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Contents
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Week 1: |
- Fundamentals of Systems Biology: Basic Concepts (systems biology, molecular biology) - From DNA to Proteins : chromosomes, genes, gene expression, protein synthesis, folding |
Week 2: |
Cellular Networks: Metabolic reaction networks, Gene-regulatory networks, Signalling networks |
Week 3: |
Cellular Networks and Graph Theory, Use of Cytoscape Quiz |
Week 4: |
Experimental techniques of genome sciences I: Genomics, Transcriptomics Homework |
Week 5: |
Experimental techniques of genome sciences II: Proteomics, Metabolomics, Fluxomics, Interactomics Quiz |
Week 6: |
Normalization of Raw Omics Data, Methods and Challenges Homework |
Week 7: |
Statistical Significance Tests I: Parametric and nonparametric significance tests, ROC Curves Quiz
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Week 8: |
Statistical Significance Tests II: Use of MATLAB for Gene Expression Omnibus database, Gene Ontology (GO) Analysis Homework |
Week 9: |
- Similarity Tests : Parametric and nonparametric similarity tests - Clustering techniques Quiz |
Week 10: |
Unsupervised Dimension-reduction techniques I: Principal Component Analysis Basics Homework |
Week 11: |
Unsupervised Dimension-reduction techniques II: Principal Component Analysis, Independent Component Analysis, and application to genome-scale data Quiz |
Week 12: |
Supervised Dimension-reduction techniques: Fisher Discriminant Analysis, Support Vector Machines Homework Project Assignment |
Week 13: |
Cell metabolism and modeling techniques I: Enzyme kinetics, Dynamic metabolic models, Lin-log kinetic approximation Quiz |
Week 14: |
Cell metabolism and modeling techniques II: Flux Balance Analysis, Flux Variability Analysis Homework |
Week 15*: |
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Week 16*: |
Project Presentations |
Textbooks and materials: |
1. Edda Klipp, Wolfram Liebermeister, Cristoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig. “Systems Biology”, Wiley-Blackwell, 2009. |
Recommended readings: |
1. Brian P. Ingalls, "Mathematical Modeling in Systems Biology: An Introduction", The MIT Press, 2013 |
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* Between 15th and 16th weeks is there a free week for students to prepare for final exam.
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