Independent Studies in Computational Biology

Schedule


This two semester course trains students in core research competencies such as reading scientific literature, writing literature reviews and research proposals, and delivering oral presentations. Instruction includes research design and methods as well as skills in R programming and quantitative trait locus analysis. Students write an NIH-style research proposal in the first semester, and carry out research in the second semester using Center-generated data and tools.

Week

Topics

Presenters

Assignments

1 Introduction to ISCB
Complex Traits
Gary Churchill Mouse Genetics: Concepts and Applications by Lee M. Silver
chapters 1 - 3.3
2 Scientific Inquiry
Genetics Review
Gary Churchill
Sue McClatchy
Mouse Genetics: Concepts and Applications by Lee M. Silver
chapters 7, 9
3 Mapping Quantitative Traits
A Brief Tour of R/qtl by Karl W. Broman
Gary Churchill
Sue McClatchy
Review Article Summary
4 Next Steps in Quantitative Trait Analysis
Journal Club Demonstration
Gary Churchill
Sue McClatchy
A Brief Tour of R/qtl by Karl W. Broman
5 Journal Club Presentation
Quantitative Trait Mapping with R/qtl
Student
Sue McClatchy
Journal Club Article
6 Journal Club Presentation
Bioinformatics Toolbox
Searching PubMed
Student
Gary Churchill
Sue McClatchy
Journal Club Article
7 Journal Club Presentation
Topic Presentations
Writing NIH Grant Proposals
Student
Student Research Teams
Sue McClatchy
Journal Club Article
Data Analysis from QTL Archive
8 Journal Club Presentation
Topic Presentations
Finding Candidate Genes
Student
Student Research Teams
Gary Churchill
Journal Club Article
Proposal Idea Presentation
9 Journal Club Presentation
Gene Expression Microarrays
Student
Gary Churchill
Journal Club Article
Review Paper Outline
10 Journal Club Presentation
How to Write the Approach Section of Your Proposal
Student
Gary Churchill
Journal Club Article
Review Paper
11 Journal Club Presentation
Proposal Idea Presentations
Expression QTL (eQTL)
Student
Student Research Teams
Gary Churchill
Journal Club Article
NIH Grant Proposal - 1st draft
12 Journal Club Presentation
Causal Modeling
Student
Gary Churchill
13 Final NIH Grant Proposals and Presentations Student Research Teams Journal Club Article
NIH Grant Proposal - 2nd draft
14 Final NIH Grant Proposals and Presentations Student Research Teams Journal Club Article
Final NIH Grant Proposal
15 Summer Student Program
Proposal Review and Feedback
Randy Smith
Gary Churchill
Journal Club Article
Timeline for Research
16 Journal Club Presentation
Group Consultations
Student
Gary Churchill
Journal Club Article
Progress Updates
17 Journal Club Presentation
Progress Updates
What is Systems Genetics?
Student
Student Research Teams - NCSSM, Rockdale
Gary Churchill
Journal Club Article
Progress Updates
18 Journal Club Presentation
Progress Updates
Pairscans in R/qtl
Student
Student Research Teams - MSSM
Sue McClatchy
Journal Club Article
Progress Updates
Pairscans in R/qtl
19 Journal Club Presentation
Progress Updates
Mapping in an Outbred Population
Student
Student Research Teams - NCSSM, Rockdale
Dan Gatti
Journal Club Article
Progress Updates
20 Journal Club Presentation
Progress Updates
Bayesian Information Criterion (BIC)
Student
Student Research Teams - MSSM
Gary Churchill
Journal Club Article
Progress Updates
BIC script
21 Journal Club Presentation
Progress Updates
NextGen Sequencing
Student
Student Research Teams - NCSSM, Rockdale
Steve Munger
Journal Club Article
Progress Updates
R script
22 Journal Club Presentation
Progress Updates
Computational Approaches to RNA-Seq Data
Student
Student Research Teams - MSSM
Narayanan Raghupathy
Journal Club Article
Progress Updates
R script
23 Journal Club Presentation
Progress Updates
Student
Student Research Teams - NCSSM, Rockdale
Journal Club Article
Progress Updates
24 Journal Club Presentation
Progress Updates
Student
Student Research Teams - MSSM
Journal Club Article
Progress Updates
25 Journal Club Presentation
Progress Updates
Student
Student Research Teams - NCSSM, Rockdale
Journal Club Article
Progress Updates
26 Journal Club Presentation
Progress Updates
Student
Student Research Teams - MSSM
Journal Club Article
Progress Updates
27 Journal Club Presentation
Progress Updates
Student
Student Research Teams - NCSSM, Rockdale
Final Oral Research Presentations and Posters
28 Journal Club Presentation
Progress Updates
Student
Student Research Teams - MSSM
Final Oral Research Presentations and Posters
29 Research Presentations Student Research Teams Poster
30 Research Presentations Student Research Teams Final Research Report