The most important task as a first-year graduate student is finding the thesis lab. Why would you choose our lab for your graduate training?

1) The question.
You need to be interested in the questions our lab is asking. We are interested in the fundamental question of how cell type-specific gene expression and cell fate are regulated during spermatogenesis. Our lab will be a good fit if you are broadly interested in cell fate, epigenetics, and reproduction.
Please check out the research page and past papers.

2) Training.
As a student, the training you receive to be an independent scientist is as important as the research question. In our group:

• You will learn the logic and method of genetics. We are a developmental genetics lab. We will identify new genes through traditional genetic screens and by developing new screen systems in vivo. We will perturb protein functions by genetic knock outs, knock-ins as well as inducible degradations. Genetics will provide a foundation of logic. By removing and adding back genes, you will learn how to judge what types of data are required to support a claim.
• You will learn biological principles and approaches to study them in different contexts. Our lab will use both flies and mice as models. You will likely choose one organism as a primary model. However, exposure to different systems will help you develop a broader understanding of biology. How did gene regulation evolve differently between flies and mice? What additional layers of regulation are needed in a mammalian genome that is 20 times the size of the fly genome? On the other hand, many genes involved in spermatogenesis are conserved in flies and mice. Then, what are the core processes required for the reproduction?
• You will become proficient at experimental and computational approaches. Many current chromatin experiments involve high-throughput sequencing with billions of short reads. I expect and will help my students to do basic analyses of these sequencing data using command line, R, etc. Biology is increasingly becoming a 'data science.' I hope that experience in our group will prepare students to understand, evaluate, and handle large datasets, even when new methods appear in the future.
• In the end, I want students trained in my lab to be good scientists. Being a critical scientist involves more than becoming proficient in your techniques. You will learn to evaluate evidence and claims critically and effectively communicate your assessments and opinions. These skills will help you to have a fulfilling career in whatever career you choose, be it in academia, industry, or any area you pursue.

3) The Fit.
I think there is no universally 'better' choice for everyone. It is a matter of preference. If you prefer a faster pace of experiment to results, working with flies or mice may seem too slow for you. On the other hand, if you are interested in the function of proteins in the context of tissue or animals, our lab is a better fit for you than, for example, structural biology or cell biology labs. Professor styles are also different. Being in a new lab, you will have more frequent interactions with me than big labs with many students and postdocs. It is up to you to decide what kind of mentoring style suits you.

The fit will be hard to judge without in-person interactions. So, come rotate with me and find out if our lab will be the right place for you.

Good luck in finding your thesis lab!

Goal of Rotation Projects
The purpose of a rotation project is to help you evaluate if the lab is the right fit for your PhD training. Over the span of 8 weeks, your goals are:

• Familiarize yourself with lab techniques: Do experiments and see if you enjoy the day-to-day experience in the lab. You cannot work in a mouse/fly lab if you find yourself dreading handling mice or flies.
• Engage in scientific discussions: Use your project to actively participate in scientific exchanges with PIs and lab members to learn if the lab is the right scientific home for you.
• Evaluate Lab Fit: Observe the lab's research focus, culture, and mentorship style to determine if it is compatible with you. Is it easy to get help with your experiments? Do you like the frequency and interactions with the PI? Do you find the research questions interesting?

Though the rotation is short, the aim is to make tangible progress—whether by testing a hypothesis, generating reagents, or analyzing data. You will give a final presentation that puts your findings within the larger scope of the research.

Example Projects for 2024-2025

[COMPUTATIONAL]
• Project: 1) Analysis of Cbx7 KO scRNA-seq data; 2) Computational screen to identify perturbations affecting gene silencing.
• Approach: Learn how to process and analyze single-cell RNA sequencing data using computational pipelines. Use publicly available gene expression data to identify genetic perturbations resulting in 'aberrant' gene expression.
[POLYCOMB]
• Project: Characterization of Cbx7 knockout (KO) mice for cellular defects.
• Project: Characterization of CBX2 paralog domain insertion mice.
• Approach: Perform immunofluorescence (IF) staining, microscopy, and sperm counts to assess cellular changes in KO mice.
[KUMGANG]
• Project: Characterization of Kumgang domain mutant flies.
• Project: Characterization of destabilization domain fused Kumgang flies.
• Project: Characterization of Kumgang homolog (Hunchback) overexpressed flies.
• Approach: Utilize techniques like IF staining, microscopy, and western blotting to study the developmental and cellular impact of various genetic manipulations in flies.
[TECHNOLOGY]
• Project: Perform a FISH-based chromatin-structure assay for Cbx7 and/or Kmg mutant flies
• Project: Develop a FISH-based in-situ 3C assay.
• Approach: Learn and implement advanced chromatin conformation and visualization techniques based on FISH.

* Please note: while genomic techniques (RNA-seq, Cut&Run, etc) are one of the main tools used in the lab, they are challenging to complete within eight weeks, so they are not a part of potential projects.

Final Presentation
At the end of your rotation, summarize your work within the broader research context. Highlight:

• Background and significance: What was known and what was unknown? Why answering your question is important?
  
• Methods and Approaches Used: Detail the experimental/computational techniques and rationale.
  
• Key Findings: Summarize what was learned, including successful results or challenges faced.
  
• Next Steps: Propose future experiments or analyses that build on your rotation work.
  

This guide will help structure your rotation so that you can anticipate what was expected. The projects listed are examples. We can discuss the project further to fit your background and interests.

Jongmin Kim (Aug 2024)

I worked as a research technician before going to graduate school. There are two major reasons you may consider this type of position.

1) To learn what you want. Graduate (or medical) school is a long commitment and will determine a big part of your subsequent career path. Do I like research? It is hard to know without doing it. After two years of full-time research, you will know if you like doing experiments, computational analyses, and discussing science. You will learn whether you find joy in basic science by making discoveries, or you are attracted to using that knowledge to directly help people by developing therapies in companies or treating people as a physician.

2) To be competitive in graduate (or medical) school applications. Research experience is critical for successful professional school applications in biomedicine. A big part of admissions are the statement of purpose and in-person interviews; these are based in large part on your prior research experience. Furthermore, prior research experience will serve you well in pursuing your thesis projects in graduate school.

I learned the basics of how to do experiments, present and communicate my research from my time as a technician. I joined the lab of a starting assistant professor. The experience of setting up a lab was exciting. The professor and I unboxed new equipment together, worked side by side to do the lab's first microarray experiment, and debugged codes to analyze the results. I got a chance to present my data to physicians in the collaborating medical school. I had opportunities (and responsibilities) that were not usually available to postbacs, as I was one of the few members of the lab.

If this is the type of experience you want, please contact me. I will do my best to mentor you so that you can contribute to our group's science and successfully advance to the next stage of your chosen career.