Genomics (ALWAYS UNDER CONSTRUCTION)
BIOL 4400--01 Fall 2025
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 | Due |
|---|---|---|---|---|
| 1 | Aug. 20Aug. 22 | Intro. & SyllabusHow to read a paper | For Class: Various Online articles (see Canvas) | Pre-course quiz--Aug. 22Questions about scientific papers--Aug. 22 |
| 2 | Aug. 25Aug. 27Aug. 29 | How to read a paper pt. 2Overview of genetics and genomicsStructural components of the genome | For Class:Various Online articles (see Canvas) | Discussion signup--Aug. 27 |
| 3 | Sep. 1Sep. 3Sep. 5 | NO CLASS--LABOR DAYSanger sequencing and the Human Genome ProjectDiscussion on HGP | For Class:Watson 1990Bentley 2000For Discussion:Nurk et al. 2022 | Selection of Project Subject--Sep. 5Precis Sep. 5 |
| 4 | Sep. 8Sep. 10Sep. 12 | Human Genome ProjectImplications and applications of HGPDiscussion: All of Us Project | For Class:Gibbs 2020Mao and Zhang 2022For Discussion:All of Us introKlein et al. 2025 | Precis Sep 12 |
| 5 | Sep. 15Sep. 17Sep. 19 | Next generation sequencing methodsThird generation sequencingDiscussion Comparing Sequencing Methods | For Class:Shendure et al. 2017Heather and Chain 2016For Discussion:Veselovsky et al. 2025 | Precis Sep. 19 |
| 6 | Sep. 22Sep. 24Sep. 26 | Output from sequencing methodsInvestigate SRA, setup Galaxy AccountDiscussion on Galaxy/Open tools | For Class:Galaxy 2024For Discussion Goclowski et al. 2025 | Precis Sep. 26 |
| 7 | Sep. 29Oct. 1Oct. 3 | Genome assembly methodsGenome assembly methodsDiscussion on Genome Assembly | For Class:Li and Durbin 2024For Discussion:Antipov et al. 2025 | Exam 1 Due Oct. 3Precis Oct. 3 |
| 8 | Oct. 6Oct. 8Oct. 10 | Genome polishing and annotationGenome annotation and BUSCODiscussion on Assessing Genome Quality | For Class:Yandell and Ence 2012For Discussion:Hjelmen 2024 | Outline and Annotated Bibliography due Oct. 10Precis Oct. 10 |
| 9 | Oct. 13Oct. 15Oct. 17 | Genome assembly assignmentBUSCO and annotation hands onFALL BREAK--NO CLASS | Recommended Reading:Dunn et al. 2019 | - |
| 10 | Oct. 20Oct. 22Oct. 24 | Sequence alignments and substitution modelsPhylogeneticsPhylogenomics Hands on | For Class:Kapli et al. 2020 | Hands on Activities due Oct. 22 |
| 11 | Oct. 27Oct. 29Oct. 31 | Phylogenomics hands onPhylogenomicsDiscussion on Phylogenomics | For Class:Steenwyk et al. 2023For Discussion:Gupta et al. 2025 | Phylogenetics Hands on by Oct. 29 Meet with Dr. Hjelmen by Oct. 31Precis by Oct. 31 |
| 12 | Nov. 3Nov. 5Nov. 7 | Comparative GenomicsInterpreting Comparative Genomics PlotsDiscussion on Introgression | For Discussion:Blumer et al. 2025 | Precis Nov. 7 |
| 13 | Nov. 10Nov. 12Nov. 14 | WORK ON FINAL PROJECTWORK ON FINAL PROJECTPopulation Genetics | For Class:Stephan et al. 2022 | Poster Draft Due Nov. 10Peer Review for Posters Due Nov. 14 |
| 14 | Nov. 17Nov. 19Nov. 21 | Poster Prep DayPoster Prep DayDiscussion on Comparative Genomics | For Class:Webster et al. 2023For Discussion:Yoo et al. 2025 | Final Posters Due by Nov. 20Precis Nov. 21 |
| - | Nov. 24Nov. 26Nov. 28 | THANKSGIVING BREAK--NO CLASS | ||
| 15 | Dec. 1Dec. 3Dec. 5 | Population Genomics cont.Discussion on Population GenomicsFINAL POSTER PRESENTATIONS | For Discussion:Liu et al. 2025 | Exam 2 due Dec. 5Precis Dec. 3 |