Course Information
Class Description
Seminar on Bioinformatics this semester will review selected topics in translational bioinformatics (TBI). Simply put, TBI is the application and development of bioinformatics methods for better medication. Join if you are interested in knowing various sub-topics covered in TBI. The book that we will cover is open and can be found in: PLoS Computational Biology: Translational Bioinformatics
All students participating in the seminar (registered or not registered) are expected to take turns presenting each Ch. If few students participate, expect to present a lot. Remember, even if you plan to take the class without registering, I will still expect you to participate fully. My roll will be to explain the content that you may not understand by simply reading the Chs and to provide more information relating to the presented topics. I may go over some of the chapters myself if we have very few participating.
Instructor
Assistant Professor
Sael Lee
Office: Academic Bldg. B422
Email: sael at sunykorea dot ac dot kr
Phone: +82 (32) 626-1215
Meeting time
Mon 14:30~15:20 Academic Bldg. B206
Office Hours
Wed. 10:30-12:00 (or send emails for appointments)
Course Materials
| #
| DATE('14)
| CONTENT
| READING
| ASSIGNMENTS
|
| 1 |
8/25 |
NO CLASS |
|
|
| 2 |
9/01 |
Introduction to Translational Bioinformatics |
|
|
| 3 |
9/7-10 |
NO CLASSES: Chuseok, Korean Thanksgiving Day |
|
|
| 4 |
9/14 |
Ch01. Biomedical Knowledge Integration |
PLoS CompBiol |
|
| 5 |
9/21-27 |
NO CLASSES: Fall break |
|
|
| 6 |
9/28 |
Ch02. Data-Driven View of Disease Biology |
PLoS CompBiol |
|
| 7 |
10/06 |
Ch03. Small Molecules and Disease |
PLoS CompBiol |
|
| 8 |
10/13 |
Ch04. Protein Interactions and Disease |
PLoS CompBiol |
|
| 9 |
10/20 |
Ch05. Network Biology Approach to Complex Diseases |
PLoS CompBiol |
|
| 10 |
10/27 |
Ch06. Structural Variation and Medical Genomics |
PLoS CompBiol |
|
| 11 |
11/03 |
Ch07. Pharmacogenomics |
PLoS CompBiol |
|
| 12 |
11/17 |
Ch08. Biological Knowledge Assembly and Interpretation |
PLoS CompBiol |
|
| 13 |
11/24 |
Ch09. Analyses Using Disease Ontologies |
PLoS CompBiol |
|
| 14 |
12/01 |
Ch13. Mining Electronic Health Records |
PLoS CompBiol |
|
| 15 |
12/08 |
Ch16. Text Mining for Translational Bioinformatics |
PLoS CompBiol |
|
| F |
12/15-19 |
NO FINAL EXAM |
|
|
Course Policy
Attendance policy
Everyone is strongly urged to attend class regularly and actively participate.
You will be responsible for learning all the materials covered in class.
Notes and supplementary handouts will cover most of the material; however, in-class participation through engaging in discussions and asking questions should be valued learning activity.
Assignments grading policy
Assignment will be handed out in class and are due in class of the due date.
Total points of each assignment will be different depending on the difficulty of the problems.
However, the maximum total point of an assignment will be less than or equal to two times the minimum total point of an assignment. Expect to see difficult problems towards the end of semester.
You have budget of 6 days that you may submit your assignments late in total throughout the semester. Spend them as you will. There will be 10% late penalty for each day late exceeding the 5 day grace. There are no extensions given to individuals unless it is an extreme case of a proven emergency (this does not include family emergencies).
Academic misconduct policy
There is no excuse in cheating. Cheating will be considered as an academic misconduct and handled according to the Stony Brook regulations. If cheating has occurred during exam or is evident in submitted assignments, your will get a grade of F.
Discussion of assignments is acceptable, however, returned assignments must show originality. This means near duplicate assignments with your peers or duplications of materials found on the web will be considered cheating. All involved personals in cheating will be penalized.
University Policy
Americans with Disabilities Act
If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC(Educational Communications Center) Building, Room 128, (631)632-6748. They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation is confidential.Disability Support
Services.
Academic Integrity
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific
procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at Academic Judiciary
Critical Incident Management
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further
information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.
