Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-002--Spring 2022

Syllabus

Learning Objectives

Upon completion of this course, students will be able to:

1. Distinguish the process of science from other ways of understanding the world.

2. Evaluate evidence to solve problems using scientific thinking.

3. Describe the basic terminology and principles of the bioinformatic “omics” - such as genomics, transcriptomics, proteomics, etc.

4. Contrast the different methodologies of DNA sequencing.

5. Effectively use databases, websites, and computational methods for studying biological data in relation to the evolution of genes, proteins, and whole genomes.

6. Interact with the practical applications of bioinformatics, including some basic coding

Schedule (Subject to change)

Week of Class Dates
(Month/Day)
Topic(s) Assignments/
Activities
Recommended
Reading
Additional Reading
(on Canvas)
Week 1 01/11 T

01/13 R
Intro. to Bioinformatics
Nature of Science: Scientific Process
Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 01/18 T

01/20 R
Evolution Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7 -
Week 3 01/25 T

01/27 R
Inheritance

Variation and Selection
Evolution Worksheet - -
Week 4 02/01 T

02/03 R
Central Dogma: DNA Structure

Central Dogma: DNA Replication
Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 02/08 T

02/10 R
RNA Transcription

Protein Translation
DNA Structure Assignment Lesk: 88-122 -
Week 6 02/15 T

02/17 R
Central Dogma--Omics

Genome Sequencing Intro
TAKE HOME EXAM 1
DUE FEB 15
Lesk: 57-67 -
Week 7 02/22 T

02/24 R
Next and 3rd Generation Sequencing

Steps of Sequencing Processing
What are -omics? - Shendure et al. 2017
Sims et al. 2014
Logsdon et al. 2020
Heather & Chain
Goodwin et al. 2016
Week 8 03/01 T

03/03 R
Genome Assembly Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
- 03/08 T

03/10 R
SPRING BREAK--NO CLASS
Week 9 03/15 T

03/17 R
BLAST

Other uses of NCBI
BLAST/NCBI Assignment Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 10 03/22 T

03/24 R
Phylogenetics Building your own Phylogeny Lesk: pp. 154-171 Kapli et al. 2020
Week 11 03/29 T

03/31 R
DNA Kits/Genetic Privacy

Transcriptomics/Proteomics
TAKE HOME EXAM 2
DUE MAR 29
Lesk: pp. 356-372, 378-393 Stark et al. 2019
Week 12 04/05 T

04/07 R
Biology and Computers

Introduction to R
Interpreting figures assignment - -
Week 13 04/12 T

04/14 R
Using R R Assignment - -
Week 14 04/19 T

04/21 R
Subsetting Data
Writing a Function
R Assignment - -
Week 15 04/26 T

04/28 R
Identifying Types of chromosomes

No Class Thursday
TAKE HOME EXAM 3
DUE APRIL 26
- -
Final 05/03 T FINISH FINAL PROJECT FINAL PROJECT
DUE MAY 3
- -


Questions/Comments