Course name: Computational Systems Biology: Next generation experiment
data analysis
Course ID: BIOS 497/897 - Section 001, Spring 2014
Instructor: Chi Zhang
Classroom: BEAD 176
Office Hour: Tue/Thu 1:30 pm - 2:00 pm, BEAD N107
Prerequisites: LIFE 120, LIEF 121, BIOS101, or equivalent; STAT 218 or
equivalent; BIOS 206 and CSCE 155T are recommended, but not required.
Some documents
Syllabus
Class Schedule:
| Date | Topics | Notes and documents etc. | HWs, Quizs, Exams |
| 1/14, 1/16 | Introduction, graph theory |
Syllabus NGS Lecture 1 NGS Lecture 2 |
|
| 1/21, 1/23 | NGS |
NGS Lecture 3 NGS Lecture 4 |
|
| 1/28, 1/30 | NGS |
NGS Lecture 5 NGS Lecture 6 |
|
| 2/4, 2/6 | NGS |
NGS Lecture 7 NGS Lecture 8 |
HW4 due by 2/17 11:59PM |
| 2/11, 2/13 | NGS |
NGS Lecture 9 NGS Lecture 10 |
HW5 due by 2/24 11:59PM |
| 2/18, 2/20 | microarray data analysis |
NGS Lecture 11 Microarray Lecture 1 |
HW6 due by 3/3 11:59PM |
| 2/25, 2/27 | microarray data analysis |
Microarray Lecture 2 Microarray Lecture 3 |
HW7 due by 3/10 11:59PM |
| 3/4, 3/6 | Transcriptome |
Microarray Lecture 4 Transcriptome Lecture 1 Transcriptome Lecture 2 |
Solutions for HW5 (edgeR) Solutions for HW7 |
| 3/11, 3/13 | Transcriptome, GO databae and function annotation |
Transcriptome Lecture 3 Transcriptome Lecture 4 |
You need to decide which paper you will present. |
| 3/18, 3/20 | Midterm Exam | No class this week |
Midterm Exam Due by 3/23, Sunday, 11:59PM Midterm Exam Solutions R code for Question 3 |
| 3/25, 3/27 | Spring break | ||
| 4/1, 4/3 | Graph theory |
Graph Theory Lecture 1 Graph Theory Lecture 2 |
HW8 due by April 10, 11:59PM |
| 4/8, 4/10 | PPI network |
PPI Lecture 1 PPI Lecture 2 |
|
| 4/15, 4/17 | PPI network |
PPI Lecture 3 PPI Lecture 4 |
HW9 due by April 29, 11:59PM ATH_PPI_small.list |
| 4/22, 4/24 | Student Presentation | Aderson, Kim, Kolman, Kusuma, Liu, Maldonado, Shao, Thelen | |
| 4/29, 5/1 | Gene network and Data integration |
Gene regulatory networks Data integration |
|
| Final Exam |
Final exam due by May 7, 11:59PM |
For more information please contact:
Chi Zhang, Assistant Professor
School of Biological Sciences
Center for Plant Science Innovation
Office: N107 Beadle
University of Nebraska-Lincoln
Lincoln, NE
Tel: 402-472-1396
Email: czhang5@unl.edu