Computational Systems Biology

Course name: Computational Systems Biology: Next generation experiment data analysis
Course ID: BIOS 426/826 - Section 001, Fall 2015
Instructor: Chi Zhang
Time: Tue/Thu 2:00 am - 3:15 pm
Classroom: BEAD 176
Office Hour: Tue/Thu 3:15 pm - 4:15 pm, BEAD N107

Some documents
Syllabus

Class Schedule:

Date	Topics	Notes and documents etc.	HWs, Quizs, Exams
8/25, 8/27	Introduction	Syllabus NGS Lecture 1 NGS Lecture 2	HW1 due by 8/31 at 11:59PM
9/1, 9/3	NGS	NGS Lecture 3 NGS Lecture 4	An example of a fastq file example of QC results
9/8, 9/10	NGS de novo assembly	NGS Lecture 5 NGS Lecture 6	HW2 due by 9/16 at 11:59PM Solutions for HW2 Discussion
9/15, 9/17	NGS genome variations	NGS Lecture 7 small genome assembly NGS Lecture 8
9/22, 9/24	NGS aligners	Introducation to R NGS Lecture 9	HW3 due by 9/28 at 11:59PM exp_dat.txt
9/29, 10/1	RNA-seq	NGS Lecture 10 NGS Lecture 11: RNA-seq analysis	HW4 due by 10/5 at 11:59PM refgenome.fa 50_reads.fastq
10/6, 10/8	Application of RNA-seq	Lecture 12 Lecture 13: ChIP-seq	HW5 due by 10/12 at 11:59PM RNA_seq_data.txt
10/13, 10/15	Microarray data analysis	Lecture 14: Metagenomics Microarray Lecture 1	HW6 due by 10/22 at 11:59PM
10/20 (fall break), 10/22	Microarray data analysis	Fall Break Microarray Lecture 2	You need to decide which paper you will present. HW7 due by 11/1 at 11:59PM
10/27, 10/29	Transcriptome, GO databae and function annotation	Transcriptome Lecture 1 Transcriptome Lecture 2	solutions for HW5 solutions for HW6
11/3, 11/5	Midterm Exam	Transcriptome Lecture 3 No class on Thursday	Midterm Exam due by 11/11 at 11:59PM RNAseq_data_noreplicate.txt RNA_seq_data.txt
11/10, 11/12	Graph theory	Graph Theory Lecture 1 Graph Theory Lecture 2	HW8 igraph in R due by 11/19 at 11:59PM graph.list graph_windows.list
11/17, 11/19	PPI network	PPI Lecture 1 PPI Lecture 2	HW9 due by 12/1 at 11:59PM ATH_PPI.list
11/24, 11/26 (Thanksgiving)	Student Presentation	Baral, Daharsh, DasGupta, Du, Kesinger
12/1, 12/3	Student Presentation	12/1:Levine, Mao, Moore, Yang 12/3:Kumar, Mediratta, Payne, Ronish, Neal
12/8, 12/10	Gene network and Data integration	Gene regulatory networks Data integration
	Final Exam		Final exam due by Dec 14, 11:59PM

For more information please contact:

Chi Zhang
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