Suggested reading: Ahn et al. (2006) The clinical applications of a systems approach. PLoS Medicine. 3(7):e209. Ahn et al. (2006) The limits of reductionism in medicine: Could systems biology offer an alternative? PLoS Medicine. 3(6):e208 Aoki and Kanehisa (2005) Using the KEGG database resource. Current Protocols in Bioinformatics. Chapter 1:Unit 1.12 Butcher et al (2004) Systems biology in drug discover. Nature biotechnology. 22(10):1253-1259. Draghichi et al (2007) A systems biology approach for pathway level analysis. Genome Research. 17:1537-1545. Ellis et al (2007) Metabolic fingerprinting as a diagnostic tool. Pharmacogenomics. 8(9):1243-1266. Gunnarsson et al (2003) Multivariate analysis of G protein-coupled receptors. Journal of Chemometrics. 17:82-92. Gusev et al (2007) Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs i Hood et al (2004) Systems biology and new technologies enable predictive and preventative medicine. Science. 306:640-643. Ideker (2004) Systems biology 101 - what you need to know. Nature Biotechnology. 22(4):473-475 Kaddurah-Daouk et al (2008) Metabolomics: A global biochemical approach to drug response and disease. Annual Reviews in Phamacol Kitano (2002) Computational systems biology. Nature. 420:206-210. Kleemann et al (2007) Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcr PDF file Laaksonen et al (2006) A systems biology strategy reveals biological pathways and plasma biomarker candidates for po Long et al (2004) Multivariate analysis of 5 GPCR receptor classes. Chemometrics and intelligent laboratory systems. 73:95-104. Nikkila et al (2008) Gender-dependent progression of systemic metabolic states in early childhood. Molecular Systems Biology. 4: Trygg and Lundstedt (2007) Chemometrics techniques for metabonomics. The Handbook of Metabonomics and Metabolomics. Chapter 6:17 Trygg et al (2007) Chemometrics in metabonomics. Journal of Proteome Research. 6:469-479. van der Greef (2006) Metabolomics-based systems biology and personalized medicine: moving towards n=1 clinical trials. 7(7):1087 van der Greef (2007) The art and practice of systems biology in medicine: Mapping patterns of relationships. 6:1540-1599. Weston and Hood (2004) Systems biology, proteomics, and the future of health care: Towards Predictive, Preventative, and Persona Winzeler (2006) Applied systems biology and malaria. Nature Reviews in Microbiology. 4:145-151. Young et al (2008) Systems biology of persistent infection: tuberculosis as a case study. Nature Reviews in Microbiology. Lectures: Systems Biology - Introduction History of the omics cascade Introduction to proteomics Introduction to transcriptiomics Introduction to metabolomics Introduction to chemometrics Bioinformatics, metabolomics and personalized medicine Introduction to KEGG Learning KEGG -Pathway (very large file, 18 MB) Learning KEGG - Chemical data Introduction to genome informatics Introduction to glycome informatics Introduction to computer programming languages Introduction to algorithms A human protein atlas for normal and cancer tissues. Peter Nilsson What is so special with systems biology? Examples from cancer studies. Serhiy Souchelnytskyi Metabolomic phenotyping in medical systems biology. Matej OrešičHandouts: Introduction to programming Perl Programming Perl (answer to Problem 3 in a Perl format - file is a .pl file) Programming Perl Programming Perl (answers) Bioinformatics database worksheet Bioinformatics database worksheet (answers) Publicly available databases and resources for systems biology
