Class Syllabus

CMSC702 - Computational Systems Biology and Functional Genomics - Spring 2016

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Instructor: Dr. Zia Khan (my first name)(at symbol)cs.umd.edu
Day and Time:
Tuesday 3:30pm-4:45pm
Thursday 3:30pm-4:45pm
Location: Computer Science Instructional Center (CSIC) Room 3120
Instructor Office Hours: By appointment.
Teaching Assistant: Josh Bradley, jgbrad1(at)cs.umd.edu
TA Office Hours: TBD
CMSC702 Piazza Page

Course Description

Major advances in technology for genomic studies are bringing the prospect of personalized and individualized medicine closer to reality. Many of these advances are predicated on the ability to generate DNA sequencing data at an unprecedented rate, posing a significant need for computational data analysis that is clinically and biologically useful and robust. This course will concentrate on the fundamental computational and statistical methods required to meet this need. It will cover topics in functional genomics, population genetics and epigenetics. Machine learning methods will be a core component of this class. No prior knowledge of biology is required. Image source: Nature 518, 337–343 (19 February 2015).

Final Project

The goal of this course is to give you the chance to propose and pursue a new line of risky research, using systems biology and functional genomics as an application area. Perhaps you'll find this area so fascinating it will become the primary topic of your PhD or masters research. You can read the current final project guidelines here: CMSC702_Spring2016_Project_Guidelines.pdf.

Quizzes

Systems biology and functional genomics are highly active research fields. One of the goals of this course is to bring everyone up to date. You will be asked to complete a short quizzes throughout the semester. You can discuss quizzes on Piazza. Some of them will be designed to elicit some discussion on the readings. In that case, you will be evaluated on the thoughtfulness of your response. Attending lecture and participating in class discussions will be the easiest way to complete these quizzes so you are encouraged to stay engaged with the class material throughout the semester. The Department and the University requires that I administer a final exam. Questions closely related to the reading quizzes will appear on the final exam. Quizzes have a 1 week deadline. Answers must be submitted 1 week after the corresponding lecture or no points will be awarded.

Grade Distribution

The grade distribution is below

10% class participation and attendance
35% reading quizzes
35% final project
20% take-home final exam

Grades will be available on grades.cs.

Attendance Policy

Please read the UMDCP attendance policy. Please do email me if you find yourself falling behind in class. I’m here to help.

Academic Integrity

Maintaining your reputation is critical in science. Please read the UMDCP academic integrity policy.

Course Evaluations

I encourage you to provide me with input and feedback during the semester. At the end of the semester, you'll be asked provide formal evaluations at www.courseevalum.umd.edu. Your evaluations will be used to improve the class in following years.

Schedule

Course Schedule

The schedule will be updated frequently over the semester.Please check back regularly. TBD designates "to be determined." Note that some of the readings are quite challenging and lecture is designed to help. My expectation is that you've taken a first shot at understanding the computational concepts underlying the reading material.

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Date Lecture Topic + Slides Associated Reference Material Quiz
Week 1
1/26 CAMPUS CLOSED DUE TO SNOW
1/28 L1:Intro to DNA
Slides/Notes
Illumina Sequencing Video
Single Cell Sequencing Video
Flow Cell Video
PacBio SMRT Sequencing Video
Nanopore Sequencing Video
Wikipedia: DNA
Cell Snapshot: HTSeq Applications
Illumina Intro
L1, Survey
Week 2
2/2 L2:The Genomic Data Deluge
Slides/Notes
DOI: 10.1371/journal.pbio.1002195 L2, Big Data Qs
2/4 L3:Genome Assembly Using Minimap and miniasm
Slides/Notes
arXiv:1512.01801 L3 Quiz
Week 3
2/9 L4:BWA Alignment + SAM Format
Slides/Notes
doi: 10.1093/bioinformatics/btp324
SAMv1 Spec
L4 Quiz
2/11 L5:CRAM data compression
Slides/Notes
DEADLINE TO FORM GROUPS OF 1-3
doi: 10.1101/gr.114819.110
CRAMv3 Spec
L5 Quiz
Week 4
2/16 L6:Bayesian Variant Detection + VCF Format
Slides/Notes
FreeBayes Draft Paper
VCFv4.2 Spec
L6 Quiz
2/18 L7:Short Tandem Repeats
Slides/Notes
doi: 10.1101/gr.135780.111 L7 Quiz
Week 5
2/23 NO CLASS INSTRUCTOR AT MEETING
2/25 L8:Structural Variation
Slides/Notes
doi:10.1093/bioinformatics/bts378
doi: 10.1101/gr.114876.110.
L8 Quiz
Week 6
3/1 L9:Genotype Query
Slides/Notes
doi:10.1038/nmeth.3654 L9 Quiz
3/3 L10:PCA and Population Structure
Slides/Notes
DEADLINE TO SELECT PROJECT
PCA Tutorial: arXiv:1404.1100
FastPCA: bioRxiv:/10.1101/018143
L10 Quiz
Week 7
3/8 L11:Statistical Phasing
Slides/Notes
doi:10.1038/nmeth.2307 L11 Quiz
3/10 L12:GWAS + Linear Mixed Models
Slides/Notes
doi:10.1038/nrg1916
doi: 10.1371/journal.pcbi.1002822
kbroman: LMMs and R/lmmlite
L12 Quiz
Week 8
3/15 NO CLASS SPRING BREAK
3/17 NO CLASS SPRING BREAK
Week 9
3/22 L13:Spliced RNA-seq Alignment
Slides/Notes
doi:10.1038/nmeth.3317
doi: 10.1093/bioinformatics/bts635
L13 Quiz
3/24 L14:RNA-seq analysis using k-mer counting and EM
Slides/Notes
doi:10.1038/nbt.2862 L14 Quiz
Week 10
3/29 L15:de novo Transcript Assembly
Slides/Notes
doi:10.1038/nbt.1883
bioRxiv:10.1101/021626
L15 Quiz
3/31 L16:RNA-seq batch effects
Slides/Notes
doi:10.1371/journal.pgen.0030161
doi:10.1093/nar/gku864
L16 Quiz
Week 11
4/5 L17:Predicting Alternative Splicing using DNNs
Slides/Notes
10.1093/bioinformatics/btu277 L17 Quiz
4/7 L18: DeepBind
Slides/Notes
doi:10.1038/nbt.3300 L18 Quiz
Week 12
4/12 L19:DNAse and Deep Learning
Slides/Notes
biorxiv:10.1101/028399 L19 Quiz
4/14 L20:Non-coding Variants + Deep Learning
Slides/Notes
doi:10.1038/nmeth.3547 L20 Quiz
Week 13
4/19 L21:Chromatin Segmentation
Slides/Notes
doi:10.1038/nmeth.1937 L21 Quiz
4/21 L22:Chromatin Imputation
Slides/Notes
doi:10.1038/nbt.3157 L22 Quiz
Week 14
4/26 L23:Enhancer Promoter Interactions
Slides/Notes
doi:10.1038/ng.3539 L23 Quiz
4/28 L24:Single Cell Sequencing Clustering and Psuedo-Time
Slides/Notes
t-SNE
doi:10.1038/nbt.2859
L24 Quiz
Week 15
5/3 L25:Course Summary
Slides/Notes
5/5 NO CLASS ZIA OUT OF TOWN
Week 16
5/10 L27: Project Presentation Day
5/15 LAST DAY TO TURN-IN FINAL PROJECT REPORT/CODE
5/18 LAST DAY TO TURN-IN TAKEHOME FINAL