Fall 2026 · Utah Valley University

Genomics

BIOL 4400-001  ·  Dr. Carl Hjelmen  ·  Fall 2026
Mon / Wed / Fri Upper Division · 3 Credits 15 Weeks Discussion & Seminar Format

Course Info

CourseBIOL 4400-001
SemesterFall 2026
FormatM / W / F in-person
Prereq.BIOL 3500 Genetics
InstructorDr. Carl Hjelmen
OfficeSB 242b
EmailCarl.Hjelmen@uvu.edu
Download Syllabus

Questions & Contact

Email is the best way to reach me. Check the contact page for office hours and my calendar.

Learning Objectives

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

  1. Summarize sequencing methods and strategies, bioinformatics and sequence comparison, sequence alignment and phylogenetic reconstruction, comparative genomics, genome organization and structure, 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/SNPs
  4. Employ critical thinking skills in discussions about genomics

Course Schedule

Subject to change — check Canvas for updates
Discussion day Exam / major deadline No class / break Reading
1
W Aug. 19
F Aug. 21
Intro & Syllabus
How to Read a Scientific Paper
Pre-Course Quiz — due Aug. 21
Questions about Scientific Papers — due Aug. 21
Various online articles (Canvas)
2
M Aug. 24
W Aug. 26
F Aug. 28
How to Read a Paper pt. 2
Overview of Genetics and Genomics
Structural Components of the Genome
Discussion Sign-Up — due Aug. 26
Various online articles (Canvas)
3
M Aug. 31
W Sep. 2
F Sep. 4
Sanger Sequencing & Human Genome Project
Human Genome Project
Discussion on HGP
Selection of Project Subject — due Sep. 4
Précis — due Sep. 4
Watson 1990; Bentley 2000; Nurk et al. 2022
4
M Sep. 7
W Sep. 9
F Sep. 11
Labor Day — No Class
Implications & Applications of HGP
Discussion on All of Us Project
Précis — due Sep. 11
Gibbs 2020; Mao & Zhang 2022; All of Us Intro; Chen et al. 2026
5
M Sep. 14
W Sep. 16
F Sep. 18
Next Generation Sequencing Methods
Third Generation Sequencing
Discussion: Comparing Sequencing Methods
Précis — due Sep. 18
Shendure et al. 2017; Heather & Chain 2016; Treichel et al. 2026
6
M Sep. 21
W Sep. 23
F Sep. 25
Output from Sequencing Methods
Investigate SRA, Set Up Galaxy Account
Discussion on Galaxy / Open Tools
Précis — due Sep. 25
Galaxy 2024; Galaxy Community 2026; Bacon et al. 2026
7
M Sep. 28
W Sep. 30
F Oct. 2
Genome Assembly Methods
Genome Assembly Methods (cont.)
Discussion on Genome Assembly
📋 Exam 1 — due Oct. 2
Précis — due Oct. 2
Li & Durbin 2024; Michael 2026
8
M Oct. 5
W Oct. 7
F Oct. 9
Genome Polishing & Annotation
Genome Annotation & BUSCO
Discussion on Assessing Genome Quality
Outline & Annotated Bibliography — due Oct. 9
Précis — due Oct. 9
Yandell & Ence 2012; Challis & Blaxter 2026
9
M Oct. 12
W Oct. 14
F Oct. 16
Genome Assembly Assignment Hands-On
BUSCO & Annotation Hands-On
No Class — Fall Break
Recommended: Dunn et al. 2019
10
M Oct. 19
W Oct. 21
F Oct. 23
Sequence Alignments & Substitution Models
Phylogenetics
Phylogenomics Hands-On
Hands-On Activities — due Oct. 21
Kapli et al. 2020
11
M Oct. 26
W Oct. 28
F Oct. 30
Phylogenomics Hands-On (cont.)
Phylogenomics
Discussion on Phylogenomics
Phylogenetics Hands-On — due Oct. 29
Meet with Dr. Hjelmen — by Oct. 30
Précis — by Oct. 30
Steenwyk et al. 2023; Foley & Murphy 2026
12
M Nov. 2
W Nov. 4
F Nov. 6
Comparative Genomics
Interpreting Comparative Genomics Plots
Discussion on Introgression
Précis — due Nov. 6
Zhang et al. 2026
13
M Nov. 9
W Nov. 11
F Nov. 13
Work on Final Project
Work on Final Project
Population Genomics
Poster Draft — due Nov. 9
Peer Review for Posters — due Nov. 13
Stephan et al. 2022
14
M Nov. 16
W Nov. 18
F Nov. 20
Poster Prep Day
Poster Prep Day
Discussion on Comparative Genomics
Final Posters — due Nov. 20
Précis — due Nov. 20
Webster et al. 2023; Wong et al. 2026
15
M Nov. 30
W Dec. 2
F Dec. 4
Population Genomics (cont.)
Discussion on Population Genomics
Present Poster — Final
📋 Exam 2 — due Dec. 4
Précis — due Dec. 2
Ma et al. 2026
🏆 Final Assignment — due Dec. 8, 11:59pm
Major Deadlines at a Glance
Exam 1
Due Oct. 2
Outline & Annotated Bib.
Due Oct. 9
Poster Draft
Due Nov. 9
Peer Review of Poster
Due Nov. 13
Final Poster
Due Nov. 20
Exam 2
Due Dec. 4
Final Assignment
Due Dec. 8

Reading & PDF Repository

Papers referenced in the schedule above

Discussion and lecture readings for BIOL 4400 in one place.

Watson 1990
The Human Genome Project: Past, Present, and Future
Bentley 2000
The Human genome Project - an Overview
Nurk et al. 2022
The complete sequence of a human genome
Gibbs_2020_HGP
The Human Genome Project changed everything
Mao & Zhang 2022
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics
Shendure et al. 2017
DNA sequencing at 40: past, present and future
Heather & Chain 2016
The sequence of sequencers: The history of sequencing DNA
Li & Durbin 2024
Genome assembly in the telomere-to-telomere era
Yandell & Ence 2012
A beginner's guide to eukaryotic genome annotation
Dunn et al. 2019
Apollo: Democratizing genome annotation
Kapli et al. 2020
Phylogenetic tree building in the genomic age
Steenwyk et al. 2023
Incongruence in teh phylogenomics era
Stephan et al. 2022
Darwinian genomics and diversity in the tree of life
Webster et al. 2023
Population Genomics for Insect Conservation
Bacon et al. 2026
Ten common misconceptions about Galaxy
The Galaxy Community 2026
Galaxy for accessible,reproducible, and collaborative data analyses: 2026 update
Michael 2026
Plant genome assembly and annotation
Michael 2026
Plant genome assembly and annotation
Challis and Blaxter 2026
Snail plots are badges of genome assembly quality
Foley and Murphy 2026
Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow
Zhang et al 2026
Recovering signatures of archaic hominin introgression using ancestral recombination graphs
Wong et al 2026
Historical comparative genomics to track the evolution of fungal pathogens: a proof of concept
Ma et al 2026
Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape