Advanced Topics in Bioinformatics

Course Director:                
Kelly Ruggles
kelly.ruggles@nyumc.org

Teaching Assistant: 
Angelina Volkova
angelina.volkova@nyumc.org

Course Time: 
Tuesdays and Fridays 3-4:30PM

Location:
TRB 819

Course overview:
The course is meant to provide students with an overview of and practical experience with bioinformatics techniques. The course consists of 9 modules.  The first two and last two modules last 1 week each, and modules 3-7 have the same structure:

Learning objectives:
At the conclusion of the course, the student will have hands-on experience with common bioinformatics analysis

Course Assessment:
100% of grade will be determined by projects and course participation
Students will complete projects based on each module. These projects are to be completed in groups of 2-3 that will rotate each week. For each project an analysis plan, a project presentation, and a final report must be completed and submitted by email to the module lecturer, ccing Dr. Ruggles (kelly.ruggles@nyulangone.org) and Angelina Volkova (angelina.volkova@nyulangone.org) by the Tuesday following module completion.

General Policies:

  • Late/missed work: You must adhere to the due dates for all required submissions.If you miss a deadline, then you will not get credit for that assignment/post. 10 points will be deducted for every day late. 

  • Incompletes: No “Incompletes” will be assigned for this course unless we are at the very end of the course and you have an emergency.

  • Responding to Messages: I will check e-mails daily during the week, and I will respond to course related questions within 48 hours.

  • Announcements: I will make announcements throughout the semester by e-mail. Make sure that your email address is updated; otherwise you may miss important emails from me.

  • Safeguards: Always back up your work on a safe place (electronic file with a backup is recommended) and make a hard copy. Do not wait for the last minute to do your work. Allow time for deadlines.

  • Plagiarism: Plagiarism, the presentation of someone else's words or ideas as your own, is a serious offense and will not be tolerated in this class. The first time you plagiarize someone else's work, you will receive a zero for that assignment. The second time you plagiarize, you will fail the course with a notation of academic dishonesty on your official record.

Module 1. Historical Overview of Bioinformatics
Lecturer: Brown
Reading List:

Schedule: 

  • Tuesday September 4

  • Friday September 7

Module 2.  Publicly Available Datasets
Lecturer: Ruggles
Reading List: 

Assignment: 

  • Students present publicly available data sets in their field of interest and a brief overview of studies that have been done using this data (10 minutes per person)

    • Choose from this list of datasets here and indicate which dataset you will be presenting on

  • Due September 18th: Identify an additional publicly dataset that was not included on the original list and write up a few sentences explaining what the data is, how it was collected, and what it has been used for at this point.  

Schedule:

  • Tuesday September 11

    • Presenters: Grivainis, Hong, Narang, Yeaton, Dube

  • Friday September 14 

  • Presenters: Abebe, McCulloch, Barkley, Devlin, Wang

Module 3:  Molecular Classification of Cancer
Lecturer Brown
Reading List: 

Schedule:

  • Tuesday September 18

  • Friday September 21

  • Tuesday September 25

  • Friday September 28

Groups:

  • Group 1: Barkley, Devlin, Wang

  • Group 2: Abebe, Narang, Hong

  • Group 3: Grivainis, McCulloch, Yeaton

Module 4: Regulatory Genomics
Lecturer: Maurano
Reading List:

Schedule:

  • Tuesday October 2

  • Friday October 5

  • Tuesday October 9

  • Friday October 12

Groups:

  • Group 1: Wang, Barkley, Abebe

  • Group 2: Yeaton, Devlin, Grivainis

  • Group 3: Hong, Narang, McCulloch

Module 5: Cancer Proteogenomics
Lecturer: Ruggles
Reading List:

Schedule:

  • Friday October 19

  • Tuesday October 23

  • Friday October 26

Groups:

  • Group 1: Wang, Yeaton, McCulloch

  • Group 2: Hong, Devlin, Narang

  • Group 3: Abebe, Grivainis, Barkley

Module 6: Chromosome Conformation Capture
Lecturer: Tsirigos
Reading List:

Schedule:

  • Tuesday October 30

  • Friday November 2

  • Tuesday November 6

  • Friday November 9

Groups:

  • Group 1: Abebe, Narang, Yeaton

  • Group 2: Barkley, Devlin, McCulloch

  • Group 3: Hong, Grivainis, Wang

Module 7: Dynamics of Bacterial Communities
Lecturer: Fenyo
Reading List:  

Schedule:

  • Tuesday November 13

  • ----- OFF Friday November 16 ------

  • ----- OFF Tuesday November 20 ----

  • ----- OFF Friday November 22 -----

  • Tuesday November 27

  • Friday November 30

Groups:

  • Group 1: McCulloch, Grivainis, Wang

  • Group 2: Devlin, Abebe, Narang

  • Group 3: Hong, Yeaton, Barkley


Module 8: Software Development Best Practices
Lecturer: Grover/Grivainis
Reading List: TBD

  • Tuesday December 4

  • Friday December 7

Module 9: Publicly Available Tools
Lecturer: Ruggles/Volkova
Reading List: 

Assignment: 

  • Students present publicly available bioinformatics tools in their field of interest and a brief overview of studies that have been done using these tools including an assessment of the positives and negatives of the chosen method (10 minutes per person)

Schedule:

  • Tuesday December 11

  • Friday December 14