Yuping Li is a graduate student in the Department of Biology at Stanford. She is co-advised by Professors Gavin Sherlock and Dmitri Petrov. Her Ph.D. work has been focusing on combining a DNA-barcode lineage tracking system in S. cerevisiae and experimental evolution to understand short-term adaptation and trade-offs.
Can you tell us a bit about yourself, personally and professionally?
This is Yuping. I am a graduate student in the Department of Biology, jointly advised by Professors Gavin Sherlock and Dmitri Petrov.
I grew up in a small village in northern China, where the concept of research was foreign to most people. My interest in science started to build up through science classes in middle school. I had a special interest in physics at that time. During high school, I learned about DNA in biology classes for the first time and became fascinated about how almost all biological systems, ranging from microbes to plants and animals, were encoded by the same fundamental DNA blocks. Aiming to learn more about genomics and possibly how to crack the DNA code, I decided to major in bioinformatics in college. While I greatly enjoyed analyzing sequencing data and inferring biological insights out of it, I found myself lacking the basic skills to understand how most biological experiments were conducted. Thus, I worked as a technician in a genetics lab after college, where I finally got my hands wet.
Fortunately, I was able to pursue my interest in biology through graduate school. During my graduate school research, I combined high-throughput sequencing and experimental evolution to study evolutionary processes, which enabled me to practice and further improve my skills in both computational and experimental biology.
How did you end up here? What first got you interested in genetics and science?
I wanted to become a scientist since I was child. However, it was unclear to me what scientists really do. My impression of scientists was mainly from cartoons, where they experimented with different colors of liquids and got something cool out of them (like the magic potion that makes people shrink to the size of ants). Thinking back I am actually not sure whether I was more attracted to the idea of being able to do specific experiments or the cool things those cartoon scientists always ended up with.
I first got seriously interested in genetics in high school. It was the early years of the human genome project. I remember that I was very excited and shocked by the idea that we could crack the secrets of humans by sequencing genomes, which eventually led to my decision to major in bioinformatics in college.
Can you tell us about your current research and what you hope to achieve with it?
Evolution is the driving force of the biodiversity we are seeing on our planet today. However, our knowledge of evolution is still very limited. This limitation is largely caused by the fact that we cannot go back in time and dissect the evolutionary process step-by-step. Fortunately, microbial experimental evolution–evolving fast growing microbes under well-controlled laboratory conditions–provides the opportunity to study evolutionary processes in real time. In my current research, I evolve yeast populations in seasonal conditions and characterize different performances that are changed in order to adapt to these conditions. Moreover, by genome-wide sequencing adaptive clones, I study the genetic basis of adaption specific to each evolutionary condition.
One question I am interested in is whether and how evolution is constrained. Trade-offs have been widely assumed in the study of evolutionary and function biology; for instance, organisms adapted to cold conditions (e.g. polar bears) trade-off in hot conditions and vice versa. However, the prevalence of tradeoff and its underlying mechanisms is poorly understood. In my current research, by evolving yeast populations in one condition and measuring their performance in another, I am able to explore this question.
While evolutionary studies may sound very basic and inapplicable to our day-to-day life, I want to point out that they are actually very important in many real-world problems. For instance, human health-related problems like antibiotic resistance or cancer progression are evolutionary processes, where either pathogenic bacteria evolve to tolerate antibiotics or normal human cells happen to pick up mutations that enable them to propagate uncontrollably. Understanding these evolutionary processes will greatly contribute to our ability to design more effective treatments for these problems.
My graduate school work has been focusing on how evolution works in a population with a single species. In the next step, I am interested in continuing the study of evolution in a multi-species system and hope to characterize how species interaction contributes to the evolutionary process.
Briefly, what’s the coolest thing about your work?
Most of it would have sounded like a science fiction to me if I didn’t study biology. We are able to observe evolution in real time and, more importantly, pinpoint what mutations caused it. This to me is incredible.
Were there people (or one person) in particular to whom you would attribute your professional success?
There are a lot of people who have helped me along the way to becoming a biologist. It would have been impossible for me to get where I am today without their help.
First, I want to thank: my high school biology teacher, who introduced me to the genomics world and was a great inspiration for me to pursue a major in biology; my college mentor who taught me a lot about bioinformatics; and my mentors in the lab I worked in as a technician, who taught me how to do lab work (for instance, running PCRs and western blots).
Second, I want to thank my current advisors, Gavin and Dmitri, who have been actively involved in every part of my training in graduate school, and who have been extremely supportive. They have guided me on the way to learning how to form scientific questions, diagnose problems, write papers and eventually become an independent researcher.
Last, I want to thank my lab mates and collaborators. I have gotten so much help from them (literally) every day in the lab. I want to thank them for both their scientific and emotional support.
What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you?
First, seek advice from people around you, your fellow graduate students, lab mates, advisor, other faculty members you get a chance to have a conversation with, and so on. We are surrounded by brilliant people with different areas of expertise. They are great resources to ask for research feedback, to brainstorm new ideas, and even to form collaborations. I have been amazed by how generous people are about their time and how much I have learned from my conversations with them. So, don’t hesitate to ask for advice!
Second, go to conferences if you can. Personally, I find conferences the best opportunity to connect with the scientific community and to keep updated with the research in my subfield. Moreover, I got lost in my lab work sometimes, without thinking about the big picture. Going to conferences helps me refocus and re-analyze my own project critically.
What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?
In the short term, I am graduating this summer and going to join the Bondy-Demony lab at UCSF as a postdoc soon. I am very much looking forward to it.
I am hoping to become a professor in the later stage of my life. I enjoy doing science, and hope to get the opportunity to mentor the next-generation of scientists as well.
Can you speak a bit to the role you see CEHG playing on Stanford campus?
CEHG has played an essential role in bringing evolutionary biologists, population geneticists, human geneticists, and ecologists on Stanford campus together. It has facilitated interdisciplinary communications and collaborations among us. I have greatly enjoyed the annual CEHG symposium and EvolGenome seminars. I feel honored to be involved in the CEHG community with whom I share my research interests and am able to seek for different perspectives. Furthermore, my graduate school work has been a combination of experimental biology and quantitative biology, which would have not been possible without the collaboration with theoreticians in the CEHG community.
Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science?
I like working out, for instance, hiking, jogging, playing ping-pong, and rock climbing in my spare time. It helps me a lot to clear up my mind and refresh myself. I also love traveling, especially to places with great nature. It is always exciting for me to see unique landscapes and different plants/animals.