Download a more detailed version of the Overall Course Syllabus here.

Download a more detailed version of the Proteomics Unit Syllabus here.

Download a more detailed version of the Proteomics Unit Readings here.

Week 1           

T Sept 4              Intro to "-omics" analysis

                R Sept 6              Lecture:  Sequencing Technologies and Applications

                F Sept 7              Lab: NCBI Genomes
                   

Week 2           

T Sept 11            Discussion:  Draft Genomes

                R Sept 13            Lecture:  Sequence similarity searches and genome alignment

                F Sept 14            Lab:  Pectobacterium draft genome alignment

                       
Week 3           

T Sept 18            Discussion:  Genome Alignment

                R Sept 20            Lecture:  Gene Prediction and HMMs

                F Sept 21            Lab:  Pectobacterium Gene Prediction - Concordance and Conflict

Week 4           

T Sept 25            Discussion:  Under and Over prediction of genes

                R Sept 27            Lecture:  Assigning function based on sequence similarity

                F Sept 28            Lab:  BLAST & InterPro to predict function of Pectobacterium genes

Week 5           

T Oct 2              Discussion: Manual vs. automated annotation

                R Oct 4              Lecture:  Orthology, Paralogy, Xenology - Does it matter

                F Oct 5              Lab:  Predicting Pectobacterium orthologs using BLASTP

Week 6           

T Oct 9              Discussion: Orthologs and Function

                R Oct 11            Lecture:  Phylogeny

                F Oct 12            Lab:  Phylogeny of Pectobacterium orthologs

Week 7           

T Oct 16            Discussion: Phylogenetic Profiling to infer Function

                R Oct 18            Lecture: "Etceromics" Experimentation

                F Oct 19            Lab:  Work on your Project

Week 8           

T Oct 23            Lecture: Transcript Sequencing vs. Hybridization

                R Oct 25            Intro to section & brief overview of proteomics

                F Oct 26            Free time to work on your project

Download a more detailed version of the Proteomics Unit Syllabus here.

Download a more detailed version of the Proteomics Unit Readings here.

Week 9           

T Oct 30             Discussion: Functional Genomics using RNAi

                R Nov 1              Discussion: Chemical Genetics

                F Nov 2              Lab: RNAi web-based tools

Week 10         

T Nov 6            Discussion: 2D gel analysis

                R Nov 8            Discussion: MuDPIT

                F Nov 9            Tour of proteomics facility

Week 11         

T Nov 13            Discussion: Biological Networks: Y2H approaches

                R Nov 15            Discussion: Biological Networks: TAP tag approach

                F Nov 16            Lab:  Creating a Network using Osprey

Week 12         

T Nov 20            Lecture:  Microarray Analysis

                R Nov 22            Thanksgiving Break

                F Nov 23            Thanksgiving Break

Week 13         

T Nov 27            Discussion: Microarray Analysis

                R Nov 29            Lecture:  Clustering array data

                F Nov 30            Lab:  Microarray clustering

Week 14         

T Dec 4            Discussion:  Microarray Analysis

                R Dec 6            Lecture:  Regulatory inferences from array data

                F Dec 7             Lab:  Microarray motif finding

Week 15         

T Dec 11            Student Project Presentations

                R Dec 13            Student Project Presentations

                F Dec 14            Student Project Presentations