Syllabus and Schedule for Fall 2013
GCBA815: Tools and Algorithms in Bioinformatics
| Week | Date | Topic | Reading Material |
| Week-1 | 8/30/13 | Introduction to bioinformatics, UNIX basics | aainfo.htm, formats.htm and Week1.pdf |
| Week-2 | 9/6/13 | Public domain tools and databases | Week2.pdf |
| Week-3 | 9/13/13 | BLAST algorithm, theory and practice | NCBI_blast.pdf, Week3.pdf |
| Week-4 | 9/20/13 | Multiple sequence alignments (ClustalW) | Week4.pdf |
| Week-5 | 9/27/13 | Profiles, HMMs, PHI/PSI/RPS-Blast | Week5.pdf |
| Week-6 | 10/4/13 | Machine learning – WEKA package (Midterm1- In-class exam) |
Week6.pdf |
| Week-7 | 10/11/13 | Microarray data analysis (BRB Tools) | Week7.pdf, Gene_Expression.txt, Clinical_phenotype.xls |
| Week-8 | 10/18/13 | Interaction network analysis - Cytoscape | Week8.pdf, Cyoscape Manual |
| Week-9 | 10/25/13 | UCSC Genome Browser | Week9.pdf, Resources, Week9 Handouts, Genome Graph Example, custom_track_example, sequence_logo_example.txt, clustalw_example.fa |
| Week-10 | 11/1/13 | Pathway analysis-IPA | Week10.pdf, Example dataset, IPA tutorial, Midterm2_F13, Midterm2_datasheet |
| Week-11 | 11/8/13 | Introduction to R (Heatmaps and Scatter Plots) (Midterm2- project due) |
Week11.pdf, scatterplot.R, heatmap.R, example_data.xlsx |
| Week-12 | 11/15/13 | Gene Function Enrichment Analysis (GSEA) | Week12.pdf, GSEA_PNAS.pdf, GSEAUserGuide.pdf |
| Week-13 | 11/22/13 | NextGen–Exome-RNAseq analysis | Week13, NGScheatsheet.pdf |
| Week-14 | 12/6/13 | Protein structure and PTM analysis tools | Week14, GCBA815_Final Project, Final Project_datasheet |
| Week-15 | 12/11/13 |
Open lab for final project |
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| Week-16 | 12/20/13 | Posting grades |