145. [link]
  • R. Gottardo and A. E. Raftery (2009) Bayesian robust variable and transformation selection: A unified approach, Canadian Journal of Statistics, 37: 1-20. [link]

2008

  • V. T. Chu, R. Gottardo, A. E. Raftery, R. E. Bumgarner and K. Y. Yeung (2008). MeV+R: Using MEV as a GUI for Bioconductor application. Genome Biology 9:R118. [link]
  • R. Gottardo, A. E. Raftery (2008). Markov chain Monte Carlo with mixtures of singular distributions. Journal of Computational and Graphical Statistics 17:917-943. [link]
  • K. Lo, R. Brinkman and R. Gottardo (2008). Automated gating of flow cytometry data via robust model based clustering. Cytometry A, 73:321-332. [link]
  • R. Gottardo, Li, W., Liu, S. and Johnson, E. (2008). A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. Biometrics, 64:468-78. [link]

2007

  • K. Lo and R. Gottardo (2007). Flexible empirical Bayes models for differential gene expression. Bioinformatics 23: 328. [link]

2006

  • W. E. Johnson, Li, W., Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., and Liu, X. S. (2006). Model-based analysis of tiling-arrays for ChIP-chip. PNAS 103:12457-12462. [link]
  • R. Gottardo, A. E. Raftery, K. Y. Yeung and R. Bumgarner (2006). Quality Control and Robust Estimation for cDNA Microarrays with Replicates. Journal of the American Statistical Association, 101:30-40. [link]
  • R. Gottardo, J. Besag, M. Stephens and A. Murua (2006). Probabilistic segmentation and intensity estimation for microarray images. Biostatistics, 7:85-99. [link]
  • R. Gottardo, A. E. Raftery, K. Y. Yeung and R. Bumgarner (2006). Bayesian robust inference for differential gene expression in cDNA microarrays with multiple samples. Biometrics, 62:10-18. [link]

2004

  • J. F. Challacombe, A. Rechtsteiner, R. Gottardo, L. M. Rocha, E. P. Browne, T. Shenk, M. R. Altherr, and T. S. Brettin (2004). Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol. Genomics, 18:51-62. [link]

2003

  • R. Gottardo, J. A. Pannucci, C. R. Kuske and T. Brettin (2003). Statistical analysis of microarray data: A Bayesian approach. Biostatistics, 4:597-620. [link]
  • G. Xie, C. A. Bonner, T. Brettin, R. Gottardo, N. O. Keyhani and R. A. Jensen (2003). Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria. Genome Biology, 4:R14. [link]

Invited book chapters

  • R. Gottardo (2009). Statistical methods for ChIP experiments on microarrays. Humana Press, vol. 567. This chapter will be part of a Volume in the Methods in Molecular Biology series on “Chromatin Immuno-precipitation Assays” edited by Phillipe Collas and published by Humana Press. [link]
  • R. Gottardo (2009). Bayesian Robust Inference for Differential Gene Expression (In Press). This chapter will be part of a book on “Bayesian Modeling in Bioinformatics” edited by Dipak Dey, Samiran Ghosh and Banni Mallick, and published by Taylor and Francis. [link]

Conference publications

  • A. Bashashati, K. Lo, R. Gottardo, R. Gascoyne, A. Weng, R. Brinkman (2009). A Pipeline for Automated Analysis of Flow Cytometry Data: Preliminary Results on Lymphoma Sub-Type Diagnosis, IEEE Engineering in Medicine and Biology Society (EMBC’09). [link]
  • X. Chen and R. Gottardo. An MM-Based Optimization Algorithm for Sparse Linear Modeling on Microarray Data Analysis, 3rd International Conference on Bioinformatics and Biomedical Engineering. ICBBE 2009. [link]

Technical reports and submitted manuscripts

  • K. Lo and R. Gottardo (2009). Flexible Mixture Modeling via the Multivariate t Distribution with the Box-Cox Transformation: An Alternative to the Skew t Distribution.
  • F. Caron, A. Doucet, and R. Gottardo (2007). Change point models and online estimation for RNA transcript analysis. Technical report 236, department of statistics, university of British Columbia.
  • Finak, G. and Manuel-Perez, J. and R. Gottardo (2009). Automated transformations for flow cytometry.
  • Bornn, Luke and Gottardo, Raphael and Doucet, Arnaud, Grouping Priors and the Bayesian Elastic Net, 2010.