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Computational Systems Biology |
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Schedule
| Date | Lecturer [Slides/Notes] | Lecture Topic(s) |
Reading | Hand In |
|---|---|---|---|---|
Apr 1 |
Stuart Slides [3.4M pdf] |
Logistics. Overview of the course. High-throughput biology. Data repositories for systems biology. DNA Microarrays. | Klipp, Chaps 1-4, 13. Schena 1995 [pubmed html ]. |
|
| Apr 3 (Thu) |
Stuart [328K pdf] | Genome-wide Expression Analysis. Stats. Normalization. |
Klipp, Chap 9.1. Wu et al.2004 [pdf] |
|
| Apr 8 (Tue) |
Stuart [1.4M pdf] | Genome-wide expression analysis. Differential marker identification. Null models. Statistical Analysis of Microarrays. Multiple testing corrections. Permutation testing. Bootstrap analysis. False-discovery rates. | Klipp 9.2,9.5 Golub et al. 1999 [462K pdf] Tusher et al. 2001 [428K pdf] |
|
Apr 10 |
Stuart [1.4M pdf] | Genome-wide expression analysis. Gene set enrichment analysis. Supervised Learning. Separating hyperplanes. K-nearest neighbors. Parzen windows. Kernel smoothing. Gene function prediction. Semisupervised Learning. Missing data imputation. | Brown et al. 1999 [103K pdf] Troyanskaya et al. 2001 [308 pdf] Subramanian 2005 [600K pdf] |
|
| Apr 15 (Tue) |
Stuart [100K pdf] Vaske R tutorial [1.4M zip] |
Genome-wide expression analysis. Feature selection. | Klipp 9.3-9.4 Saeys et al 2007 [178K pdf] |
|
| Apr 17 (Thu) |
Stuart [385K pdf] | Genome-wide expression analysis. Measures of similarity. Dimension reduction. Clustering. Agglomerative and devisive. Cluster Evaluation. | Klipp 11.3 |
GenFun Team Members Due |
| Apr 22 (Tue) |
David Ng [821K pdf], Melissa Cline, Thomas Juettemann (Stuart out of town) |
ClueGene search engine demo (Ng) . Visualization of large-scale data using Cytoscape (Cline) and YETI (Juettemann). | Ng et al. 2007 [359 pdf] | HW1 Due. |
| Apr 24 (Thu) |
Stuart [478K pdf] | Genome-wide expression analysis. Bi-clustering. | Cheng and Church 2000 [362K pdf] |
|
| Apr 29 (Tue) |
Stuart [1.4M pdf] | Search Engines I. | Ihmels et al 2002 [311K pdf] | |
| May 1 (Thu) |
MIDTERM | Genome-wide expression analysis exam. | ||
| May 6 (Tue) |
Stuart [1.1M pdf] Notes by David Ng, 2005 [1.3M pdf] Whiteboard Pics: [1][2][3] |
Network Models. Boolean/Linear/Relevance | Klipp 9.6. Friedman, 2004 [706K pdf] |
HW2 Due. |
| May 8 (Thu) |
Stuart [64K pdf] Whiteboard Pics: [1][2][3][4][5] |
Network Learning. Bayesian Networks. Conditional Independence. Model parameters. Explaining away. | Kevin Murphy 2007 [html] [246K pdf] | |
| May 13 (Tue) |
Stuart [37K pdf] Notes [1.3M pdf] Whiteboard Pics: [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] |
Network Learning. Inference. Exact inference. Variable elimination. Learning from perturbations. | Heckerman 1995 [484K pdf]. |
Mini-review references due. |
| May 15 (Thu) |
Stuart [238K pdf] Notes [911K pdf] |
Network Learning. Inference. Message passing. Dynamic networks. | Milo et al. 2002 [170K pdf] |
|
| May 20 (Tue) |
Stuart [823K pdf] | Pattern Discovery Within Networks: Significant patterns in networks. Topology of nets; hubs. Dense subnetwork clustering. Network Motifs. Null network models. |
Barabasi and Oltavi 2004 [384K pdf] |
HW3 Due. |
| May 22 (Thu) |
Stuart [1.3M pdf] | Pattern Discovery Across Networks. Integration of Networks. Network Alignment. Recurrent subnetworks. |
Sharan and Ideker 2006 [544K pdf] Flannick et al. 2006 [1.2M pdf] |
|
| May 27 (Tue) |
Stuart [2.3M pdf] | Additional Network Topics (if time allows): Meta-network analysis. | Hwang et al. 2005 [777K pdf] | |
| May 29 (Thu) |
FINAL | Gene networks exam. | ||
| Jun 3 (Tue) |
Students | Mini-reviews. Great papers in Systems Biology. | List of topics [html] | Mini-review Presentation Materials Due |
| Jun 5 (Thu) |
Students | Mini-reviews. Great papers in Systems Biology. | List of topics [html] | |
| Jun 10 (Tue) 12-3 |
GenFun | Gene Function Prediction Competition & Pizza Party | GenFun Programs and Write-ups Due |
