People



Flavia Bossi (Postdoc) Since college, I have always been interested in the regulation of gene expression; promoters and transcription factors are still my favorite areas of study. Following that interest, I joined Patricia Leon’s lab at the Instituto de Biotecnologia (Universidad Nacional Autonoma de Mexico) to work on the functional characterization of an AP2/ERF transcription factor involved in the glucose signaling pathway in Arabidopsis thaliana. It was a challenging Ph.D. project that excited, frustated, and at times puzzled me.

Early in 2010, I decided to join Sue Rhee’s lab to study a family of regulatory proteins important for another level of gene regulation – targeted degradation of proteins. I was drawn to the Rhee lab for several different reasons. 1- to try to grasp the way of thinking of bioinformatitians (learn basic bioinformatics along the way), 2- to be part of an interesting multidisciplinary group, 3- looking for something new and outside of my comfort zone.

Even though science eats up most of my time, I do have other interests. My most beloved hobbie has always been dance, both taking classes and enjoying dance performances. Moving to the Bay Area introduced me to another art form which is now one of my hobbies too: taiko drumming. And last but not least, I have a family-shared pastime: to play video-games. Favorite console? Nintendo DS … by far.

Peifen Zhang (Director, Plant Metabolic Network) I love the pure beauty of plants and flowers, and am amazed by the modern techniques in molecular biology in seeking out answers to the ‘what’ and ‘how’ questions. I chose to focus on plant genetics for my Ph. D. thesis and had the good fortune of training with Tom Peterson at Iowa State University. I learned how to connect the dots and make a fact-backed story. After some additional years of postdoctoral research, I no longer had the extreme but necessary patience waiting for results at the bench, nor the nerve to take the seemingly endless failures of experiments. So I moved on to the field of bio-database development and biocuration and was fortunate enough to work on the TAIR and, later, PMN projects. I enjoy, very much, the multidisciplinary environment of bio-database development and biocuration, ranging from wet-lab results, to computational predictions, to ontology development and database implementation, and overall, the operation as a whole.

Outside of work and two small kids, I am interested in observing things that are visually beautiful, architectures of houses and gardens, interior designs and more.

Hye-In Nam (Research Assistant) I got a Master’s degree in Chemistry from Washington State University. During my masters program, I worked on characterizing protein-protein interactions of HELA cells using mass spectroscopy. I joined Sue Rhee's group in November 2009. I am engaged in several projects discovering the function of unknown genes and abiotic stress adaptation in plants. I get to do all the crazy and unfunded research projects including experimental evolution in duckweeds, macronutrient and micronutrient signaling integration in plants, and quantiative genetics of salinity adaptation in fitness in higher plants using deep sequencing and a new mapping method we developed in the lab called target-enriched extreme QTL (TEX-QTL) mapping. Outside of work, I love to watch movies and TV shows. Also, I enjoy cooking and baking.

Michael Banf (Postdoc) During my Ph.D., I enjoyed reading about a wide variety of fields in science and stumbled upon Genetics. As a computer scientist with a background in Electrical Engineering, I became increasingly fascinated about how information is encoded in the DNA and the circuit-like genetic pathways and networks in biological systems. I started asking questions about how machine learning and mathematical modeling can contribute to the analysis of the regulation of these complex mechanisms. In finishing my Ph.D. project on auditory image understanding for the visually impaired, I started searching for a postdoctoral position in the area of computational systems biology and came across the Rhee lab.

The lab is engaged in systematically elucidating the regulation of metabolic and signaling pathways in plants using experimental as well as computational approaches, which allows me to start my research on developing computational models of transcriptional gene regulation in these pathways and collaborate with experienced biologists. The focus on plants is a great research opportunity, because little is known about the regulatory mechanisms, in comparison to animals and microbes, although plants provide the essentials to allow life on Earth.

Apart from the scientific stuff, I love to read inspiring biographies or the works by great analytical thinkers, such as J. Polkinghorne, C.S. Lewis or B. Pascal, on some of life’s tough questions. To clear my head, I enjoy training Krav Maga, playing the piano, watching movies or Brazilian Jiu-Jitsu and listening to music… especially Hans Zimmer soundtracks.

Pascal Schläpfer (Postdoc) When I was 15 years old, I decided against further high school education and started a training program to be an IT technician. Although I enjoyed the work, I was not challenged by the daily tasks I had to cope with. Therefore, after four years, I decided to get my high school degree. At this time I got interested in natural sciences and embarked on a journey at the ETH Zurich, Switzerland, where I studied Biology for my bachelor’s degree. In the last half of my university education, I discovered the potential of simulating the world, organisms, and pathogens computationally. I started my master’s degree in Plant Biology, also at the ETH and started to simulate metabolism of plants. I continued these studies for my Ph.D. in the laboratory of Willhelm Gruissem. After a successful PhD, my wife and I decided to get experience on the other side of the pond and we both found positions at the Carnegie Institution for Science. In today’s work I focus on simulation of host and pathogen metabolism, how they communicate with each other and how they benefit from the presence or absence of the counterpart. I not only focus on improving the quality of the already present metabolic networks for plants, but also extend our capabilities to investigate plant pathogens. Aside from our work, my wife and I enjoy the many jewels of the Californian nature, discovered diving, and use the astonishing variety of products to cook at home.
Yanniv Dorone (Graduate student) I am an international (half-French, half-Israeli) graduate student in the Stanford Biology department. During my “Classes Préparatoires aux Grandes Ecoles” years at the Lycée Henri IV in France, I focused my education in physics, chemistry and mathematics. However, the biological applications these fields provide stoked my interest in biology. Therefore, after getting into the Ecole Normale Supérieure de Lyon, I decided to make a special request to change my major to biology. While this was a risky and challenging change to make during the last year of my B.S., I look back at this as one of the three best decisions I have made career-wise (the other two being applying to Stanford and joining the Rhee lab!). I was really excited about biology in general and had finally found a passion: plant genetics. Since then, I had the privilege of working in four different labs on four different continents: I worked on the initiation of translation at the Mechulam lab (Ecole Polytechnique, France), meiosis in the autotetraploid plant A. arenosa at the Bomblies lab (Harvard, US), temperature perception in A. thaliana at the Wigge lab (Cambridge, UK) and projects related to meiosis in A. thaliana at the Levy lab (Weizmann Institute, Israel). As a PhD student, my goal is to identify and characterize novel mechanisms of transcriptional regulation in A. thaliana. When I’m not doing science, my free time is devoted to movies, reading and traveling.
Arvind Chavali (Postdoc) I am a bioengineer by training with interests in systems biology, bioinformatics, and computational methods development. Previously, I received a doctoral degree from the University of Virginia for work on metabolism of pathogens causing neglected tropical diseases, and I also spent some time at Yale University studying transcriptional regulation in the context of HIV latency. My latest foray into plant biology is a wholly new endeavor for me, but one that I am truly very excited about. The study of specialized plant metabolism may lead to the discovery of new natural products with widespread medicinal use. Additionally, understanding the significance behind recently discovered biosynthetic gene clusters in various plant species will likely provide fascinating insights into how secondary metabolism may have evolved over time. Outside of research, I have a passion for science communication and public policy. I hold a Master's degree in Public Policy from Princeton University's Woodrow Wilson School where I mainly specialized in health policy and international development.
Kangmei Zhao (Postdoc) I got my Ph. D from The University of Oklahoma and joined the Rhee lab in July, 2016. During my graduate study, I worked on the characterization of novel cell wall associated transcription factors in grasses, especially focusing on members that can control grass-specific cell wall biosynthesis genes. Then, I got to be really interested in further understanding pathway evolution and plants adaptation to the environment. After the graduate training with Dr. Laura Bartley, I decided to join the Rhee lab. I really enjoy the multidisciplinary research environment. Currently, I am working on the regulation and evolution of plant specialized metabolic genes as well as discovering novel secondary metabolites that could potentially promote plants resistance to different stress stimuli. Outside of research, I love reading and running.
Hatem Rouached (Visiting Faculty) I gained scientific and managerial skills during my PhD (University of Montpellier II, France, 2002-2005), my Postdoc (University of Lausanne, Switzerland, 2005-2009), and as Senior Scientist in Crop Design (BASF Company, Ghent, Belgium, 2010-2012). In 2010, I obtained the academic diploma of habiliation to direct research work « HDR » (University of Bourgogne, France). During my PhD and postdoctoral periods, I acquired expertise in the area of molecular and physiological aspects of plant nutrition. In particular, I studies the molecular mechanisms controlling the sulfate and phosphate transport and signaling in Arabidopsis through the study of the SULTR and PHO1 gene family. In 2012, I was hired at INRA- Montpellier -FRANCE. Since then, I am developing an original research program in the “Biochemistry and Molecular Biology of Plants” (B&PMP) Research Unit, aiming at decoding the genetic and molecular basis of the interaction between the homeostasis of macro-and micronutrients, particularly phosphate and metals, in plants.
  JeanAe Ruth Kim (Research Assistant)
  Bo Xue (Research Assistant)

Group Photo, Summer of 2016

Group Photo, Summer of 2015