T-61.6080 Special Course in Bioinformatics II P (3-10 cr)

Additional reading

Introduction to machine learning

Introduction to molecular biology and bioinformatics



  • Madeira, S. and Oliveira, A. Biclustering Algorithms for Biological Data Analysis: A Survey. IEEE Tr. CCB 1(1):24-45, 2004.
  • Segal, E. et al. From signatures to modules: Understanding cancer using microarrays. Nature Genetics 37(suppl):S38-S45, 2005. 
  • Ideker, T. and Sharan R. Protein networks in disease. Genome Research 18(4):644-652, 2008.

Learning the Structure of a Graphical Model
  • Schmidt, M. et al. Optimizing Costly Functions with Simple Constraints: A Limited-Memory Projected Quasi-Newton Algorithm. AISTATS, 2009.
  • Friedman, J. et al. Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9(3): 432-441, 2007.
  • Lee, S.-I. et al. Eficient structure learning of markov networks using l1-regularization. NIPS, 2006.
  • Elidan, G. et al. "Ideal parent" structure learning for continuous variable Bayesian networks. Journal of Machine Learning Research 8:1799-1833, 2007.
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