People



Flavia Bossi (Senior Research Associate) 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.

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.

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.
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.
Fan Lin (Postdoc) I received my PhD degree from the University of Oklahoma with a focus on cell wall biology and cellulosic biofuel. I analyzed large-scale data such transcriptomic and proteomic data to identify candidate cell wall genes that are important for grass development and biomass quality. I joined Sue Rhee’s lab in Sep 2017 and currently working on developing a machine-learning algorithm to prioritize causal genes in Quantitative Trait Loci (QTL). Tradition methods to identify causal genes are time-consuming and labor-intensive, e.g. fine mapping. This algorithm utilizes publically available genomics and functional genomics data to predict which QTL genes are more likely to be causal, which will accelerate the discovery of novel functional genes that determine agronomic traits such as biomass yield. I live a simply life and enjoy biking, reading, and writing.
Benjamin Jin (Research Assistant) I graduated in the spring of 2017 from Stanford with a bachelor's degree in biology and a minor in feminist, gender, and sexuality studies. I also completed an honors thesis in the Gordon Li lab of neurosurgery at the Stanford Medical School, investigating kinase regulation of the tumorigenic c-myc pathway within medulloblastoma cell lines. This experience, alongside internships at Gilead Sciences and some light thinking about feminist/queer ecology, ultimately lead me to pursue work in the plant/ecological sciences, and thus I joined the Rhee lab in November 2017. I firmly believe that we currently ought to prioritize learning information about and expending scientific labor upon how the non-human organisms of this world (such as Arabidopsis) operate and how we can better coexist with them, and thus feel very privileged to be working at an institute and lab that studies all of this! Alongside labwork, biology, and feminist/queer studies, I enjoy tinkering on the piano, writing & reading & doodling, long commutes, and listening to the whole spectrum of words and thoughts that others have to share.
Bo Xue (Bioinformatics Research Assistant)

Jiun Yen (Postdoc) I received my Ph.D. in Biological Systems Engineering from Virginia Tech in April of 2017. I was trained in both computational and experimental biology in graduate school. My focus was on utilizing genome-scale models to generate metabolic engineering strategies and model plant metabolism in Arabidopsis. I wrote a MATLAB software package, called Node-Reward-Optimization toolbox (NR-Opt), to quickly design concise and accurate metabolic engineering strategies to obtain the desired metabolic phenotypes. I also demonstrated how genome-scale models can be used to simulate the relationship between starch metabolism and growth in wild-type and transgenic Arabidopsis, and validated the model predictions experimentally. I joined the Rhee lab in October of 2017 to develop a pipeline that leverages state-of-the-art machine learning algorithms to predict transporter class and substrate specificity using only sequence data. I moved to the US from Taiwan when I was little. I like to cook. Very carnivorous! I like chocolate and unproductive philosophical conversations that ends with "we're all just trying to survive." Besides human, my favorite animal is a whale shark because it is huge but it eats the smallest things and it is a shark and you can swim next to it without fear and I'm a still a kid inside.

 

Kevin Radja (Bioinformatics Research Assistant) I graduated in 2018 from Arizona State University with a bachelors in biomedical engineering focusing on computer science. I was introduced to bioinformatics as a summer intern at Carnegie where I did data manipulation and visualizations of phage metagenomic data as well as creating an interactive webpage comparing the alignment of cyanophages. The following summer I worked as a bioinformatics intern at a startup called EpiBiome. I built a pipeline to determine if phages were present within metagenomic samples using genome assembly. I joined the Rhee lab in June of 2018 to aid in developing a pipeline that uses machine learning to predict plant metabolism functions. I wanted to expand my knowledge of bioinformatics to later pursue higher education. Outside of work, I teach and train for competitions in a martial art called Taekwondo. I love to eat foods from around the world and then learn how to cook them myself.
Bharti Parihar (Summer Intern) I am a licensed clinical Histotechnician and have been in the field of Anatomic Pathology & Histology for 12 years. I am employed full time with Kaiser Permanente in their Regional Histology Lab in Berkeley. My responsibilities include all aspects of routine histology, immunohistochemistry and special stains. I am embarking on a wonderful journey of plant biology and am currently completing my Bachelor of Science degree in Biology through California State University, East Bay. My experience in the clinical histology lab will be implemented in the Rhee Lab by way of bringing forth structural knowledge of the desert extremophile, Tidestromia oblongifolia (Arizona honeysweet). I welcome the work required to gather structural information of this plant, as well as the inevitable learning of various histological methods used for plant tissue in contrast to my professional experience with human and veterinary tissues. The fascinating world of plants spark many questions within me such as, “Why don’t plants get cancer?”, “Can plants ‘learn’ by making associations?”. While I plan to pursue a doctorate program in plant biology, my specific area of interest is yet to be determined. I just love all things plant!
Angela Xu (Curator Assistant) I graduated Spring 2018 from UCSB’s College of Creative Studies with a bachelor’s in biology and a minor in statistical sciences. I got my first start with scientific research in the Trkola lab at University of Zurich where I examined the cell stoichiometry of HIV-1 entry for a summer. I was introduced to bioinformatics when I joined the Valentine lab at UCSB where I scripted an automated way to construct phylogenetic trees. I joined the Rhee lab June 2018 as a curator assistant where I’m excited to learn more about plant enzymes while figuring out what specific field I will pursue for a doctorate in the future. Other than science, I also enjoy painting and writing Chinese calligraphy during my free time.
Ankush Bharadwaj (Summer Intern) I'm an undergraduate student at University of California, Los Angeles, majoring in Microbiology, Immunology, and Molecular Genetics. The aspects of plant biology that I am most interested in is exploring the different compounds that plants produce and the pathways used for these compounds. I aim to apply this understanding into brainstorming potential applications of research on these molecules and pathways, specifically in medicine. My hopes for working with the Rhee Lab revolve around not only in perfecting my science communication skills, but also on gaining experience working with a multidisciplinary lab where many approaches on the same goal are brought together. Outside of science, I keep myself as occupied as possible, mainly by tossing around existentialist phrases I've heard on Rick and Morty, skateboarding, kayaking, hiking, and playing loud rock on the guitar.
Cheng Zhao (Postdoc) I got my P.hD. degree from Texas A&M University. My P.hD research focused on developing metabolic engineering strategies for terpene production in photosynthetic systems. In August 2018, I joined Dr. Rhee's group to develop metabolic network models to guide metabolic engineering efforts and agriculture applications for higher biomass yield under drought using sorghum and Setaria. In my spare time, I like playing ping-pong and basketball.

 

Group Photo, Spring of 2018