BIO322 Advanced Topics in Genomics

The course is divided into four main modules:

1. Genomic evolution between species
2. Genomic variation between individuals
3. Genomic regulation within an individual
4. Research project (group work)

Each module includes a mix of theoretical lectures and hands-on exercises every week.

At the end of each of the first three modules, there is a quiz on Canvas, which can be taken multiple times. Students must score at least 80% to pass each module.

In Module 4, students will work in groups to develop a research project proposal. This includes a presentation where they receive feedback, followed by the submission of a written report.

BIO210 and/or BIO200.

This course requires basic knowledge of molecular biology and genetics, including the structure and function of DNA, RNA, and proteins, as well as fundamental principles of genetic inheritance and mutations. Basic understanding of probability distributions, p-values, and statistics is necessary. Basic bioinformatics skills in R are required.

Attendance does not affect the evaluation, but students are expected to attend regularly to stay updated on lecture content and announcements.

Group work starts early, so students should register for the course as soon as possible.

Evaluation

Evaluation will be based on group presentations and group reports (Module 4) at the end of the course. Students will be randomly assigned to groups and will create "a hypothetical research project" using the theories and techniques learned throughout the course. These projects will be presented during the final weeks.

Length and Level of Detail

The recommended length is 2-3 pages. While slight deviations will not result in automatic penalties, students are encouraged to be concise and stay within this range. Writing excessively will not improve the evaluation; rather, clarity and effective communication of ideas are more important.

Students must collaborate with their group to identify a relevant and compelling research question. They may choose from a list of provided questions or propose their own. It is essential that all group members are motivated by the chosen topic. Possible focus areas include, but are not limited to, health, sustainability, conservation, evolution, precision breeding, new technology, and fundamental biological research using genomics.

Regarding the level of detail, students should ensure that their proposal is specific and well-structured. A well-defined hypothesis makes it easier to outline methods and structure the research. For example:

• Vague hypothesis: "Genetic and non-genetic factors contribute to disease resistance in plants."
• Specific hypothesis: "Transposable elements in the wheat genome increase susceptibility to rust disease."

For the Materials and Methods section, while students are not required to perform actual experiments, they should provide a clear plan for how the necessary data would be obtained or generated. This includes specifying species, populations, traits, and tissues relevant to the study. Additionally, students must determine whether the required data is available in existing databases. If suitable datasets exist, the specific databases should be mentioned. If no suitable data is available, students must outline how they would design experiments to collect the necessary information. For example:

• How would samples be collected? From where and how many?
• What methods would be used to measure or analyze traits?
• How would the data be processed and analyzed to address the hypothesis?

Similarly, the Expected Results and Interpretation section should consider both expected outcomes that support the hypothesis and alternative outcomes that do not support it. Students should discuss potential biological mechanisms that explain the results and, in the case of unexpected findings, how they would adjust their interpretations accordingly.

This project is designed to mimic the structure of a PhD/Master’s research proposal or a grant application. Therefore, students should approach it with a conceptual understanding of how research is designed and justified.

1. Weekly Assignment (Module 1 - 3)

Each week, students must submit their exercises in groups on Canvas. The goal is not perfection but engagement and effort. Students are encouraged to attempt the exercises to the best of their ability. If they encounter difficulties, they may include comments such as: "We got this far but don’t fully understand" or "We encountered this error." These submissions will not be penalized for being incomplete, as long as there is a demonstrated effort. Model answers will be provided after the deadline to allow students to compare their work and identify areas for improvement.

2. Integrated Quizzes (Module 1 - 3)

At the end of each module, students will take a quiz available on Canvas. These quizzes serve both as a review and as an assessment of understanding. To ensure mastery of key concepts, quizzes can be attempted multiple times, allowing students to improve their scores through repeated engagement. A passing score of at least 80% is required for each module's quiz. This system encourages continuous learning and provides opportunities for students to identify and address gaps in their understanding.

3. Final Group Project (Module 4)

In the final module, students will work in groups to develop a research project proposal, applying the theories and techniques they have learned throughout the course. Each group will collaborate to choose a research question, either from a provided list of topics or by proposing their own. The final proposal should be 2-3 pages long, with slight deviations permitted, though conciseness is encouraged. A well-defined hypothesis will make structuring methods and analysis easier. The proposal must include a clear Materials & Methods section, detailing how data will be collected and analyzed. Additionally, students should discuss expected results, considering both potential supporting findings and alternative outcomes that do not align with their hypothesis.

4. Group Work & Attendance Policy

For all group assignments and the final project, students must document each member’s contributions to ensure accountability. Attendance is not mandatory; however, students are responsible for ensuring that their absence does not negatively affect their group’s progress. Group members are expected to communicate effectively and coordinate their responsibilities independently.