Nienke Besbrugge (Postdoctoral Associate)
My PhD from VIB, Belgium focused on developing a multifunctional tag (GSyellow) that can be used to unravel localization patterns as well as protein-protein and protein-DNA interactions in plants. In the Rhee lab, I will study transcriptional regulation of plant metabolism in Arabidopsis, and assess the function of the different players involved. Besides transcriptional regulation I also have a strong interest in the socio-economic value of plant research and its applications for small farmers. With drought stress as one of the biggest challenges in agriculture in the future, I will study the metabolism of Lathyrus sativa, one of the most drought resistant crops that is commercially available. This orphan crop, better known as grass pea, is of great value in emerging and developing economies, but has not been deeply studied before. As such, I hope my work will contribute to the development of sustainable and economically important products. In my free time I like to travel and be out of my comfort zone. Learning new things is one of my favorite things to do, and this can go from new recipes to languages to circus tricks, basically anywhere my curiosity takes me. When I am not running around, I try to sit still in nature and appreciate the beauty of it all.
Navadeep Boruah (Postdoctoral Associate)
My PhD research involved predictive modeling of plant metabolism and 13C metabolic flux analysis in the lab of Ganesh Sriram at University of Maryland, College Park. A major focus of my dissertation was employment of plant genome-scale metabolic networks to investigate hitherto unexplained metabolic phenomena, e.g. selection of glutamine as the predominant nitrogen transport amino acid for seasonal nitrogen recycling in poplar, and the predominance of specific amino acids in seed storage proteins of maize. In the Rhee lab, I will study plant-pathogen interactions and extremophile metabolism, with a focus on development of testable hypothesis by metabolic network modeling and their validation with 13C isotope labeling experiments.
Prior to joining Ganesh Sriram's lab for my PhD, I had worked on a Master's thesis on dynamics of microfluidic droplets in the lab of Panagiotis Dimtrakopoulos at UMD. I am a chemical engineer by training, Before I relocated to USA for graduate school, I had worked in a petroleum refinery for 4 years in multiple roles. Apart from research, I enjoy attending rock concerts, photography and brewing beer.
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.
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.
Emily Fryer (Research Assistant)
I received my B.S. in Biology concentrating in Ecology, along with a minor in Computing from San Francisco State University in Fall 2018. During my undergrad I was a member of the CoDE (Coding to Understand Disease Evolution) lab where I was introduced to the principles of population genetics and computational biology. My research focused on utilizing computational methods to understand the fitness costs associated with drug resistance mutations in HIV. In addition I've had the opportunity to dabble in front-end web development, data mining and topic modeling to understand sentiment on social media. My passions have always been rooted in the world of plants, their ecology and coevolution with other organisms. I am excited to be a member of the Rhee lab where I will apply computational methods to understanding metabolic processes in plants. My ultimate goal is to pursue a PhD and am interested in understanding the effect of varying ploidy levels on evolution. In my spare time I enjoy hiking, baseball, cooking and grazing my way through the culinary savanna of the the Bay Area.
Charles Hawkins (Biocurator)
I received my Ph.D. from U. Maryland under Dr. Zhongchi Liu, where I studied the ways in which gene expression and hormones come together to shape the parts of the flower and worked on a new model of the role of auxin in fruit development. I also worked on pipelines for genomic analysis in strawberry and identified the mutation behind yellow strawberries’ color. I previously received a BA in physics and computer science from U. Maryland. After receiving my Ph.D., I worked for two years as a postdoc at the USDA-ARS Plant Germplasm Introduction and Testing Research Unit in Prosser, WA under Dr. Long-Xi Yu, working on automated pipelines for genomic selection for abiotic stress tolerance in alfalfa. I joined Rhee lab in August of 2018 as BioCurator of the Plant Metabolic Network. I am currently working to curate the PlantCyc database, to improve the accuracy and capabilities of our prediction pipelines, and to make the pipelines more automated. Building tools and resources that people use to do cool science is a passion of mine. Outside of work, I enjoy baking, electronics, programming, and going for walks.
Suryatapa Ghosh Jha (Postdoctoral Associate)
I received a Ph.D. from the U. Vermont. I am broadly interested in knowing about the cellular pathways that regulate plant growth and function, how they evolved, and the molecular mechanisms behind them. My long-term goal is to understand how plants can help us fulfill the need of sustainable agriculture and sustenance of an expanding biosphere. To proceed towards that goal, one of the first steps is to understand the workings of plant cells in more detail, in order to reveal the mechanisms of cell development and how it translates to the development of the whole organism. I am excited to join the Carnegie Institution and will be working as a part of a team to develop a plant cell atlas, which will delineate the subcellular localization and functional networks of cellular proteins and their pathways. Outside of lab, I like to spend my time reading, painting, and trying out new recipes.
Benjamin Jin (Laboratory 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 so 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, driving and/or commuting, and listening to the whole spectrum of words and thoughts that others have to share.
Fan Lin (Postdoctoral Associate)
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.
Hye In Nam (Laboratory Technician)
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.
Karine Prado (Postdoctoral Fellow)
I received my PhD from the University of Montpellier (France) where I studied the molecular and cellular mechanisms controlling the hydraulic properties of Arabidopsis thaliana rosette in response to environmental stresses. Then I joined the University of Edinburgh (UK) as a postdoctoral research associate. I studied the contribution of non-transcriptional mechanisms to biological timekeeping of the pico-alga Ostreococcus tauri that has become a new relevant model for plant Systems Biology. Then I studied how light and thermo-sensitive phytochrome photoreceptors regulate chloroplast RNA processing and photosynthesis.
At the Carnegie Institution, I am going to study mechanisms of thermoadaptation of a desert extremophile C4 plant. The long term goal of this project is to improve crops and to address relevant challenges in response to worldwide climate changes.
When I am not working in lab, I like hiking, dancing, swimming, reading and watching movies.
Kevin Radja (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.
Angela Xu (Research 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.
Jiun Yen (Postdoctoral Associate)
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.
Cheng Zhao (Postdoctoral Associate)
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.
Kangmei Zhao (Postdoctoral Associate)
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.