Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-002--Fall 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 08/23 T

08/25 R		 Intro. to Bioinformatics
Nature of Science: Scientific Process		 Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 08/30 T

09/01 R		 Evolution Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7 -
Week 3 09/06 T

09/08 R		 Inheritance

Variation and Selection		 Evolution Worksheet - -
Week 4 09/13 T

09/15 R		 Central Dogma: DNA Structure

Central Dogma: DNA Replication		 Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 09/20 T

09/22 R		 RNA Transcription

Protein Translation		 DNA Structure Assignment Lesk: 88-122 -
Week 6 09/27 T

09/29 R		 Central Dogma--Omics

Genome Sequencing Intro		 TAKE HOME EXAM 1
DUE SEP. 27		 Lesk: 57-67 -
Week 7 10/04 T

10/06 R		 Next and 3rd Generation Sequencing

Steps of Sequencing Processing		 Sequencing Intro Assignment - Shendure et al. 2017
Sims et al. 2014
Logsdon et al. 2020
Heather & Chain
Goodwin et al. 2016
Week 8 10/11 T

10/13 R		 Genome Assembly

FALL BREAK--NO CLASS		 Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
Week 9 10/18 T

10/20 R		 Genome Assembly pt. 2

BLAST		 BLAST/NCBI Assignment (Due Thursday) Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 10 10/25 T

10/27 R		 Biology and Computers

Introduction to R		 -- Lesk: pp. 154-171 Kapli et al. 2020
Week 11 11/01 T

11/03 R		 Using R TAKE HOME EXAM 2
DUE NOV. 01		 Lesk: pp. 356-372, 378-393 Stark et al. 2019
Week 12 11/08 T

11/10 R		 Subsetting Data

Writing a Function		 R assignment - -
Week 13 11/15 T

11/17 R		 Transcriptomics/Proteomics

Identifying Types of Chromosomes		 R Assignment - -
- 11/22 T

11/24 R		 THANKSGIVING BREAK--NO CLASS
Week 14 11/29 T

12/01 R		 Other Uses of NCBI
Phylogenetics		 -- - -
Week 15 12/06 T

12/08 R		 Phylogentics Pt. 2

DNA kits/Genetic Privacy		 TAKE HOME EXAM 3
DUE DEC. 6
Building your own Phylogeny		 - -
Final 12/13 T FINAL PROJECT FINAL PROJECT
DUE DEC. 13		 - -


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