Course Director:                
Kelly Ruggles
kelly.ruggles@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
Students will complete projects based on each module. These projects are to be completed in groups of 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 Dr. Ruggles (Kelly.ruggles@nyumc.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.
  • 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)

Schedule:

  • Tuesday September 11
  • Friday September 14 


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

Schedule:

  • Tuesday September 18
  • Friday September 21
  • Tuesday September 25
  • Friday September 28


Module 4: Regulatory Genomics
Lecturer: Maurano
Reading List:

​​Schedule:

  • Tuesday October 2
  • Friday October 5
  • Tuesday October 9
  • Friday October 12


Module 5: Cancer Proteogenomics
Lecturer: Ruggles
Reading List:

​Schedule:

  • Tuesday October 16
  • Friday October 19
  • Tuesday October 23
  • Friday October 26

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

Schedule:

  • Tuesday October 30
  • Friday November 2
  • Tuesday November 6
  • Friday November 9


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

​Schedule:

  • Tuesday November 13
  • Friday November 16

**WEEK OFF FOR THANKSGIVING**

  • Tuesday November 27
  • Friday November 30


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
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



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