This training initiative in Environmental Genomics at the MDI Biological Laboratory seeks to guide research towards understanding how gene function is influenced by environmental conditions while accounting for variation that exists within and among natural populations. Two significant advances create opportunities to finally link gene-environment interactions to the fitness of individuals and to population-level outcomes affecting biodiversity and ecosystem functioning:
- Genome and transcriptome sequences are now available for a growing number of species whose ecology and physiology are well understood.
- Sophisticated tools for high-throughput biology, statistical analysis and informatics are rapidly becoming more accessible to single investigators.
This course is built on the paradigm that the research field will most effectively grow by training early career environmental scientists to properly design comprehensive, large-scale, experiments enabled by drastically increased sample-throughput and lower costs. Most importantly, the challenges of manipulating and analysing population-level genomics (big) data must be addressed.
Topics covered in seminar and laboratory formats:
- bioinformatics, including sequence analysis workflows and use of R statistical analysis tools
- experimental design for environmental genomics research and laboratory training
- robotic platforms for sample preparation as well as preparing RNA-sequencing libraries.
The course provides a significant introduction and some hands-on training experience for PhD students and early career scientists, who will acquire sufficient knowledge, and build an important network of experts and peer investigators, to initiate their own environmental genomics study and launch Environmental Scientist careers in academia and industry.
- Gary Churchill, Ph.D.Professor, Karl Gunnar Johansson ChairThe Jackson Laboratory
- Thomas H. Hampton, Ph.D.Senior Bioinformatics AnalystGeisel School of Medicine at Dartmouth
- Michael A. Herman, Ph.D.Co-director, Ecological Genomics InstituteUniversity of Nebraska-Lincoln
- W. Kelley Thomas, Ph.D.Director, Hubbard Center for Genome StudiesUniversity of New Hampshire
- Andrew Whitehead, Ph.D.Assistant ProfessorUniversity of California, Davis
Institute for Systems Biology
University of Chicago
Sample Schedule, subject to change
|7-8pm||Introduction and Welcome
Introduction to Environmental Genomics
Overview of class experiment, bioinformatics, lab training & the Analysis Jamboree Graduation
|8-10pm||Guest Lecture: Ecological Genomics: Theory and Practice|
|8am-6pm||Laboratory Training: RNA-Seq library preparation
(People versus Robot)
|9-10:30am||Lecture: Introduction to Sequence Data Workflow|
|10:30am-12pm||Bioinformatics Training: Introduction to R
|1-4pm||Laboratory Training: Quality assurance tests of RNA-Seq libraries|
|4-6pm||Bioinformatics Training: Visualization of sequence data for quality assurance (FastQC hands-on workshop)|
|8-9:30am||Workshop Presentation: Review of the sequencing technology, its strengths and its limitations|
|9:30-11:30am||Bioinformatics Training: Visualizing complex data
(presentation & hands-on workshop)
|11:30-12:30pm||Robotics Training: Introduction to automation systems|
|1:30-3pm||Synthesis Session: “Models in search of Ecology vs Ecology in search of Models”|
|3-6pm||Jamboree Working Groups Formed
One-on-One Questions & Answers With Faculty (Skill Sets)
1. Transcriptional variation / Differential expression
2. Functional interpretation / Enrichment analysis
3. Pathways and networks
4. Genomic variation
5. Data visualization
|9-11pm||Synthesis Session: John Colbourne moderates: “Why not extract ______ from the sequence data for my investigations?”|
|Wednesday, August 6|
|8-9am||Bioinformatics Training: Navigating the command line|
|9-11am||Bioinformatics Training: Data analysis workshop using R to analyze Tuxedo output (hands-on workshop) PART 1|
|11-12pm||Workshop Presentation: RNA-Seq Alignment to Individualized Genomes|
|1-2:30pm||Workshop Presentation: Statistical Considerations for Analyzing Genome-Scale Data|
|2:30-4pm||Bioinformatics Training: Data analysis workshop using R to analyze Tuxedo output (hands-on workshop) PART 2|
|4-6pm||Bioinformatics Training: Biological inference using pathway analysis (hand-on workshop)|
|8-9am||Workshop Presentation: Exploring Genome Sequence Variation|
|9-11am||Bioinformatics Training: Exploring genome sequence variation|
|11-12pm||Synthesis Session: Integrating omics data|
|1-2pm||Bioinformatics Training: Gene Set Enrichment Analysis|
|9am-12pm||Bioinformatics Synthesis Training: Analysis Jamboree help desk|
|1-3pm||Bioinformatics Synthesis Training: Analysis Jamboree help desk|
|3-6pm||Results! Adjudication of the “Analysis Jamboree” team results by distinguished panel|
|10am-12pm||Q&A: “How do I obtain funding for my Environmental Genomics project?”|
Included in tuition. Housing is assigned. Please call 207-288-9880 ext 102 if you have any questions.
Double occupancy dormitory rooms and shared cottages are all within short walking distance of course activities. Single occupancy rooms, if available, can be purchased for an additional fee. Parking and wi-fi is available at the housing units.
This course is supported by a research education grant from the National Institute of Biomedical Imaging and Bioengineering (1R25EB022367-01).