PCB 5596/ BSC 4434 Biomedical Informatics: Sequence Analysis

Fall 2024, Monday and Wednesday 10:30-11:45am
Office hour: Monday and Wednesday 9:30-10:30am
Instructor: Xiaoman Li

Description

This course will introduce basic concepts and tools in bioinformatics. Topics include next generation sequencing, programming with Python, gene information retrieval, DNA sequence analysis, cis-regulatory analysis, and so on. Different from classical Bioinformatics courses that focus on method development, this course is more like a computational biology lab course, which enables students to be familiar with useful tools and resources for their biomedical or bioinformatics research.

This course is for Biomedical Science undergraduate/graduate students and Computer Science undergraduate/graduate students. All Biomedical Science students and all computer science students can take this applied bioinformatics course. If you are not sure whether you can take this course, you are welcome to talk with the instructor.

Textbook: No required textbook. All class contents are provided in the lecture slides and published papers.

Assignments and grading:
Graduates: choose one topics you are interested in and read two papers. The preferred topics include but not limited to miRNA, single cell, metagenomics, drug resistance, and enhancers. The papers must be from Science, Nature, Nature Genetics, Nature biotech, Nature methods, or cell after 2021. All papers should utilize next generation sequencing data for their analyses. The instructor should be informed of the selected topic by Sept 11 and the slides should be submitted by email no later than Oct 9 (20%). 30-minute presentation and discussion on the selected papers (40%). Write a 1 page summary of future directions of the topic you presented based on your own thoughts (30%). Due on Nov 27. The review must include at least two points about what can be done for future research by yourself.

Undergraduates: choose one topics and read one paper. The preferred topics include but not limited to miRNA, single cell, metagenomics, drug resistance, enhancers. The paper must be from Science, Nature, Nature Genetics, Nature biotech, Nature Methods, or cell after 2021. The main paper should be based on next generation sequencing data analyses. The instructor should be informed of the selected topic by Sept 11 and the slides should be submitted by Oct 9 (20%). 20-minute presentation and discussion on the selected paper (40%). Write a 1 page description of the future directions of the topics you present based on your own thoughts (30%). Due on Nov 27. The description must include why the directions are important and novel.

All students:

The random attendance: 0 points.

Class writing questions: 6 points; there will be a simple and short question on item emphasized in the previous class each time for six times.

Presentation participation: 4 points; asked at least one question in at least four classes; one point for questions asked in one class and at most four points will be given.

A: 95-100; A-:90-94; B+:87-89; B: 83-86; B-:80-82; C+:77-79; C:73-76; C-:70-72; D+:67-69; D:63-66; D-: 60-62; F: <60.

Academic Policies:
All students are required to show up in the zoom video if you come to the class. Absolutely no cheating is allowed. Please read the policy on Academic misconduct and cheating on http://www.goldenrule.sdes.ucf.edu/2e_Rules.html. Please also read the BSBS Academic Integrity Statement.

In order to document that you began this course, please complete the following the first assignment at the webcourse site by the end of the first week of classes or as soon as possible after adding the course. Failure to do so may result in a delay in the disbursement of your financial aid.