This course will cover translational bioinformatics in the context of human diseases. Students will be provided with the practical skills to implement what they have learned in class. Specifically, when the course is finished, students will be able to analyze multi-omics data to understand human disease. The objective of this course is expose students to the topics and technologies used in modern bioinformatics studies. The course covers a mix of biological and computational topics, including:
- Genetic variation and Genome-Wide Association Studies
- Current high throughput sequencing assays (DNA-Seq, RNA-Seq, ChIP-Seq)
- Differential gene expression techniques
- Microbiome/metagenomics techniques
- Metabolomics
- Proteomics
- Systems, network, and integrative biology
- Basic linux cluster usage
- Python and R scripting
- Computational workflow and replication strategies
- Genomics data visualization techniques
- Biological databases
- Number: GMS6804, Translational Bioinformatics
- Semester: Spring 2023
- Units: 3
- Instructor: Dominick Lemas (djlemas@ufl.edu)
- Place: Harrell 128 or Communicore CG-24
- Time: 11:45-2:45 pm, Tuesdays
- Class start date: Tuesday January 9, 2018
- Class end date: Thursday March 8, 2018
- Submission deadline for final exam report: 11:59 pm Sunday March 18, 2018
- Student presentation (for final exam) date: Thursday March 8, 2018
| Week | Dates | Topic | Programming | Assignments |
|---|---|---|---|---|
| Wk 1 | 01/10 | Course overview & objectives | Github/Rstudio/Docker/Twitter | quiz-01/quiz-02 |
| Wk 2 | 01/17 | Bioinformatic Tools & Databases | Datacamp | quiz-03/reaction paper #1 |
| Wk 3 | 01/24 | Translational Bioinformatics: Past, Present, and Future | Docker/Asciinema | quiz-04/ cover-letter-V1 |
| Wk 4 | 01/31 | Biomolecules, Data and Diseases | Docker/Asciinema | quiz-05/ biosketch |
| Wk 5 | 02/7 | Collaboration & Reproducibility | Github Learning Lab | quiz-06 |
| Wk 6 | 02/14 | Sequencing, Assembly & Interpretation | Datacamp | reaction paper #2/proposal outline/cover-letter-V2 |
| Wk 7 | 02/21 | Genetic Variation & Gene-Environment Interactions | Datacamp | quiz-07 |
| Wk 8 | 02/28 | Interdisciplinary Center for Biotechnology Research (ICBR) Tour | reaction paper #3/specific aims-V1 | |
| Wk 9 | 03/07 | Microbiome & Microbe Host Interactions | Datacamp | quiz-08/specific aims-V2 |
| Wk 10 | 03/14 | NO CLASS/ SPRING BREAK | ||
| Wk 11 | 03/21 | Research Computing Center (RCC) Field Trip | reaction paper #4 | |
| Wk 12 | 03/28 | Metabolomics | Datacamp | research plan |
| Wk 13 | 04/04 | Late Breaking Topics | Datacamp | peer-review |
| Wk 14 | 04/11 | Innovation Hub & Technology Transfer Tour | reaction paper #5 | |
| Wk 15 | 04/18 | Group Project Presentations | full proposal | |
| Wk 16 | 04/25 | NO CLASS | final exam |
- by appointment only.
- You will get a homework every Thursday.
- The expected level of homework is that whoever attended and followed well on the Thursday hands-on course should be able to answer the homework questions in a few hours.
- Homework is due by the following Friday at midnight (11:59 pm).
- Turn in the homework to CANVAS.
- Show all codes with answers to the questions.
- Create a hands-on session document to perform data analysis with your own data (public or private data) similar to MED 263 class
- Following this document, students (or others) should be able to conduct a data analysis in the context of bioinformatics
- Turn in the hands-on session document to TA (affaustino@ucsd.edu) prior to the last class (deadline 11:59 pm Sunday March 18, 2018)
- Present the hands-on session during the class Thursday March 8, 2018 (10-minute presetation each)