
Our lab combines computational and experimental approaches to reveal molecular mechanisms underlying adaptive strategies in plants. We focus on metabolic traits at multiple scales including individual genes, pathways, and networks. We also uncover novel functions, mechanisms, and pathways of 'unknown' genes (those that are not similar to any known genes), which is taking us to areas of research we never thought of studying before.
Seung Yon (Sue) Rhee
Email: srhee@carnegiescience.edu
Lab website: rheelab.org
Lab Tabs
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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.
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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 like to read novels about dystopian futures and rewatch Broad City episodes for the tenth time - I'm also a recently retired collegiate track/XC runner who still enjoys a good trail run!
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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.
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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.
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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.
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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 interation 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.
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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.
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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.
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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.
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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.
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Selena Rice (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.
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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.
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Evan Saldivar (Graduate 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!
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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.
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I graduated in 2015 from University of Minnesota, Twin Cities with a Master's degree in Computer Science focusing on data mining and recommender systems. Discovering new and relevant 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 tools for visualizing our databases. If I'm not working, you'll probably find me trying to catch a movie. I love the theater going experience.
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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.
Selected recent references
Papers from our group are highly cited with a current h-Index (as of July 2020) of 50 on Google Scholar (See ciation page). Some of our papers are listed below.
- Zhao K, Kong D, Jin B, Smolke CD, Rhee SY* (2021) A novel form of bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis. eLife doi: 10.7554/eLife.69508
- Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, and Rhee SY* (2021) Plant Metabolic Network: A comprehensive resource of plant metabolic information. Journal of Integrated Plant Biology https://doi.org/10.1111/jipb.13163
- Dorone Y, Boeynaems S, Jin B, Bossi F, Flores E, Lazarus E, Michiels E, De Decker M, Baatsen P, Holehouse AS, Sukenik S, Gitler AD*, Rhee SY* (2021) Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress. Cell 184(16):4284-4298.e27 DOI: 10.1016/j.cell.2021.06.009 [PubMed]
- Kang S-H*, Pandey RP, Lee C-M, Jeong J-T, Choi B-S, Sim JS, Jung M, Won SY, Oh T-J, Yu Y, Lee OK, Kim HH, Lee T-H, Kim N-H, Bashyal P, Kim T-S, Kim C-K, Kim J-S, Ahn B-O, Rhee SY*, Sohng JK* (2020) Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nature Communications 11:5875. DOI: 10.1038/s41467-020-19681-1 [PubMed][Correction][pdf]
- Lin F, Lazarus E, Rhee SY* (2020) QTG-Finder2: a generalized machine learning algorithm for prioritizing QTL causal genes in plants. Genes|Genomes|Genetics 10(7): 2411–2421. DOI: 10.1534/g3.120.401122 [PubMed][full text]
Selected recent reviews and perspectives
- Plant Cell Atlas Consortium, Ghosh Jha S, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY (2021) Vision, challenges and opportunities for a Plant Cell Atlas. eLife DOI: 10.7554/eLife.66877
- Eckelbarger M, Rice S, Osano A, Peng J, Ullah H, Rhee SY (2021) Recognizing Pioneering Black Plant Biologists in Our Schools and Society. Trends in Plant Science http://doi.org/10.1016/j.tplants.2021.07.021
- Demirer GS, Silva TN, Thomas JB, Jackson CT, Ehrhardt DW, Rhee SY, Mortimer JC, and Landry MP (2021) Nanotechnology to advance CRISPR/Cas genetic engineering of plants. Nature Nanotechnology 16:243–250. [pdf]
- Rice S, Fryer E, Jha SG, Malkovskiy A, Meyer H, Thomas J, Weizbauer R, Zhao K, Birnbaum KD, Ehrhardt DW, Wang Z, Rhee SY, and The Plant Cell Atlas Consortium (2020) First Plant Cell Atlas Workshop Report. Plant Direct 00: 1– 10. https://doi.org/10.1002/pld3.271 [pdf]
- Rhee SY*, Birnbaum KD*, Ehrhardt DW* (2019) Towards Building a Plant Cell Atlas. Trends in Plant Science. DOI: https://doi.org/10.1016/j.tplants.2019.01.006 [full text]
ALL PEER REVIEWED PUBLICATIONS (* corresponding author)
Zhao K, Kong D, Jin B, Smolke CD, Rhee SY* (2021) A novel form of bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis. eLife doi: 10.7554/eLife.69508
Plant Cell Atlas Consortium, Ghosh Jha S, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW*, Birnbaum KD*, Rhee SY* (2021) Vision, challenges and opportunities for a Plant Cell Atlas. eLife In press. DOI: 10.7554/eLife.66877
Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, and Rhee SY* (2021) Plant Metabolic Network: A comprehensive resource of plant metabolic information. Journal of Integrated Plant Biology https://doi.org/10.1111/jipb.13163
Eckelbarger M, Rice S, Osano A, Peng J, Ullah H, Rhee SY* (2021) Recognizing Pioneering Black Plant Biologists in Our Schools and Society. Trends in Plant Science http://doi.org/10.1016/j.tplants.2021.07.021
Cole B, Bergmann D, Blaby-Haas C, Blaby I, Bouchard K, Brady S, Ciobanu D, Coleman-Derr D, Leiboff S, Mortimer J, Nobori T, Rhee SY, Schmutz J, Simmons BA Singh A, Sinha N, Vogel J, O’Malley R*, Visel A*, Dickel D* (2021) Plant Single-Cell Solutions for Energy and the Environment. Communications Biology 4:962.
Dorone Y, Boeynaems S, Jin B, Bossi F, Flores E, Lazarus E, Michiels E, De Decker M, Baatsen P, Holehouse AS, Sukenik S, Gitler AD*, Rhee SY* (2021) Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress. Cell 184(16):4284-4298.e27 DOI: 10.1016/j.cell.2021.06.009 [PubMed] [highlighted by Developmental Cell, PNAS, Nature Chemical Biology, Science, F1000, Science]
Demirer GS, Silva TN, Thomas JB, Jackson CT, Ehrhardt DW, Rhee SY*, Mortimer JC*, and Landry MP* (2021) Nanotechnology to advance CRISPR/Cas genetic engineering of plants. Nature Nanotechnology 16:243–250.
Kang S-H*, Pandey RP, Lee C-M, Jeong J-T, Choi B-S, Sim JS, Jung M, Won SY, Oh T-J, Yu Y, Lee OK, Kim HH, Lee T-H, Kim N-H, Bashyal P, Kim T-S, Kim C-K, Kim J-S, Ahn B-O, Rhee SY*, Sohng JK* (2020) Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nature Communications 11:5875. DOI: 10.1038/s41467-020-19681-1 [PubMed][Correction][pdf]
Rice S, Fryer E, Jha SG, Malkovskiy A, Meyer H, Thomas J, Weizbauer R, Zhao K, Birnbaum KD, Ehrhardt DW, Wang Z, Rhee SY*, and The Plant Cell Atlas Consortium (2020) First Plant Cell Atlas Workshop Report. Plant Direct 00: 1– 10. https://doi.org/10.1002/pld3.271
Parry G, Provart NJ, Brady SM, Uzilday B, The Multinational Arabidopsis Steering Committee (2020) Current status of the multinational Arabidopsis community. Plant Direct 00:1-9.
Lin F, Lazarus E, Rhee SY* (2020) QTG-Finder2: a generalized machine learning algorithm for prioritizing QTL causal genes in plants. Genes|Genomes|Genetics 10(7): 2411–2421. DOI: 10.1534/g3.120.401122 [PubMed][full text]
Bouain N, Korte A, Satbhai SB, Rhee SY, Busch W, Rouached H* (2019) Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation. bioRxiv 460360; doi: https://doi.org/10.1101/460360 PLOS Genetics 15(11): e1008392
Rhee SY*, Birnbaum KD, Ehrhardt DW* (2019) Towards Building a Plant Cell Atlas. Trends in Plant Science 24(4):303-310
Banf M*, Zhao K, Rhee SY* (2019) METACLUSTER - an R package for context-specific functionality analysis of metabolic gene clusters. Bioinformatics btz021, https://doi.org/10.1093/bioinformatics/btz021
Lin F, Fan J, Rhee SY* (2019) QTG-Finder: a machine-learning algorithm to prioritize causal genes of quantitative trait loci in plants bioRxiv 484204; doi: https://doi.org/10.1101/484204 Genes|Genomes|Genetics 9(10): 3129–3138
Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee SY, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol. 175(4):1499-1509. doi: 10.1104/pp.17.01490. PubMed PMID: 29208732; PubMed Central PMCID: PMC5717721. [pdf]
Bossi F, Fan J, Xiao J, Chandra L, Shen M, Dorone Y, Wagner D, Rhee SY* (2017) Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC Genomics 18(1):480
Rouchard H* and Rhee SY* (2017) System-level understanding of plant mineral nutrition in the big data era. Current Opinion in Systems Biology 4:71-77
Schalpfer P, Zhang P, Chuan W, Kim T, Banf M, Chae L, Dreher K, Arvind C, Nilo-Poyanco R, Bernard T, Kahn D, and Rhee SY* (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiology 173(4):2041-2059
Chavali A* and Rhee SY* (2017) Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Briefings in Bioinformatics. bbx020. doi: 10.1093/bib/bbx020
Banf M and Rhee SY* (2017) Enhancing gene regulatory network inference through data integration with markov random fields. Nature Scientific Reports 7:41174
Banf M* and Rhee SY* (2016) Computational inference of gene regulatory networks: approaches, limitations and opportunities. BBA Gene Regulatory Mechanisms S1874-9399(16)30188-2
Walsh JR, Schaeffer ML, Zhang, Rhee SY, Dickerson JA, Sen TZ* (2016) The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. BMC Systems Biology 10:129
Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni JJ, Zhao PX, Rhee SY, Fei Z* (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant S1674-2052(16)30223-4
Rhee SY*, Parker J, and Mockler T (2016) A glimpse into the future of genome-enabled plant biology from the shores of Cold Spring Harbor. Genome Biology 17(1):3
Fiume E, de Klein N, Rhee SY, and Magnani E* (2015) A framework for discovering, designing, and testing microProteins to regulate synthetic transcriptional modules. Methods in Molecular Biology 1482:175-88
Guo J, Fan J, Hauser B, and Rhee SY* (2015) Target enrichment improves mapping of complex traits by deep sequencing. Genes | Genomes | Genetics 6(1):67-77
Ladics G*, Bartholomaeus A, Bregitzer P, Doerrer N, Gray A, Holzhauser T, Jordan M, Keese P, Kok E, Macdonald P, Parrott W, Privalle L, Raybould A, Rhee SY, Rice E, Romeis J, Vaughn J, Wal J-M, and Glenn K (2015) Genetic basis and detection of unintended effects in genetically modified crop plants. Transgenic Research 24(4):587-603
Kim T, He K, Dreher K, Lee I, Moon S, Bais P, Dickerson J, Dixon P, Fiehn O, Lange BM, Sumner LW, Welti R, Wurtele ES, Nikolau BJ, and Rhee SY* (2015) Patterns of metabolite changes from large-scale gene perturbations in Arabidopsis thaliana using genome-scale metabolic networks. Plant Physiology 167(4):1685-98
de Klein N, Magnani E, and Rhee SY* microProtein Prediction Program (miP3): a software for predicting microProteins and their target transcription factors. (2015) International Journal of Genomics Article ID 734147. 1-4
Peng J, Uygun S, Kim T, Wang Y*, Rhee SY*, and Chen J* (2015) Measuring genome-specific semantic similarities using Gene Ontology and Gene Co-Function networks. BMC Bioinformatics 16(1):44
Xu M and Rhee SY* (2014) Becoming data-savvy in a big-data world. Trends in Plant Science 19(10):619–622 [pdf]
Jones AM, Xuan Y, Xu M, Wang R-S, Ho C-H, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder JI, Albert R, Rhee SY*, and Frommer WB* (2014) Border control – a membrane-linked interactome of Arabidopsis. Science 344:711-716. [highlighted in F1000]
Chae L, Kim T, Nilo-Poyanco R, and Rhee SY* Genomic signatures of specialized metabolism in plants. (2014) Science 344:510-513. [highlighted in F1000]
Magnani E, De Klein N, Nam H-I, Kim J-G, Pham KL, Fiume E, Mudgett MB, and Rhee SY* (2014) A comprehensive analysis of microProteins reveals their potentially widespread mechanism of transcriptional regulation. Plant Physiology 165(1):149-159
Rhee SY* and Mutwil M* (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science 19(4):212-221
Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, and Smet ID* (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24(10):3859-75
Chen J, Lalonde S, Obrdlik P, Noorani Vatani A, Parsa SA, Vilariño C, Revuelta JL, Frommer WB, and Rhee SY* (2012) Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Frontiers in Plant Science 3(124):1-14
Moon S, He Kun, Bais P, Dickerson J, Dixon P, Rhee SY, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange B, Cortes D, Shuman J, Shulaev V, Huhman D, Sumner L, Roth M, Welti R, Ilarslan H, Wurtele E, Brachova L, Campbell A, Perera A, and Nikolau B* (2012) Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. Frontiers in Plant Science 3(15):1-12
Chae L, Lee I, Shin J, and Rhee SY* (2012) Towards an understanding of how molecular networks evolve in plants. Current Opinion in Plant Biology 15(2):177-184
Hwang S, Rhee SY*, Marcotte EM*, and Lee I* (2011) Systematic prediction of gene function using a probabilistic functional gene network for Arabidopsis thaliana. Nature Protocols 6(9):1429-1442
Sun Y, Fan X-Y, Cao D-M, He K, Tang W, Zhu J-Y, He J-X, Bai M-Y, Zhu S, Oh E, Patil S, Kim TW, Ji H, Wong WH, Rhee SY, and Wang J-Y* (2010) Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis. Developmental Cell 19(5):765-77
Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi MA, Parsa SA, Kim D-Y, Acharya BR, Stein EV, Hu H-C, Villiers F, Takeda K, Yang Y, Han YS, Schwacke R, Chiang W, Kato N, Loqué D, Assmann SM, Kwak JM, Schroeder J, Rhee SY, and Frommer WB* (2010) A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2. Frontiers in Plant Science 1(24):1-14
Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, and Rhee SY* (2010) Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants. Plant Physiology 153(4):1479-91
Bais P, Moon S, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau B, Rhee SY, and Dickerson JA* (2010) PlantMetabolomics.org: A web portal for Plant Metabolomics Experiments. Plant Physiology 152(4):1807-16
Lee I, Ambaru B, Thakkar P, Marcotte E*, and Rhee SY* (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature Biotechnology 2(28):149-156. [highlighted in F1000]
Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLOS Computational Biology 5(7): e1000431
Chen J, Ji L, Hsu W, Tan K-L, and Rhee SY* (2009) Exploiting Domain Knowledge to Improve Biological Significance of Biclusters with Key Missing Genes. IEEE Technical Committee on Data Engineering Conference ICED.2009.205: 1219-1222
Aceituno FF, Moseyko N, Rhee SY, and Gutierrez RA* (2008) The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics 9:438
Howe D*, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St. Pierre S, Twigger S, White O, and Rhee SY* (2008) The future of biocuration. Nature 455:47-50
Rhee SY*, Wood V, Dolinski K, and Draghici S* (2008) Use and Misuse of the Gene Ontology (GO) Annotations. Nature Review Genetics 9(7):509-15
Pennycooke JC, Cheng H, Roberts SM, Yang Q, Rhee SY, and Stockinger E* (2008) The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements. Plant Molecular Biology 67(5):483-97
Lalonde S*, Ehrhardt D, Loqué D, Chen J, Rhee SY, and Frommer WB (2008) Molecular and cellular approaches for the detection of protein-protein interactions and generation of protein interaction maps. Plant Journal 53(4):610-35
Avraham S, Tung C-W, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, and Ware D* (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research 36:D449-D454
Fiehn O*, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, and Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3(3):195-201.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, and Karp PD* (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 38(Database issue):D473-9
The Gene Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Research 36(Database issue):D440-4
Ilic K, Kellogg E, Jaiswal P, Zapata F, Stevens P, Vincent L, Pujar A, Avraham S, Reiser L, McCouch SR, Sachs S, Schaeffer M, Ware D, Stein L, and Rhee SY* (2006) Plant Structure Ontology: A Unified Vocabulary for Flowering Plants. Plant Physiology 143(2):587-99
Stein LD, Beavis WD, Gessler DD, Huala E, Lawrence CJ, Main D, Mueller LA, Rhee SY, and Rokhsar DS* (2006) Save our data! Scientist 20(4):24-25
Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser R, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, and McCouch S* (2006) Whole Plant Growth Stage Ontology: History, Development and Application. Plant Physiology 142(2):414-28
Leebens-Mack J*, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Kellogg EA, Koonin EV, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevens P, Stevenson DW, Warnow T, and Zmasek C. (2006) Taking the First Steps Towards a Standard for Reporting on Phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237
Rhee SY*, Dickerson J*, and Xu D* (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology 57: 335-360
Zimmermann P*, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee SY, Wagner U, and Hennig L. (2006) MIAME/Plant – adding value to plant microarrray experiments. Plant Methods 2:1-3
Gene Ontology Consortium (2006) The Gene Ontology Project in 2006. Nucleic Acids Research 34(Database issue):D322-6
Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, and Karp P* (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 34(Database issue):D511-6
Li S, Ehrhardt D, and Rhee SY* (2006) Systematic Analysis of Arabidopsis Protein Localization and Software Tools for Fluorescent Tagging of Full-Length Arabidopsis Proteins. Plant Physiology 141(2):527-39. [highlighted in F1000]
Jaiswal P*, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, and Zapata F. (2005) Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Functional and Integrated Genomics 6:388-397
Rhee SY* (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology 138(2):569-70
Yan T, Yoo D, Berardini T, Mueller L, Weems D, Weng S, Cherry JM, and Rhee SY* (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Research 33(Web Server issue):W262-6
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp P, and Rhee SY* (2005) MetaCyc and AraCyc: metabolic pathway databases for plant research. Plant Physiology 138(1):27-37
Bard J, Rhee SY, and Ashburner M* (2005) An ontology for cell types. Genome Biology 6:R21
Schlueter SD, Wilkerson MD, Huala E, Rhee SY, and Brendel V* (2005) Community-based gene structure annotation. Trends in Plant Science 10(1):9-14
Jenkins H*, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka K, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee SY, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wurtele ES, and Kell DB (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology 22(12):1601-6
Zhang X, Fowler S, Cheng H, Lou Y, Rhee SY, Stockinger EJ, and Thomashow MF* (2004) Freezing Sensitive Tomato has a Functional CBF Cold Response Pathway, but a CBF Regulon that Differs from that of Freezing Tolerant Arabidopsis. Plant Journal 39(6):905-19
Berardini TZ, Mundodi S, Reiser R, Huala E, Garcia-Hernandez M, Zhang P, Mueller LM, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, and Rhee SY* (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiology 135(2):1-11
Tian GW, Mohanty A, Chary SN, Li S, Paap B, Drakakis G, Kopec C, Li J, Ehrhardt E, Jackson D, Rhee SY, Raikhel N, and Citovsky V* (2004) High-Throughput Fluorescent Tagging of Full-Length Arabidopsis Gene Products in Planta. Plant Physiology 135(1):25-38. [highlighted in F1000]
Dolan EL, Soots BE, Lemaux PG, Rhee SY, and Reiser L* (2004) Strategies to Avoid Reinventing the Pre-college Education and Outreach Wheel. Genetics 166:1601-1609
Weems D, Miller N, Garcia-Hernanzez M, Huala E, and Rhee SY* (2004) Design, implementation, and maintenance of a model organism database for Arabidopsis thaliana. Comparative and Functional Genomics 5(4):362-369
Thimm O, Bläsing YG, Nagel, A, Meyer, S, Kruger, P, Selbig, J, Müller, L, Rhee, SY, and Stitt M* (2004) MapMan: A User-Driven Tool to Display Genomics Data Sets onto Diagrams of Metabolic Pathways and other Biological Processes. Plant Journal 37(6):914-39. [highlighted in F1000]
Bard JL* and Rhee SY* (2004) Ontologies in biology: design, applications and future challenges. Nature Review Genetics 5(3):213-22
Rhee SY* (2004) Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiology 134(2):543-7
Krieger CJ, Zhang P, Mueller L, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, and Karp P* (2004) MetaCyc: Recent enhancements to a database of metabolic pathways and enzymes in microorganisms and plants. Nucleic Acids Research 32 Database issue:D438-42
Harris MA*, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, and White R; Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 32 Database issue:D258-61
Rhee SY, Osborne E, Poindexter P, and Somerville CR* (2003) Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated pectinase required for pollen mother cell degradation. Plant Physiology 133(3):1170-80
Mueller LA, Zhang P, and Rhee SY* (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology 132(2):453-60
Rhee SY*, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, and Zhang P (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 31(1):224-228
Clarke BC, Lambrecht M, and Rhee SY* (2003) Arabidopsis genomic information for interpreting wheat EST sequences. Functional and Integrated Genomics 3(1):33-38
Garcia-Hernandez M*, Berardini TZ, Chen C, Crist D, Doyle A, Huala E, Knee E, Miller N, Mueller L, Mundodi S, Reiser L, Rhee SY, Scholl R, Tacklind J, Weems D, Wu Y, Xu I, Yoo D, Yoon J, and Zhang P (2002) Functional and Integrated Genomics 2(6):239-253
Reiser L, Mueller LA, and Rhee SY* (2002) Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. Plant Molecular Biology 48(1):59-74
The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11(8):1425-1433
Huala E*, Dickerman A, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang J, Huang W, Mueller L, Bhattacharyya D, Bhaya D, Sobral B, Beavis B, Somerville C, and Rhee SY* (2001) The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Research 29(1):102-5
Rhee SY* (2000) Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. Plant Physiology 2000 124(4):1460-4
Rhee SY, Weng S, Bongard-Pierce DK, Garcia-Hernandez M, Malekian A, Flanders, DJ, and Cherry JM* (1999) Unified display of Arabidopsis thaliana physical maps from AtDB, the A. thaliana database. Nucleic Acids Research 27(1):79-84
Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, and Rounsley SD (1998) Genome maps 9. Arabidopsis thaliana. Wall chart. Science 282(5389):663-7
Rhee SY and Somerville CR* (1998) Tetrad pollen formation in quartet mutants of Arabidopsis thaliana is associated with persistence of pectic polysaccharides of the pollen mother cell wall. Plant Journal 15:79-88
Rhee SY and Somerville CR* (1994) Flat-Surface Grafting in Arabidopsis thaliana. Plant Molecular Biology Reporter 13:118-123
Preuss D*, Rhee SY, Davis RW (1994) Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes. Science 264:1458-60
Ruan ZS, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, and Maloney PC* (1992) Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. Journal of Biological Chemistry 267:10537-43
Book chapters and other publications
Rhee SY (2014) An interview with Seung Yon (Sue) Rhee. Trends in Plant Science 19(4):198-199.
Ilic K, Stevens PF, Kellogg EA, and Rhee SY (2008) Plant Structure Ontology –anatomical ontology of flowering plants. In: Anatomy Ontologies for Bioinformatics: Principles and Practice. A. Burger, D. Davidson and R. Baldock (Eds). Springer. 27-42. ISBN: 184628884
Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology 138(1):1-3
Yoo D, Xu I, Berardini T, Rhee SY, Narayanasami V, and Twigger S (2005) PubSearch and PubFetch, a simple management system for semi-automated retrieval and annotation of biological information from the literature. In Current Protocols in Bioinformatics. John Wiley & Sons. Chapter 9. Unit 9.7
Reiser L and Rhee SY (2005) Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. In Current Protocols in Bioinformatics. John Wiley & Sons. Chapter 1.11
Berardini TA and Rhee SY (2004) Arabidopsis thaliana: Characteristics and Annotation of a Model Genome. In Encyclopedia of Plant & Crop Science. Marcel Dekker, Inc. 47-50
Rhee SY, Zhang P, and Foerster H, and Tissier C (2005) AraCyc: Overview of an Arabidopsis Metabolism Database and Its Applications for Plant Research. In Biotechnology in Agriculture and Forestry: Plant Metabolomics. K. Saito, R. Dixon and L. Willmitzer ed., Springer. Volume 57. pp. 141-153
Rhee SY (2001) Extending the Frontiers of Plant Biology: Large scale biology, bioinformatics, and information management. Plant Biotechnology Institute Bulletin May Issue:10-12
Rhee SY and Flanders DJ (2000) Web-based bioinformatic tools for Arabidopsis researchers. In Arabidopsis: A Practical Approach. pp. 225-265. Zoe Wilson ed., Oxford University Press, UK.
POPULAR SCIENCE ESSAYS
Rhee SY (1997) Gregor Mendel (1822-1884). Commissioned and originally published on Genetech. Reprinted at Access Excellence, a national educational program that provides high school biology teacher’s access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. Currently available at: http://www.cccbiotechnology.com/RC/AB/BC/Gregor_Mendel.php, http://www.math.usu.edu/rheal/stat1040/lecture_notes/Chapter_26.pdf, https://www.verslo.is/home/Raungreinar/lif/Itarefni/Erfdir/Gregor%20Mendel%28e%29.htm
Rhee SY (1997) Louis Pasteur (1822-1895). Commissioned and originally published on Genetech. Reprinted at Access Excellence, a national educational program that provides high school biology teacher’s access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. Currently available at: http://www.cccbiotechnology.com/RC/AB/BC/Louis_Pasteur.php
Rhee SY (1997) Linus Pauling (1901-1994). Commissioned and originally published on Genetech. Reprinted at Access Excellence, a national educational program that provides high school biology teacher’s access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. Currently available at: http://www.cccbiotechnology.com/RC/AB/BC/Linus_Pauling.php
Rhee SY (1997) Kary B. Mullis (1944 - ). Commissioned and originally published on Genetech. Reprinted at Access Excellence, a national educational program that provides high school biology teacher’s access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. Currently available at: http://www.cccbiotechnology.com/RC/AB/BC/Kary_B_Mullis.php
Collaborative Projects
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Associomics Consortium
Comprehensive membrane protein interactome of Arabidopsis thaliana -
Genomes to Natural Products Network
Plant secondary metabolic pathway discovery using bioinformatics and synthetic biology -
NeuroPlant
An interdisciplinary project to explore the relationship between plant secondary metabolites and animal neurological behavior -
Plant Cell Atlas
A collaborative iniatiative to develop a comprehensive molecular map of plant cells -
Setaria for Biofuels
Genetic architecture of drought tolerance in grasses
AraNet
Gene Functional Associations
Gene Ontology Consortium
Ontologies
The Arabidopsis Information Resource
Model Organism Database
Plant Metabolic Network
Genome-scale databases of metabolic enzymes, compounds, and pathways in plants
This page lists and makes available the programs we have developed in our lab.
Title | Description | Software |
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E2P2 version 3.1 | E2P2 version 3.1 fixes a couple of bugs [README] | E2P2V3.1 |
E2P2 version 3.0 | E2P2 version 3.0 includes expanded reference enzyme sequence libraries updated versions of component software packages. Additional updates were made to improve prediction performance detailed more in the README file. [README] | E2P2V3.0 |
E2P2 version 2.1 | E2P2 version 2.1 includes expanded reference enzyme sequence libraries and improved performance assessment and base classifier integration schemes. [README] | E2P2V2.1 |
SAVI version 3.02 | Semi-Automated Validation Infrastructure version 3.02 processes predicted metabolic pathways using pathway meta data such as taxonomic distribution and key reactions and makes decisions about which pathways to keep, remove, and subject to manual validation. [README] | SAVIV3.02 |
PlantClusterFinder version 1.0 | A pipeline to predict metabolic gene clusters from plant genomes [README] | PlantClusterFinder1.0 |
PlantClusterFinder version 1.2 | An updated version of Plant Cluster Finder to handle species with complex GeneID to ProteinID mappings [README] | PlantClusterFinder1.2 |
PlantClusterFinder version 1.3 | A major update with improved user friendliness and easier interpretation of results [README] [Release Notes] | PlantClusterFinder1.3 |
miP3 version 2 | microProtein Prediction Program (miP3) version 2 predicts microProteins in a sequenced genome. It is more streamlined and simplified than version 1. [README] | miP3V2 |
GRACE | GRACE (Gene Regulatory network inference ACcuracy Enhancement) is an algorithm that enhances the accuracy of transcriptional gene regulatory networks by using a Markov Random Field approach. [README] | GRACE |
QTG-Finder version 1.1
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A machine learning algorithm to prioritize causal genes in quantitative trait loci. [README]
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QTG-FinderV1.1 |
QTG-Finder2 | A generalized machine learning algorithm to prioritize causal genes in quantitative trait loci for any plant species. [README] | QTG-Finder2 |
We always look forward to adding new members to the team. For prospective graduate students and postdocs: feel free to send inquiries at any time, even if no specific openings are listed, by emailing Sue Rhee (srhee at carnegiescience dot edu). We encourage and welcome applicants who are Black, Indigenous, People of Color, First Generation College, Low Income, LBGTQ, or underrepresented in STEM fields in other ways.
Current Specific Position Openings:
No openings at the moment.
General Summer Internships:
Undergraduate students are encouraged to apply for a summer internship in our lab. We typically accept 2-3 interns each summer. A stipend is available for an internship though the number of paid internships varies from year to year depending on funding availability. Due to space and mentor limitations, we cannot accept applications from high school students. Applications for a Carnegie Summer Internship are due March 18th, 2022 at 5pm PST. Applications can be submitted here. Applications submitted after this deadline will be considered as space permits. Accepted interns typically work full-time (8 hrs per day excluding lunch break) from June to August for 10-12 weeks. Each intern will be mentored by a postdoc, a grad student, a research assistant, or Dr. Sue Rhee, depending on the available project. Regardless of the mentor, the intern will meet with Dr. Sue Rhee once every 1-2 weeks. There are lunch-time seminars from 2 plant faculty every Friday (pizza provided) for all the interns and a poster-session in August where the interns show off their work and the entire Carnegie and Stanford plant community is invited. For questions, please reach out to Dr. Sue Rhee (srhee at carnegiescience.edu) directly.
Rhee Lab Policies and Expectations
- Start your path to independence. You are expected to lead and ‘own’ your projects, whether you developed it from scratch, inherited from a former member, or assigned a problem when you start. Think hard and critically about the problem you develop to work on and understand why it is the most important problem to solve. No one, including me, will think as hard about your project as you. Your goal should be to be the world’s expert on what you are studying. I, and others, will throw ideas at you. You must make sure that those ideas are sound before pursuing them at length. If you are not sure, consult me or anyone in the lab, your cohort, former collegues, online discussion boards, etc. Create your own advisory board to help your professional and personal development. Depending on prior experience, this path to independence will take different amount of time to reach for different people. Learn to identify and solve problems on your own by using resources in the Web, asking labmates and colleagues near and far, or consulting me. I expect to see some degree of independence in all lab members within six months.
- Communicate. I encourage you to talk with people around you as much as possible to get the most out of your research experience. Everyone in my lab collaborates with others (mostly other lab members but also members of other labs) and most of the collaborations are initiated by the trainee. Be open to others’ ideas and keep an open mind about different ways of looking at your results. Let me and your labmates know, constructively, if you think we are wrong about something scientifically. At the same time, don’t worry about saying the wrong thing. Everyone knows different things and has different strengths. It is fine to not know something. We are all here to help each other and maintain a rigorous, engaged scientific community. Constructive criticism is key to improving ourselves and helping others. Openness is also a secret to a great research environment. Don’t keep your data a secret within the lab. Openness in the lab comes with an understanding that it is privileged information that you should respect and keep confidential within the lab. Be generous with your ideas, your time, and your expertise. You learn the most by teaching others. Being a researcher is a privileged occupation and you must give back by helping others. I meet with most of my trainees weekly or biweekly. The meetings are an opportunity for you to discuss your progress, failures, and needs. Consider me as your pro bono consultant. It works best if you come prepared. Don’t expect me to remember all the details of your project and where our conversations ended last time. Start with the big picture (project management chart, overall project objectives, or the main problem at hand in the context of the big picture, etc.).
- Be safe, courteous, respectful, helpful, proactive, grateful, and neat. You must be considerate and respectful of your labmates and colleagues. We want to have only good citizens in our lab. Always treat others how you would like to be treated. Strive to do more than your share to keep the research environment in safe, clean, working order. In the least, keep your own work bench and desk area clean and participate in lab chore responsibilities. Taking initiatives and being proactive are highly valued in our lab. If you notice something broken or not right, notify the appropriate person immediately (lab manager, facilities manager, safety officer, or me). Double your courteousness when you are borrowing others’ space or equipment. Unless you have been told otherwise, you should always ask to borrow a piece of equipment or reagent, even if you have used it before. No profanity, whether directed at oneself or others, is allowed. Always be grateful and courteous to each other and especially to the support staff.
- Keep good records. If you haven’t written it down, you might as well not have done it. Be prepared to show me your data. Back-up your electronic data daily. Regularly enter verified constructs and seeds in the lab spreadsheet and other repositories. You agree to keep all lab data private and confidential unless we discuss making the data public or sharing with others. Document your software, scripts and pipelines thoroughly and keep them up to date. We often publish our codes online before publications and it is essential that the codes are fully debugged and well documented.
- Don’t be afraid to fail. Science is full of failures. You will not be discouraged from or reprimanded for failing in this lab. Talk about your failures with others and let me know if something is taking longer than expected because the experiment, algorithm, or simulation didn’t work as expected. The most important thing is to not repeat the same mistakes and to learn from the failures. Think of every failure as an opportunity and come up with something positive.
- Give credit where credit is due. Authorship will be based on established guidelines by the International Committee of Medical Journal Editors (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html). I generally communicate with the first author(s) to establish authorship and order to reach an agreement.
- Set your own schedule. You are responsible for making sure that your projects and other responsibilities are not overly disrupted by your absences. We follow vacation and sick leave set by Carnegie. I am flexible about work hours so long as you work full time (40 hours a week excluding lunch, commute time, excessive/numerous breaks) and you overlap sufficiently with others in the lab. Working off-site is permissible as long as it’s not too frequent. A longer period of off-site work time is allowed upon request on a case-by-case basis. We ask that people note their absences in the lab Google calendar.
- Attend scientific conferences. Funds permitting, I would like everyone working full-time to have the opportunity to attend a conference a year. For the most part, attending a conference will mean that you have something worthwhile to present. Please be sure to leave plenty of time to prepare for conference and other presentations. All abstracts and posters should be approved by me before submission.
- Be a leader and engage. I expect people in my lab to participate and lead in lab, department, and institution-wide activities or other types of activities that bring their research to a wider audience. Attending our weekly lab meetings and Friday department seminars is required. Examples of engaging widely include organizing seminars or journal clubs, participating in professional societies, recruitment activities, or dept-wide programs such as summer internships or organizing work parties/social activities. We foster a culture that emphasizes boldness, creativity, diversity, empathy, equity, flexibility, freedom, innovation, respect, scientific rigor, and transparency.
- When you leave. I expect a postdoc to commit to at least 3 years in the lab and an RA for at least 2 years. I expect a Ph.D. student to graduate within 5-6 years. I encourage each trainee to discuss career plans and professional development with me every six months. Depending on their plans, I am flexible about incorporating off-site training such as internships and courses into their tenure in the lab. I am fine with trainees taking the projects they developed in the lab so long as we communicate and agree on the scope and nature. Solid documentation and organization of materials and data are expected at least 2 weeks before departure.
Outreach in the Rhee Lab
In addition to performing scientific research, members of the Rhee Lab are also engaged in a number of community outreach projects that we create, plan, and execute. While some of these projects focus on a specific demographic, such as our Virtual Classroom Visits program, others such as Science on the Screen extend to a broader audience and welcome participation from the general public. Information about current outreach activities and events can be found below.
outreach projects
Science on the Screen
Live broadcasts of popular films followed by Q & As with famous filmmakers and scientists
Designing Videogames using Plant Science
Drafting and creation of video games with the intention of increasing general knowledge of plant science
PLEDGE (Source: Sammy Katta's Diversity Posters)
Thank you for showing your support for racial justice, diversity, and inclusion in your lab! Rather than charging for these posters, we are asking you to make a commitment to continuous allyship for marginalized and underrepresented communities if you print and display this poster in your lab.
This means, at a minimum:
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Educating yourself about racial justice and systemic discrimination against marginalized communities.
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Participating in the Diversify Plant Science Initiative from ASPB.
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Listening to and uplifting voices from these communities even when they challenge your assumptions and make you uncomfortable.
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Speaking out and pushing for change when you see microaggressions or institutional policies that disadvantage these communities, both within your lab and within the larger campus community (from staff and low-wage workers to students and faculty).
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Making space and time for trainees to heal, take care of their communities, or fight for justice, and continuing to provide financial, career, and other support while they do so (if you think this is not possible at your institution, see the point above).
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Donating, when you have the means, to organizations that promote the success and well-being of marginalized communities in STEM or in the larger community. Examples include (but are not limited to):
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Fellowship for the Future by 500 Women Scientists
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If you share this poster with others, I ask that you share this link, rather than sharing the files or directly linking the poster, to ensure that anyone who displays this poster in their lab understands what it really means. If you’ve made a modified version for your model organism, please share this pledge along with your version of the poster.
If you commit to these actions, click the button below to download the posters.
This page lists talks that have been given by members of our lab as well as talks that we produced.
Talks given by us
- "A journey through biophysics, seed physiology, and ecology to discover a water sensing molecule that controls seed germination", 2021 Synapsis Symposium: Cultivation & Culture, Cornell University, April 23, 2021, Sue Rhee and Yanniv Dorone
- "Challenges and opportunities in studying genes of unknown function" ASPB's Plantae Presents, June 16, 2020, Sue Rhee
- Dr. Rhee's talk starts at 33 minutes in the youtube video.
- "Speeding up gene discovery to understand the genetic basis of natural variation" DOE JGI Gnomics of Energy & Environment Meeting, 2015, Sue Rhee
- "Towards rational assessment of changes in metabolites from genetic modification: Opportunities and challenges in genomics, metabolomics, and metabolic network modeling", HESI: Genetic Basis of Unintended Effects in Modified Plants, 2014, Sue Rhee
Talks we produced
- Carnegie Plant Biology Summer Internship Program, 2010
- This 5-min video captures the essence of a summer internship research expereicnece at Carnegie Science's Plant Biology department using the 2010 year as an example.
- Living Legends: Winslow Briggs, 2010
- Dr. Winslow Briggs of Carnegie Institution for Science, Department of Plant Biology, speaks about how he started his illustrious career in science and his exciting and inspiring journey through orchids, fern, blue light and bruellosis and shares some endearing anecdotes. Dr. Briggs, Director Emeritus of Carnegie's Department of Plant Biology, is one of the preeminent biologists of our time and is the recipient of numerous awards including the prestigious International Prize for Biology from the Japan Society for the Promotion of Science.
- Living Legends: Mike Freeling, 2010
- Living Legends: Charley Yanofsky, 2010