Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-002--Fall 2021


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
Topic(s) Assignments/
Additional Reading
(on Canvas)
Week 1 08/24 T

08/26 R
Intro. to Bioinformatics
Nature of Science: Scientific Process
Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 08/31 T

09/02 R
Nature of Science: Evolution
Nature of Science: Evolution and Inheritance
Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7
Week 3 09/07 T

09/09 R
Nature of Science: Variation and Selection

Hardy-Weinberg and Central Dogma
Evolution and Inheritance Lesk: pp. 9-17, 49-58 Crick 1970
Week 4 09/14 T

09/16 R
Central Dogma: Structure of DNA

Central Dogma: DNA Replication and Transcription
Selection and Population Genetics assigment Lesk: pp. 88-122
Week 5 09/21 T

09/23 R
Central Dogma: Transcription and Translation
Central Dogma and -omics
Week 6 09/28 T

09/30 R
Biology and Computers
Introduction to R
Translate RNA into Protein
Week 7 10/05 T

10/07 R
Biology and Computers: using R PICK PAPER FOR PROJECT Lesk: pp. 57-67 Shendure et al. 2017
Sims et al. 2014
Logsdon et al. 2020
Heather & Chain
Goodwin et al. 2016
Week 8 10/12 T

10/14 R
Biology and Computers

Lesk: pp. 68-73 Rice and Green 2017
Week 9 10/19 T

10/21 R
Biology and Computers
Intro. to Sequencing
TAKE HOME EXAM 2 Salzburg 2019
Week 10 10/26 T

10/28 R
Genome Sequencing Abstract and Figure Explanation (Final) Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 11 11/02 T

11/04 R
Genome Assembly Setting up a sequencing project Lesk: pp. 116-122 Tam et al. 2019
Shraiber and Akey 2015
Week 12 11/09 T

11/11 R
Genome Annotation
DNA Databases
Seqeunce alignments Lesk: pp. 154-171 Kapli et al. 2020
Week 13 11/16 T

11/18 R
Comparative Genomics and Phylogenetics TAKE HOME EXAM 3 Lesk: pp. 356-372 Stark et al. 2019
- 11/23 T

11/25 R
Week 14 11/30 T

12/02 R
Submit Draft Poster for Peer Review(Final) Lesk: pp. 378-393
Week 15 12/07 T

12/09 R
Work on Final Project Submit Peer Review Comments for Final