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Systems Biology and the Omics Cascade

Suggested reading

Ahn et al. (2006) The limits of reductionism in medicine: Could systems biology offer an alternative? PLoS Medicine. 3(6):e208
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Ahn et al. (2006) The clinical applications of a systems approach. PLoS Medicine. 3(7):e209.
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Aoki and Kanehisa (2005) Using the KEGG database resource. Current Protocols in Bioinformatics. Chapter 1:Unit 1.12
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Butcher et al (2004) Systems biology in drug discover. Nature biotechnology. 22(10):1253-1259.
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Draghichi et al (2007) A systems biology approach for pathway level analysis. Genome Research. 17:1537-1545.
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Ellis et al (2007) Metabolic fingerprinting as a diagnostic tool. Pharmacogenomics. 8(9):1243-1266.
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Gunnarsson et al (2003) Multivariate analysis of G protein-coupled receptors. Journal of Chemometrics. 17:82-92.
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Gusev et al (2007) Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics. 8(Suppl 7):S16.
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Hood et al (2004) Systems biology and new technologies enable predictive and preventative medicine. Science. 306:640-643.
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Ideker (2004) Systems biology 101 - what you need to know. Nature Biotechnology. 22(4):473-475
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Kaddurah-Daouk et al (2008) Metabolomics: A global biochemical approach to drug response and disease. Annual Reviews in Phamacology and Toxicology. 48:653-683.
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Kitano (2002) Computational systems biology. Nature. 420:206-210.
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Kleemann et al (2007) Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis. Genome Biology. 8(9):R200
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Laaksonen et al (2006) A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS One. 1:e97.
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Long et al (2004) Multivariate analysis of 5 GPCR receptor classes. Chemometrics and intelligent laboratory systems. 73:95-104.
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Nikkila et al (2008) Gender-dependent progression of systemic metabolic states in early childhood. Molecular Systems Biology. 4:197.
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Trygg and Lundstedt (2007) Chemometrics techniques for metabonomics. The Handbook of Metabonomics and Metabolomics. Chapter 6:171-199.
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Trygg et al (2007) Chemometrics in metabonomics. Journal of Proteome Research. 6:469-479.
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van der Greef (2006) Metabolomics-based systems biology and personalized medicine: moving towards n=1 clinical trials. 7(7):1087-1094.
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van der Greef (2007) The art and practice of systems biology in medicine: Mapping patterns of relationships. 6:1540-1599.
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Weston and Hood (2004) Systems biology, proteomics, and the future of health care: Towards Predictive, Preventative, and Personalized Medicine. Journal of Proteome Research. 3:179-196.
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Winzeler (2006) Applied systems biology and malaria. Nature Reviews in Microbiology. 4:145-151.
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Young et al (2008) Systems biology of persistent infection: tuberculosis as a case study. Nature Reviews in Microbiology.
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Lectures

Systems Biology - Introduction
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History of the omics cascade
PDF file
Introduction to proteomics
PDF file
Introduction to transcriptiomics
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Introduction to metabolomics
PDF file
Introduction to chemometrics
PDF file
Bioinformatics, metabolomics and personalized medicine
PDF file
Introduction to KEGG
PDF file
Learning KEGG -Pathway (very large file, 18 MB)
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Learning KEGG - Chemical data
PDF file
Introduction to genome informatics
PDF file
Introduction to glycome informatics
PDF file
Introduction to computer programming languages
PDF file
Introduction to algorithms
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A human protein atlas for normal and cancer tissues. Peter Nilsson
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What is so special with systems biology? Examples from cancer studies. Serhiy Souchelnytskyi
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Metabolomic phenotyping in medical systems biology. Matej Orešič
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Handouts
Introduction to programming Perl
PDF file
Programming Perl
PDF file
Programming Perl (answers)
PDF file
Programming Perl (answer to Problem 3 in a Perl format - file is a .pl file)
Perl file
Bioinformatics database worksheet
PDF file
Bioinformatics database worksheet (answers)
PDF file

Publicly available databases and resources for systems biology

Excel file

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