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Principal Investigator
Dr. Rhee is a Senior Staff Member of Plant Biology Department at Carnegie Institution for Science. She received her B.A. in biology from Swarthmore College and her Ph.D. in biology from Stanford University. She has been an investigator at the Plant Biology Department of Carnegie Institution for Science since 1999.
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Managers and Coordinators
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.
Charles Hawkins (Curator & Plant Metabolic Network Director)
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.
Selena Rice (Curator & Scientific Coordinator)
I received my Ph.D. from Johns Hopkins University in the lab of Dr. Juliette Lecomte. My thesis research involved the investigation of the structure, function, and chemistry of a truncated hemoglobin (THB1) found in Chamlydomonas reinhardtii. Since earning my Ph.D. in 2015, I have been working as a lab manager, first in the lab of Dr. John Kim at Johns Hopkins and then in the lab of Dr. Jeremy Reiter at UCSF working on various projects and ensuring that the lab ran smoothly. I joined the Rhee lab in April of 2020 as a Biocurator of the Plant Metabolic Network. I am currently working to curate the PlantCyc database, identifying new metabolic pathways to improve the coverage and usability of the database for scientists around the world. In my free time I volunteer for the AI Village and Women in Security and Privacy, two non-profits in the information security space. I also enjoy reading, exercising, spending time with my cats and husband, and eating good food.
Karine Prado (Senior Research Associate)
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.
Elena Lazarus (Assistant Scientific Coordinator)
I received my B.S. in chemistry with a minor in English and an ACS certification in biochemistry from the University of Portland in 2019. While in college, I worked in two laboratories (the Hoffman lab and the Weilhoefer lab) on research focused on extracting, identifying, and quantifying compounds from plants. In 2018, I was a National Science Foundation Boyce Thompson Institute Plant Genome Research Intern in the Moghe lab at Cornell University. Prior to joining Carnegie, I also worked at the Oregon Health and Science University on the Patient-Centered Outcomes Research Institute’s peer review editorial board from 2017 to 2019. In the Rhee lab, I work on a variety of interdisciplinary projects using molecular and chemical techniques to study novel genes and mechanisms. In my free time, I love to cook and bake, read, and go hiking.
Bioinformatics
Bo Xue (Programmer)
I graduated in 2015 from University of Minnesota, Twin Cities with a Master's degree in Computer Science focusing on data mining and recommender system. Discovering new information from data has always been an interesting topic to me. After working at the Chinese Academy of Science on the systematic characterization of mice miRNA expression, I developed a fondness for bioinformatics. Since joining Sue Rhee's lab in 2015, I have been working on many interesting projects, mainly the Plant Metabolic Network. Which includes developing computational pipelines and the visualization of our databases. If I'm not working, you'll probably find me trying to catch a movie. I love the theater going experience.
Postdoctoral Fellows
Sterling Field (Postdoctoral Fellow)
I finished my PhD in Biochemistry & Cellular and Molecular Biology at the University of Tennessee. My dissertation research focused on autophagy mediated turnover of mRNA-Protein complexes during flooding in Arabidopsis, and how RNA granules are regulated during stress. For my masters, I worked on miRNA mediated tassel development in Maize at East Carolina University, in North Carolina. I earned my bachelors at the Ohio State University, where I researched transcriptional regulation of floral development in Arabidopsis, and majored in Plant Cellular and Molecular Biology. Outside of the lab I co-lead the LGBTQ+ Plant Scientist Network, advocate for LGBTQ+ visibility and support in STEM, and enjoy hiking, gardening, and reading science fiction.
Purva Karia (Postdoctoral Fellow)
I received my PhD from University of Toronto in the lab of Dr. Keiko Yoshioka. My PhD research focused on the subcellular localization, function and the importance of post-translational modification of Arabidopsis tail-anchored protein, Triphosphate Tunnel Metalloenzyme 1 (TTM1). I have always been interested in understanding plant hormone signaling and the significance of the protein post-translational modification. In the Rhee and Ehrhardt labs, I will be working on the Sorghum Metabolic Atlas project to unravel the localization and functions of Sorghum metabolic enzymes. Outside of the lab, I enjoy camping, hiking, baking and visits to the dog park with my furbaby.
Megan Ruffley (Postdoctoral Fellow)
I am interested in using machine learning algorithms to understand selection across plant genomes in response to stress. I received my PhD in Bioinformatics and Computational Biology at the University of Idaho where I focused on performing simulation-based model inference using machine learning algorithms in areas ranging from demographic inference and phylogenetics to community-wide assembly mechanisms. This research was concentrated on disjunct plants of the Pacific Northwest temperate rainforest, but also focused on community-wide plant ecosystems, such as island plant communities. I am currently interested in continuing to apply machine learning algorithms to novel problems in evolutionary biology that can aid in solving our world’s most challenging problems. In the Moi and Rhee labs, I continue to investigate these algorithms as I study the relationship between genetic adaptation and response to stress in economically and agriculturally important crop plants. Investigating such adaptations to stress aid in our struggle to understand the future impacts of climate change.
Jason Thomas (Postdoctoral Fellow)
My name is Jason Thomas, and I am from Omaha Nebraska. I went to the University of Nebraska-Lincoln and graduated with a Degree in Biological Systems Engineering. I then went to earn a Ph.D. in Plant Biological Sciences University of Minnesota Twin Cities where I worked on improving floral nectar production in the biofuel cover crop field pennycress (Thlaspi arvense). As a post doctoral researcher in the Rhee lab I’ll work on a variety of molecular and computation plant biology projects. When not in the lab I may be playing ultimate frisbee, dodgeball, piano or guitar. I am also fond of learning languages, identifying plants, and bad puns.
Kangmei Zhao (Postdoctoral Fellow)
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.
Joanna Feehan (Postdoctoral Fellow)
My scientific career has formed from diverse experiences. I completed a Bachelor's Degree in Nursing before a Masters Degree in Cell Biology studying retinopathies using Xenopus laevis tadpole models at the University of British Columbia. For my PhD, I joined the lab of Jonathan Jones at The Sainsbury Laboratory in Norwich, UK where I used biochemical approaches to understand signalling mechanisms in plant-pathogen defence responses. As a postdoc here at Carnegie, I am working in the lab of Sue Rhee to understand the mechanisms of extreme heat-adaptation by Tidestromia oblongifolia using population genomics approaches.
Matt Stata (Postdoctoral Fellow)
Matt Stata is an evolutionary biologist with an interest in the convergent evolution of complex traits. One of the most prominent examples of such a trait is C4 photosynthesis in terrestrial plants. Despite requiring specialized leaf anatomy and highly regulated tissue-specific expression of numerous enzymes and transporters, C4 photosynthesis has evolved from C3 ancestors independently over 60 times in flowering plants. C4 photosynthesis thus represents an excellent system in which to ask questions about how evolution by natural selection solves a significant problem such as photorespiration and the limitations of Rubisco, and how many different ways such a solution can be achieved. Matt's PhD research at the University of Toronto focused on C4 evolution in Blepharis (Acanthaceae). In this genus, C4 photosynthesis evolved independently five times, and a large diversity of extant C3-C4 intermediate phenotypes exist. During Matt's time at UofT he also helped to establish a large genomics project focused on the evolution of C4 photosynthesis named C4 Phylomics. At the Carnegie Institute, Matt works in the lab of Dr. Sue Rhee to further develop this project, focusing on obtaining additional germplasm with the ultimate goal of having genomic resources available for every independent C4 lineage on the planet, and analyzing these data to identify previously unknown features of C4 evolution. Besides research, Matt is interested in electronic music, photography, gardening, and cycling.
Graduate Students
Evan Saldivar (Ph.D. Student)
I graduated from UC San Diego in 2019 with a major in Molecular Biology and a minor in Mathematics. My previous research focused on small-molecule specialized metabolism in maize (Zea mays) roots, with a specific focus on terpenoid biochemistry. I am broadly interested in plant biochemistry, as well as the application and development of new techniques, both experimental and computational. I am starting a PhD in Stanford's Biology Department in Fall 2020, and am excited to engage with the broader scientific community, at both Stanford and the Carnegie Institute!
Elena Dep Pup (M.Sc. student)
I received my B.S. in Agricultural Sciences at the University of Pisa, Italy. During my B.S. I was an Honors’ Student at the Sant’Anna School of Advanced Studies. I worked at the UN Food and Agriculture Organization and at ECBF, a sustainable venture capital fund. I am now finishing my M.Sc. in Plant Sciences at Wageningen University in the Netherlands, specializing in Plant Breeding and Genetic Resources. In my M.Sc. thesis I applied GWAS and genomic prediction in potatoes to develop diagnostic markers for 20 traits. I have also been a part-time Research Assistant at the Plant Breeding group for about 1 year. I am doing my M.Sc. internship at the Rhee Lab under the supervision of Kangmei Zhao (Postdoc) to integrate different omics data in the prediction of plant metabolic gene clusters. I am passionate about science policy and currently developing the concept of science-as-a-service as founder of The Good Scientists platform
Research Assistants
William Dwyer (Research Assistant)
My name is Will, I am a 2020 graduate of Vassar College (in New York) where I received a B.A. in Biochemistry with a secondary concentration in sociology. I grew up in France, near Versailles, but my family is originally from Belgium, Japan, and Boston. I was first introduced to research as an undergraduate student - working in chemistry and genetics labs - and during a summer fellowship at the Icahn School of Medicine in New York City, where I investigated a novel therapy for a rare genetic disorder. After my experiences in the biomedical world, my interests shifted towards plant biology as I grew increasingly concerned over the effects of impending climate changes and developed an appreciation for kingdom Plantae. Outside of work, I enjoy backpacking, reading novels about dystopian futures and binging anime - I'm also a recently retired collegiate track/XC runner who still enjoys a good trail run!
Maxwell Eckelbarger (Research Assistant)
My name is Maxwell Eckelbarger, and this year I am a sophomore at Stanford University studying a self-designed major called Botanical Engineering. I am from Spencerville Indiana and grew up on a farm and in the forests, and this instilled in me a love for nature and plants. I want to study how plants and other biological vectors can be used to fix environmental issues and repair Earth's ecosystems and make modern life more sustainable. I am most interested in cold sensation and toxin processing in plants' secondary metabolism as of recent. I am also an art minor and pursuing a notation in science communication, and am passionate about communicating science to the public through images.
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 savannah of the the Bay Area.
Danny Ginzburg (Research Assistant)
I was born and raised in Chicago. I did my undergrad at Northwestern where I studied Earth Sciences and Environmental Policy. I then worked as a sustainability data analyst for 2 years before moving to Israel to get my masters degree in agricultural sciences at Hebrew University's Faculty of Agriculture. I completed my graduate research at the Israel Ministry of Agriculture studying the interaction of incident light spectra and seed priming techniques to improve the growth efficiency and drought tolerance of leafy greens. After graduate school, I moved to New York City to work in commercial hydroponics growing leafy greens and herbs on the rooftops of commercial and industrial buildings. I'm an introvert who loves a quiet and comfortable environment to read. My physical sustenance mostly comes in the form of coffee, oats, peanut butter, hummus, and burritos.
Jack Cox (Research Assistant)
I received my master's degree at San Jose State University working to characterize scribbler, a gene involved in the development of Fruit Flies. Since graduating, I have worked with a couple of startups developing covid sensors using a variety of technologies from electrochemical analysis of bio-chips to CRISPR to produce a colorimetric signal.
INTERNS
Sandeep Mangat (Intern)
Sandeep is a sophomore from Winnipeg, Canada. He is studying chemistry at Princeton University and hopes to earn certificates in Neuroscience and History and the Practice of Diplomacy. In the past, he has done research on neurodegenerative diseases and metabolic disorders. Sandeep also enjoys writing and serves as an editor for the college newspaper. In his free time, he enjoys watching movies and going on walks
Maxine Gutierrez (Intern)
I received my B.S. in kinesiology with an emphasis in rehabilitation sciences and a minor in Spanish from San José State University in 2020. Prior to Carnegie, I explored my interests in biology and chemistry and worked as an instructional laboratory assistant for the chemistry department at Mission College. In the Rhee lab, I am working on the sorghum metabolic atlas and field pennycress projects. I am excited to be exploring the natural world, particularly through the many facets of plant biology research, due to the global, agricultural, medicinal, material, and ecological significance of plants. In my free time, I enjoy art, music, reading, quidditch, sports, being outdoors, and spending time with my dog and three chickens.
Ruby Tebbutt (Intern)
I am currently a biological sciences student at Durham University in the UK. I live in a very small village just outside London. I aspire to work in agricultural research to improve crop productivity. I hope this will beneficially impact the quality of life in the developing countries most affected by climate change. Outside of my studies I enjoy rowing, lacrosse and volunteering at my local wildlife rescue centre.
Julia Gershon (Intern)
Julia is a sophomore at Stanford University pursuing a major in Bioengineering and a minor in Creative Writing. She is interested in a career that uses genetic engineering as a way to create positive change and is researching carboxysome evolution in cyanobacteria with the Rhee Lab. In her free time, she loves writing, walks with friends and dogs, rambling about TV shows, and playing Dungeons & Dragons.
