Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-001--Spring 2026

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 01/06 T

01/08 R		 Intro. to Bioinformatics

Scientific Process video		 Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 01/13 T

01/15 R		 Evolution video

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

01/22 R		 Inheritance

Inheritance		 Evolution Worksheet - -
Week 4 01/27 T

01/29 R		 Central Dogma: DNA Structure

DNA Replication		 Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 02/03 T

02/05 R		 RNA Transcription

Protein Translation		 DNA Structure Assignment Lesk: 88-122 -
Week 6 02/10 T

02/12 R		 Central Dogma--Omics

Genome Sequencing Intro		 TAKE HOME EXAM 1
DUE FEB 10		 Lesk: 57-67 -
Week 7 02/17 T

02/19 R		 Genome Sequencing Intro

Next and 3rd Generation Sequencing		 Sequencing Intro Assignment - Shendure et al. 2017
Sims et al. 2014
Logsdon et al. 2020
Heather & Chain
Goodwin et al. 2016
Week 8 02/24 T

02/26 R		 Steps of Sequencing Processing

Genome Assembly		 Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
Week 9 03/03 T

03/05 R		 Genome Assembly pt. 2

BLAST		 - - -
- 03/10 T

03/12 R		 SPRING BREAK--NO CLASS
Week 10 03/17 T

03/19 R		 Other uses of NCBI

Phylogenetics		 BLAST/NCBI Assignment (in class) Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 11 03/24 T

03/26 R		 Phylogenetics Hands on

Biology and Computers		 TAKE HOME EXAM 2
DUE MAR. 24
Building your own phylogeny (in class)		 Lesk: pp. 154-171 Kapli et al. 2020
Week 12 03/31 T

04/02 R		 DNA Kits/Genetic Privacy

Introduction to R		 - Lesk: pp. 356-372, 378-393 -
Week 13 04/07 T

04/09 R		 Using R

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

04/16 R		 Subsetting Data

Writing a Function		 R Assignment - -
Week 15 04/21 T Identifying Types of chromosomes TAKE HOME EXAM 3
DUE APR. 21		 - -
Final 04/27 T FINISH FINAL PROJECT FINAL PROJECT
DUE APR. 27		 - -


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