Syllabus 2014

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)
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
(Final project due on 12/14/13)

Week-16 12/20/13 Posting grades