15 Lab01: Find and describe a Genome Analysis Paper
15.1 Lab 1
In class we will read and discuss a recent genome analysis paper that illustrates the three perspectives on genomics (cell, organism, tree of life) and the balance between hypothesis‑driven and discovery‑driven research introduced in Chapter 11–3.
After class, you will search PubMed for a scientific study that includes some form of genome analysis. Avoid “double‑dipping” by reusing papers assigned for other courses or lab meetings. Ideally, choose:
- a genome paper on your study organism, or
- a paper that follows a workflow similar to one you plan to use in your own research, or
- a recent paper that excited you and presents a genome analysis.
Before you start, skim the “Types of Genome Analysis Research Projects” section in Chapter 1 and, if needed, review Appendix Section A.1 for a refresher on reading primary literature1–4.
By the end of this lab, you should be able to:
- Identify the main hypothesis (or questions) of a genomics paper.
- Classify the study using the three perspectives from Chapter 1 (cell, organism, tree of life).
- Describe whether the study leans more hypothesis‑driven, discovery‑driven, or combines both.
- Summarize key genome features (assembly size, chromosome number, basic QC metrics) reported in the paper.
15.2 Deliverables
- Paper and methods diagram
- Upload the PDF of your chosen paper to Canvas.
- Upload a one‑page diagram of the methods used to test the main hypothesis. Give your diagram a descriptive title and include:
- data types (e.g., short‑read WGS, long‑read assembly, RNA‑seq),
- main analysis steps (alignment, assembly, variant calling, comparative analyses),
- which of the three perspectives your paper emphasizes
- whether it is hypothesis-drive, discovery-based, or both.
- data types (e.g., short‑read WGS, long‑read assembly, RNA‑seq),
- Upload the PDF of your chosen paper to Canvas.
- 2–3 minute video summary
- Record an informal 2–3 minute Panopto video summarizing the paper’s goals, methods, and main findings, and how it fits into the perspectives from Chapter 1.
- Upload the video to the “Lab Activity #1” Panopto assignments folder as described on Canvas.
Please refer to the syllabus for late policies. Detailed step‑by‑step instructions for recording and uploading Panopto videos are provided on Canvas rather than here.
15.3 Resources and Refreshers:
If you do not have much experience finding and reading primary literature, complete Appendix Section A.1 (“How to Read Scientific Literature”) before or alongside this lab. That appendix walks through hypothesis identification, concept mapping, and designing follow‑up experiments using a concrete example.