Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-001--Spring 2024

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 01/09 T

01/11 R		 Intro. to Bioinformatics

Scientific Process		 Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 01/16 T

01/18 R		 NO CLASS TUES. JAN. 16

Evolution		 Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7 -
Week 3 01/23 T

01/25 R		 Evolution pt. 2

Inheritance		 Evolution Worksheet - -
Week 4 01/30 T

02/01 R		 Variation and Selection

Central Dogma: DNA Structure		 Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 02/06 T

02/08 R		 DNA Replication

RNA Transcription		 DNA Structure Assignment Lesk: 88-122 -
Week 6 02/13

02/15 R		 Protein Translation

Central Dogma--Omics		 TAKE HOME EXAM 1
DUE Feb 13		 Lesk: 57-67 -
Week 7 02/20 T

02/22 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 02/27 T

02/29 R		 Steps of Sequencing Processing

Genome Assembly		 Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
Week 9 03/05 T

03/07 R		 Genome Assembly pt. 2

BLAST		 BLAST/NCBI Assignment (in class) - -
- 03/12 T

03/14 R		 SPRING BREAK--NO CLASS
Week 10 03/19 T

03/21 R		 Other uses of NCBI

Phylogenetics		 NCBI activity Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 11 03/26 T

03/28 R		 Phylogenetics hands on

DNA Kits/Genetic Privacy		 TAKE HOME EXAM 2
DUE MAR. 26
Building your own phylogeny (in class)		 Lesk: pp. 154-171 Kapli et al. 2020
Week 12 04/02 T

04/04 R		 Biology and Computers

Introduction to R		 - Lesk: pp. 356-372, 378-393 -
Week 13 04/09 T

04/11 R		 Using R R Assignment - -
Week 14 04/16 T

04/18 R		 Subsetting Data

Writing a function		 R Assignment - -
Week 15 04/23 T Identifying Types of chromosomes TAKE HOME EXAM 3
DUE APR 23		 - -
Final 04/29 M FINISH FINAL PROJECT FINAL PROJECT
DUE April 29		 - -


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