Course Syllabus

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Bioinformatics: Biol 435, 535, 535DDNA_wind_sculpture.jpg

Cramer 129, M,W,F 11:00-11:50

"It's just this playground of incredibly rich data"

Dr. Elizabeth Blackburn, Nobel laureate, co-discover of telomerase

 

Instructor: Dr. Rebecca Reiss, 313 Jones Annex, reiss@nmt.edu

I.  Rationale

This course will teach biologists to analyze microarray and Next-Generation Sequencing (NGS) gene expression data. User-friendly software is now available that facilitates the completion of a post-sequencing workflow from quality control to data visualization, so computer-scripting skills are not required; although a basic understanding of statistics is crucial. A toy box with tools for analyses allows biologists to play in this data-rich environment and develop hypotheses from the massive amount of data generated over the past 20 years.

II. Course Aims and Outcomes

Aims

Participants will gain skills in high-throughput genetic analyses (microarrays and NGS) that can be applied to any gene expression dataset.

Specific Learning Outcomes

By the end of this course, participants should successfully be able to:

  • Understand workflows for high-throughput gene expression data
  • Download expression data from public databases
  • Manipulate data files with JMP®
  • Create informative networks using Cytoscape
  • Locate and utilize public-domain bioinformatic resources
  • View genome alignments with the Integrated Genome Viewer

III. Course Prerequisites

 Senior or graduate standing is required. NMT students must have completed Biol 111 (General Biology), Biol. 333 (Genetics), and Biol 331 (Cell Biology). Students from other schools must have completed similar courses. Instructor permission is required if any prerequisite is missing.

 IV.  Format and Procedures 

The course is taught as a live lecture (435 and 535) or a distance education course (535D only). Registration for the distance section is subject to a $350 fee. The course will be managed through the Canvas portal https://nmt.instructure.com/login/canvashttps://nmt.instructure.com/login/canvas ).

This Bioinformatics course consists of four modules, the first will focus on data mining and visualization using publically available microarray data. The next will be an introduction to the wide variety of bioinformatics databases, including The Cancer Genome Atlas (TCGA) and genome browsers, and the last third of the course will focus on next-generation sequencing protocols and data analysis. The Topic(s) for the fourth module (‘TBA”) will be determined by the students.

 Grades will be based the timely completion of assignments within each module, which include quizzes, reports, and presentations. Graded assignments are marked with an * within each module. A final project will be required, The topic and format will selected by the student in collaboration with the instructor.

V.  Course Materials 

There is no required text as readings will be from the literature. Access to a computer (laptop preferred) that can run the following programs is necessary for each participant:

 

  1. Tentative Course Schedule

Week date

Topics

Module/Assignments

1

8/17

The Gene Expression Omnibus (GEO)

GEO part A

2

8/24

Data Mining: Searching GEO

GEO part B

3

8/31

Data Analysis: GEO2R, JMP

GEO part C

4

9/9

Data Visualization: Cytoscape, Gene Ontology (GO), and gene enrichment analysis

GEO part D

5

9/14

Data Visualization: Merging data with networks

GEO part E

6

9/21

Presentations

GEO part F

7

9/28

Genome Sequencing Projects and Browsers

DB Part A

8

10/5

The Cancer Genome Atlas (TCGA)

DP Part B

9

10/12

Nucleic Acids Research Database Issue, Presentations

DP Part C

10

10/19

Next-Generation Sequencing (NGS): Methods

NGS Part A

11

10/26

NGS: Post-Sequencing Workflows

NGS Part B

12

11/2

NGS: Integrated Genome Viewer (IGV)

NGS Part C

13

11/9

NGS: Data visualization, Cytoscape

NGS Part D

14

11/16

TBA

 

15

11/23

TBA

 

16

11/30

TBA

 

Finals week

 

Final Project Due

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Course Summary:

Date Details Due