Introduction to Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 1011-003--Fall 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 08/24 R Intro. to Bioinformatics Syllabus Quiz Lesk: Preface, pp. 34-37 Gauthier et al. 2019
Markowetz 2017
Week 2 08/29 T

08/31 R		 Scientific Process

Evolution		 Case Study: Does sugar cause hyperactivity Lesk: pp. 1-7 -
Week 3 09/05 T

09/07 R		 Evolution

Inheritance		 Evolution Worksheet - -
Week 4 09/12 T

09/14 R		 Variation and Selection

Central Dogma: DNA Structure		 Inheritance Assignment Lesk: pp. 9-17,49-58 Crick 1970
Week 5 09/19 T

09/21 R		 DNA Replication

RNA Transcription		 DNA Structure Assignment Lesk: 88-122 -
Week 6 09/26

09/28 R		 Protein Translation

Central Dogma--Omics		 TAKE HOME EXAM 1
DUE SEP 26		 Lesk: 57-67 -
Week 7 10/03 T

10/05 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 10/10 T

10/12 R		 Steps of Sequencing Processing

Genome Assembly		 Sequencing Assignment Lesk: pp. 68-73 Rice and Green 2017
Week 9 10/17 T

10/19 R		 Genome Assembly pt. 2

FALL BREAK		 - - -
Week 10 10/24 T

10/26 R		 BLAST

Other uses of NCBI		 BLAST/NCBI Assignment (in class) Lesk: pp. 123-143 Langmead and Nellore 2018
Erlich and Narayanan 2014
Week 11 10/31 T

11/02 R		 Phylogenetics

Phylogenetics Hands on		 TAKE HOME EXAM 2
DUE OCT. 31
Building your own phylogeny (in class)		 Lesk: pp. 154-171 Kapli et al. 2020
Week 12 11/07 T

11/09 R		 DNA Kits/Genetic Privacy

Biology and Computers		 - Lesk: pp. 356-372, 378-393 -
Week 13 11/14 T

11/16 R		 Introduction to R

Using R		 R Assignment - -
- 11/21 T

11/23 R		 THANKSGIVING BREAK--NO CLASS
Week 14 11/28 T

11/30 R		 Using R

Subsetting Data		 R Assignment - -
Week 15 12/05 T

12/07 R		 Writing a Function

Identifying Types of chromosomes		 TAKE HOME EXAM 3
DUE DEC. 05		 - -
Final 12/12 T FINISH FINAL PROJECT FINAL PROJECT
DUE DEC. 12		 - -


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