High School Comp Bio

High School Comp Bio

Introducing High School Students to Computational Biology

Independent Studies in Computational Biology (ISCB) immerses talented science and math students in systems genetics research. The course integrates genetics, statistical analysis, and the R programming language to bring a highly interdisciplinary research experience to students. Independent Studies in Computational Biology offers graduate level research experiences to high school students in order to accelerate their research careers at a very early age. Participating schools include the Maine School of Science and Mathematics, North Carolina School of Science and Mathematics, Rockdale Magnet School of Science and Technology, Mount Desert Island High School, and Falmouth High School.

Aims

Aims and Objectives

Students gain the experimental and computational knowledge necessary to embrace a systems biology approach, and experience authentic systems genetics research by designing and conducting independent research projects with guidance from Gary Churchill and bioinformatician Sue McClatchy. Read More >less

By the end of this course, students will be able to:

  • analyze scientific literature
  • summarize primary research and review articles
  • explain the purpose, methods and results of a scientific article
  • develop questions and hypotheses around a specific area of research
  • describe methods for answering research questions
  • demonstrate understanding of statistical genetics
  • demonstrate understanding of measures of gene expression
  • demonstrate understanding of quantitative trait locus (QTL) analysis
  • plan and execute a research strategy
  • write or alter existing R code to perform specific tasks
  • locate data from bioinformatics resources
  • apply QTL analysis methods to phenotype and expression data
  • report analysis results in both written and oral forms
  • demonstrate an appreciation for education and careers in computational biology

 

 
Schedule

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. Read More >less

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
 
Reading

Recommended Reading

Course reading includes current primary research articles and reviews from top tier journals including Nature and Science. Texts for background material in mouse genetics, quantitative trait locus analysis, and R programming are made available to each school as well. Read More > less

  • Lee M. Silver, Mouse Genetics: Concepts and Applications (New York: Oxford University Press 1995), http://www.informatics.jax.org/silverbook/index.shtml
  • Peter Dalgaard, Introductory Statistics with R (New York: Springer Science+Business Media LLC 2008)
  • Phil Spector, Data Manipulation with R (New York: Springer Science+Business Media LLC 2008)
  • Karl W. Broman and Saunak Sen, A Guide to QTL Mapping with R/qtl (New York: Springer Science+Business Media LLC 2009)
 
Publications

Publications by ISCB Students

Several students have published their research in scientific journals.  Read More >less

ISCB students are highlighted in bold

Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design Mol Biosyst. 2010 Oct;6(10):1890-900.

Feng M, Deerhake ME, Keating R, Thaisz J, Xu L, Tsaih SW, Smith R, Ishige T, Sugiyama F, Churchill GA, DiPetrillo K. Genetic analysis of blood pressure in 8 mouse intercross populations Hypertension. 2009 Oct;54(4):802-9. PMCID: PMC2854560 [ Full Text ]

Shockley KR, Witmer D, Burgess-Herbert SL, Paigen B, Churchill GA. Effects of atherogenic diet on hepatic gene expression across mouse strains Physiol Genomics. 2009 Nov 6;39(3):172-82. PMCID: PMC2789673 [ Full Text ]

Smith R, McGann D, Gotwals R, Symonds R, Hageman R, Vedell P, Churchill G. Independent Studies in Computational Biology NCSSSMST Journal. Fall 2009:10-16. [ Full Text ]