About Me




Princeton University, Princeton, NJ – 2010 – 2016

  • Doctor of Philosophy in Molecular Biology2018
  • Master of Arts in Molecular Biology 2013

Massachusetts Institute of Technology, Cambridge, MA – 2008 – 2011

  • Bachelor Of Science, Course 10B – Chemical-Biological Engineering
  • Bachelor Of Science, Course 7A – Physical Biology


Hello! My name is Sophia Hsin-Jung Li (李欣融), currently an HFSP postdoctoral fellow at École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. Previously, I obtained my Ph.D. in 2018 from Princeton University and graduated from Massachusetts Institute of Technology (MIT) in 2011 with a B.S. double majoring in Chemical Engineering and Biology. I grew up in Taipei, Taiwan.

My passion is to combine engineering and biology to understand how biological systems work quantitatively. Biological systems are complex, so studying individual parts could fail to elucidate how they work as a whole. We can thus apply the concepts and tools in engineering by both bottom-up and top-down methods. To achieve this, I want to build novel tools that enable us to probe systems that were previously difficult to approach. First, creating something from scratch requires the knowledge of how pieces work alone and collectively together. Second, systematic characterization allows the extraction of simple rules from the complex biological phenomenon. I am interested in using methods of both directions to discover mechanisms that drive complex behaviors of a cell or a symbiotic ecosystem.

I am currently working at EPFL to study host-microbe interactions using a novel in vitro mini-gut model (with Prof. Matthias Lutolf and Prof. Alex Persat ). I combine stem cell engineering, biophysics, and microbiology to re-create critical physiological features of the human host gut outside the body. It allows me to study the spatiotemporal dynamics of host-microbe interactions that are difficult to observe in vivo. My goal is to investigate how microbes affect the host physiology in the context of health and diseases to identify novel key regulators and potentially contribute to innovative therapeutic intervention.

My Ph.D. work at Princeton University with Prof. Zemer Gitai and Prof. Ned Wingreen focused on metabolism and growth. Using non-pathogenic Escherichia coli as a model system, I investigated how cells adapt to different growth conditions; specifically, how cells regulate their ribosome abundance and efficiency under nutrient limitations. To address these questions, I had to learn, optimize, and implement several complex new technologies, and therefore established collaborations with experts in each technology. I have obtained skills in several techniques (with related sample preparation, data processing, and statistics), interpretation of biological data, and designing well-controlled experiments. The technology includes the operation of chemostats, RNA-Seq, ribosome profiling, metabolomics, and proteomics using LC/MS. The collaborations lead to multiple co-author publications with different labs in and outside Princeton University (See CV). I collaborated with Prof. Josh Rabinowitz to develop a method for probing translation by mitochondrial ribosomes at single nucleotide resolution. It allowed us to identify defects in mitochondrial tRNA modification (Morscher et al. Nature 2018). My thesis work provides new insights into how bacterial cells make tradeoffs between growth efficiency and adaptability to changing environmental conditions (Li et al. Nature Microbiology 2018). Moreover, based on my thesis work, I lead a team of undergraduates and junior graduate students to systematically quantify the regulation of gene expression through the central dogma. I won the Best Student of the Year in 2017 for my scientific achievement during graduate school from the Department of Molecular Biology.

Outside of the lab, I enjoy sports, travel, and reading. I am a second-dan Taekwondoist certified by the World Taekwondo Federation. Right now, I am learning to thrive like a Swiss. I am eating more chocolates than ever, learning French and German, and hitting slopes of the Alps to ski. My next big trip would be visiting Peru or Africa!


This is my PhD final public oral given on November 1st, 2018 at Princeton University. I presented my PhD work on how E. coli allocate its resources. Most importantly, I focused on its ribosome abudance and activity under different nutrient limitations.


I attended the 60th Lindau Nobel Conference at Lindau, Germany in 2010. During the conference, I was fortunate to be in a film with Sr. Tim Hunt. Our conversation about systems biology is recorded by Nature and is available on Youtube.