Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-002--Spring 2023

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 01/10 T

01/12 R		 Intro. to Bioinformatics
Nature of Science: Scientific Process		 Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 01/17 T

01/19 R		 Evolution Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7 -
Week 3 01/24 T

01/26 R		 Inheritance

Variation and Selection		 Evolution Worksheet - -
Week 4 01/31 T

02/02 R		 Central Dogma: DNA Structure

Central Dogma: DNA Replication		 Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 02/07 T

02/09 R		 RNA Transcription

Protein Translation		 DNA Structure Assignment Lesk: 88-122 -
Week 6 02/14 T

02/16 R		 Central Dogma--Omics

Genome Sequencing Intro		 TAKE HOME EXAM 1
DUE FEB 14		 Lesk: 57-67 -
Week 7 02/21 T

02/23 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 02/28 T

03/02 R		 Genome Assembly Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
- 03/07 T

03/09 R		 SPRING BREAK--NO CLASS
Week 9 03/14 T

03/16 R		 BLAST

Other uses of NCBI		 BLAST/NCBI Assignment Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 10 03/21 T

03/23 R		 Phylogenetics Building your own Phylogeny Lesk: pp. 154-171 Kapli et al. 2020
Week 11 03/28 T

03/30 R		 DNA Kits/Genetic Privacy

Transcriptomics/Proteomics		 TAKE HOME EXAM 2
DUE MAR 28		 Lesk: pp. 356-372, 378-393 Stark et al. 2019
Week 12 04/04 T

04/06 R		 Biology and Computers

Introduction to R		 Interpreting figures assignment - -
Week 13 04/11 T

04/13 R		 Using R R Assignment - -
Week 14 04/18 T

04/20 R		 Subsetting Data
Writing a Function		 R Assignment - -
Week 15 04/25 T

04/27 R		 Identifying Types of chromosomes

No Class Thursday		 TAKE HOME EXAM 3
DUE APRIL 25		 - -
Final 05/02 T FINISH FINAL PROJECT FINAL PROJECT
DUE MAY 2		 - -


Questions/Comments