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README.md

README.md

MED263 Winter 2018, Bioinformatics Applications to Human Disease

Course Description

This elective course will cover the latest advances in bioinformatics in the context of human diseases. Students will be provided with the practical skills to implement what they have learned in class. Specifically, when the course is finished, students will be able to analyze multi-omics data to understand human disease.

Course Information

  • Number: MED263, Bioinformatics Applications to Human Disease
  • Quarter: Winter 2018
  • Units: 4
  • Directors: Lucila Ohno-Machado (lohnomahcado@ucsd.edu) and Jihoon Kim (j5kim@ucsd.edu)
  • TA: Andre Fonseca Faustino (affaustino@ucsd.edu)
  • Place: Room 304, Medical Education Telemedicine (MET) building
  • Time: 2-3:30 pm, Tuesdays and Thursdays (Jan 9 - Mar 8, 2018)
  • Grading: Homework 60%, Final presentation/report 40% (no mid-term)

Dates

  • Class start date: Tuesday January 9, 2018
  • Class end date: Thursday March 8, 2018
  • Submission deadline for final exam report: 11:59 pm Sunday March 18, 2018
  • Student presentation (for final exam) date: Thursday March 8, 2018

Courses

Week Date Topic Instructor
1 Tuesday 1/9 Overview & Bootcamp part 1 (docker and linux) Lucila Ohno-Machado (lohnomachado@ucsd.edu) and Jihoon Kim (j5kim@ucsd.edu)
1 Thursday 1/11 Bootcamp part 2 (conda, Jupyter notebok, and R) Jihoon Kim (j5kim@ucsd.edu)
2 Tuesday 1/16 Network Biology lecture Hannah Carter (hkcarter@ucsd.edu)
2 Thursday 1/18 Network Biology hands-on session Hannah Carter (hkcarter@ucsd.edu)
3 Tuesday 1/23 Exome-seq and variant analysis lecture Olivier Harismendy (oharismendy@ucsd.edu)
3 Thursday 1/25 Exome-seq and variant analysis hands-on session Olivier Harismendy (oharismendy@ucsd.edu)
4 Tuesday 1/30 Classification model and survival analysis in biomedicine Xiaoqian Jiang (x1jiang@ucsd.edu)
4 Thursday 2/1 Classification model and survival analysis in biomedicine hands-on session Xiaoqian Jiang (x1jiang@ucsd.edu)
5 Tuesday 2/6 RNA-seq lecture Katie Fisch (kfisch@ucsd.edu)
5 Thursday 2/8 RNA-seq hands-on session Katie Fisch (kfisch@ucsd.edu)
6 Tuesday 2/13 Prioritizing disease mutations using DNA sequence data lecture Vikas Bansal (vibansal@ucsd.edu)
6 Thursday 2/15 Prioritizing disease mutations using DNA sequence data hands-on session Vikas Bansal (vibansal@ucsd.edu)
7 Tuesday 2/20 Chip-Seq lecture Sven Heinz (sheinz@ucsd.edu)
7 Thursday 2/22 Chip-Seq hands-on session Sven Heinz (sheinz@ucsd.edu)
8 Tuesday 2/27 GRO-seq lecture Chris Benner (cbenner@ucsd.edu)
9 Thursday 3/1 GRO-seq hands-on session Chris Benner (cbenner@ucsd.edu)
9 Tuesday 3/6 Ethics, Privacy, and Policy lecture Cinnamon Bloss (cbloss@ucsd.edu)
9 Thursday 3/8 Student Presentation Jihoon Kim (j5kim@ucsd.edu)

Office Hours

  • 3:30-4:30 pm after class Tuesdays and Thursdays at room 304, MET building
  • If these hours don't work you, email to Andre (affaustino@ucsd.edu) or Jihoon (j5kim@ucsd.edu) to schdedule different hours, preferrably on Tuesdays and Thursdays.

Homework

  • You will get a homework every Thursday.
  • The expected level of homework is that whoever attended and followed well on the Thursday hands-on course should be able to answer the homework questions in a few hours.
  • Homework is due by the following Thursday right before class (1:59 pm Thursdays).
  • Turn in the homework to TA Andre(affaustino@ucsd.edu) by email.
  • Show all codes with answers to the questions.

Final Exam

  • Create a hands-on session document to perform data analysis with your own data (public or private data) similar to MED 263 class
  • Following this document, students (or others) should be able to conduct a data analysis in the context of bioinformatics
  • Turn in the hands-on session document to TA (affaustino@ucsd.edu) prior to the last class (deadline 11:59 pm Sunday March 18, 2018)
  • Present the hands-on session during the class Thursday March 8, 2018 (10-minute presetation each)