Collection of articles for T-61.6080

Using background measurement data

Large scale data mining approach for gene-specific standardization of microarray gene expression data. Yoon et al., Bioinformatics, 2006. (html)
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. Katz et al., BMC Bioinformatics, 2006. (html)
Analyzing gene expression data in terms of gene sets: methodological issues. Goeman and Buhlmann, Bioinformatics, 2007. (html)
Integrative missing value estimation for microarray data. Hu et al., BMC Bioinformatics, 2006. (html)
Logistic regression with an auxiliary data source. Liao et al., ICML 2005. (pdf)
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Carvalho et al., Biostatistics, 2007. (html)

Informative structure priors: joint learning of dynamic regulatory networks from multiple types of genomic data. Bernard et al., PSB 2005. (pdf)

Multi-task learning for classification with Dirichlet process priors. Xue et al., JMLR 2007. (pdf)
Inductive Transfer for Bayesian Network Structure Learning. Niculescu-Mizil and Caruana, AISTATS 2007. (pdf)

Classification of microarray data using gene networks. Rapaport et al., BMC Bioinformatics, 2007. (html)
Annotating gene function by combining expression data with a modular gene network. Shiga et al., Bioinformatics 2007. (html)
Supervised reconstruction of biological networks with local models. Bleakley et al., Bioinformatics, 2007. (html)

Penalized Probabilistic Clustering. Lu and Leen, Neural Computation, 2007. (html)
Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms. Tai et al., Bioinformatics, 2007. (html)
Kernel-based data fusion for gene prioritization. De Bie et al., Bioinformatics, 2007. (html)
Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression. Li et al., Biology Direct, 2006. (html)