Genomics (ALWAYS UNDER CONSTRUCTION)

BIOL 4400--01 Fall 2022

Syllabus

Learning Objectives

Upon completion of this course, students will be able to:

1. Summarize the subtopics: sequencing methods and strategies, bioinformatics and sequence comparison, sequence alignment and phylogenetic reconstruction,
comparative genomics, organization and structure of genomes, genome annotation, transcriptomics and proteomics

2. Interpret constructed evolutionary trees derived from molecular data.

3. Carry out genomic analyses such as annotation, transcriptomics, functional genomics, metagenomics, and genetic variation and SNPs

4. Employ critical thinking skills in discussions about genomics

Schedule (Subject to Change)

Week Dates Topic Readings
1 Aug. 22

Aug. 24

Aug. 26.		 Intro. & Syllabus

Overview of Genetics and Genomics

Structural Components of the Genome		 For Class:
Various Online articles (see Canvas)
2 Aug. 29

Aug. 31

Sep. 2		 Sanger Sequencing and the Human Genome Project

Human Genome Project

Discussion on HGP		 For Class:
Watson 1990
Bentley 2000

For Discussion:
Nurk et al. 2022
3 Sep. 5

Sep. 7

Sep. 9		 NO CLASS--LABOR DAY

Implications and Applications of HGP

Discussion on "All of Us" Project		 For Class:
Gibbs 2020
Mao and Zhang 2022

For Discussion:
"All of Us" Intro
Ramirez et al. 2022
4 Sep. 12

Sep. 14

Sep. 16		 Next Generation Sequencing Methods

Third Generation Sequencing

Discussion Comparing Sequencing Methods		 For Class:
Shendure et al. 2017
Heather and Chain 2016

For Discussion:
Hu et al. 2021
5 Sep. 19

Sep. 21

Sep. 23		 Output from Sequencing Methods

Investigate SRA, set up Galaxy Account

Discussion on Galaxy/Open tools
 For Class:
Exam 1 Due Sep. 21

For Discussion:
Galaxy 2020
6 Sep. 26

Sep. 28

Sep. 30		 Genome Assembly Methods

Genome Assembly Methods Cont.

Discussion on Genome Assembly		 For Class:
Rice and Green 2019

For Discussion
Hotaling et al. 2021
7 Oct. 3

Oct. 5

Oct. 7		 Genome Assembly Assignment

Genome Polishing

Discussion on Genome Polishing
 For Class:
McCartney et al. 2020

For Discussion:
Wick and Holt 2022
8 Oct. 10

Oct. 12

Oct. 14		 Genome Annotation and BUSCO

BUSCO and Annotation Hands on

FALL BREAK--NO CLASS		 For Class:
Yandell and Ence 2012

Recommended Reading:
Dunn et al. 2019
9 Oct. 17

Oct. 19

Oct. 21		 Continue Annotation Discussion

Sequence Alignments

Sequence Alignments and Substitution Models		 For Class:
Edgar and Batzoglou 2006
10 Oct. 24

Oct. 26

Oct. 28		 Phylogenetics

Phylogenomics hands on

Discussion on Phylogenomics		 For Class:
Kapli et al. 2020

For Discussion:
One Thousand Plant transcriptomes...
11 Oct. 31

Nov. 2

Nov. 4		 Phylogenomics

Phylogenomics and Human Genomics

Discussion on Introgression		 For Class:
Hibbins and Hahn 2022

For Discussion
Figeuiro et al. 2017
12 Nov. 7

Nov. 9

Nov. 11		 Comparative Genomics

Comparative Genomics Plots

Discussion on Comparative Genomics		 For Class:
Herrero et al. 2016

For Discussion:
D'Hont et al. 2012
13 Nov. 14

Nov. 16

Nov. 18		 WORK ON FINAL PROJECT

WORK ON FINAL PROJECT

Discuss any Questions		 For Class:
Exam 2 Due Nov. 18
- Nov. 21

Nov. 23

Nov. 26		 THANKSGIVING BREAK--NO CLASS
14 Nov. 28

Nov. 30

Dec. 2		 Population Genomics

Population Genomics cont.

Discussion on Population Genomics		 For Class:
Gopalan et al. 2022

For Discussion:
Aylward et al. 2022
15 Dec. 5

Dec. 7

Dec. 9		 Open Discussion on Genomics

Final Questions and Preparations for Final

PRESENT POSTER FINAL		 -


Questions/Comments