Rhee Lab

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
Phone: (650) 739-4251

Lab Tabs

Our Research

Research Interests: 2002 | 2005 | 2009 | 2012

Research Interests (JANUARY 2019)

Climate change is the single biggest threat to global human health, and is expected to cause about a quarter of a million deaths globally from malnutrition, infectious diseases and heat stress (link). Climate change is rapidly changing the habitability of many species on many places on Earth. We need innovations in science and technology to tackle global sustainability, food security, human health, and biodiversity.

Plants not only form the foundation of terrestrial ecosystems and the human food supply, but also provide renewable energy and essential medicines. Plants mediate production, transport, and storage of our primary food sources and sequester a significant proportion of the world’s carbon. Therefore meeting today’s societal challenges necessitate technological and conceptual advances in plant science.

RheeLabResearch2019.png

We aim to uncover the molecular mechanisms underlying adaptive traits in the face of heat, drought, nutrient limitation, latitude and pests. We study a variety of plants including models, orphan crops, medicinal and desert plants. More recently our work has involved studying a model nematode C. elegans, fungal pathogens, corals, and piezophilic bacterium. Our group employs computational modeling and targeted laboratory testing to study mechanisms of adaptation, functions of novel genes, organization and function of metabolic networks, and chemical and neuronal code of plant-animal interactions. We are also interested in developing translational research programs involving carbon sequestration by plants and biomass maximization under drought in bioenergy crops.

On training…

My main, perhaps the only, ambition in science is to recruit the best postdocs and students and help them become even better by the time they leave my lab. Synergistic interaction with people in my group is the most fun and rewarding aspect of my job on a daily basis and is the main driver for publishing good papers, presenting our work, and securing funding. Our group has two types of trainees: postdoctoral researchers who are in their last phase of training before launching their own groups or establishing independence in other ways, and research assistants who typically come right after college or a masters program without much, if any, research experience. Besides these opposite ends of the training spectrum, everyone has his or her unique personality, style of learning, and background. So I try to adjust the style and type of training according to the individual.

My goal is to foster an environment for the trainee to become an independent, effective, and successful leader. I strive to help them learn how to identify interesting, solvable problems and foster an engaging environment for them to learn and apply innovative methods to solve the problems. One way I do this is by having an interdisciplinary group where people with different training and cultural backgrounds come and develop a variety of projects. The synergism we have achieved through this is evident in our lively group meetings that typically last for 1.5-2 hours where essentially everyone brings up interesting suggestions and ideas.

I recruit postdocs who not only have clear potential but also have areas that I feel I can definitively help improve during their tenures in my lab. In addition to conducting phone and in-person interviews, I request a document outlining a plan of research projects, with which I communicate extensively by email before I make an offer. I feel that each new member that comes to my lab is special and unique and I feel a sense of duty to see him/her flourish intellectually and personally during his/her tenure in my lab. I advise postdocs on career development informally throughout their tenure, but formally during the interview and after 1 year into the tenure. Towards the end of the first year, I ask the postdocs to come up with a list of their strengths and weaknesses and we discuss these points, particularly with a focus on improving the weaknesses catered for their career directions.

I emphasize training postdocs on effective writing and speaking. The postdocs typically participate in writing one grant proposal during his/her tenure and write at least one first-author publication in which he/she leads the process from beginning to end, with my guidance. They also have ample opportunities in preparing and delivering presentations of their work. Informally, each postdoc gives presentations during weekly group meetings (12-14 people). There are additional opportunities for giving presentations, such as the department-wide post-doc only ‘round table’ meetings (~20-30 people) and the biweekly internal seminar series attended by the whole department (~70-80 people). Typically postdocs in my group give ~6-8 presentations/year. Much is gained also by listening to others speak about their research and, being located at a university, we have access to a number of cutting-edge seminar series. At Carnegie, postdocs have an opportunity to meet with the invited seminar speakers during lunch and post-seminar reception. My postdocs typically attend one scientific conference/year. Presenting a poster or an oral presentation is highly encouraged.

Finally, my postdocs gain opportunities to learn how to mentor and advise students who come through our lab as summer interns or voluntary research assistants. Typically 1-2 summer interns and research assistants visit my lab per year.

Besides training people in the science, I consider training of the scientist to be equally important. I value and try to foster qualities such as intellectual generosity, intellectual integrity, creativity and vision. I believe these qualities distinguish a great scientist from a good scientist. Intellectual generosity does not merely stop at being generous in sharing results and reagents, but also ideas, constructive criticisms and empathy in other people’s problems. The best way to learn this, in my view, is by examples from role models. I am surrounded by colleagues and mentors with many of these qualities and I encourage people in my group to seek, recognize and appreciate such qualities in their peers, advisors, mentors and other scientists. Intellectual integrity is another quality I emphasize, mostly to the beginning researchers. When one is starting out in designing and performing experiments, it is very easy for one’s enthusiasm to overshadow the absolute objectivity required. I see this time and again where if students are aware of the expected result, they tend not to ‘see’ the unexpected result. I am sure this behavior is not always conscious. But that makes it even more critical to emphasize intellectual honesty. I also believe there are ways of fostering creativity and vision, but will not dwell on these further here.

Last but not least, I want to emphasize the need for all of us to become the best storytellers. With all the talk and facts about the demise of federal funding for basic scientific research and available positions in academia, we forget how privileged we are to pursue our intellectual curiosities as a profession. This privileged lifestyle comes with a profound responsibility to captivate the ears, eyes, and hearts of the general public with stories that illustrate that with basic science, everything is possible, but without basic science, there will be no humanity.

Tweets by @SueRhee2

News

Jan

2019

Worms help Carnegie and Stanford biologists investigate how plant-derived neurological drugs work

By Carnegie HQ

Stanford, CA— For millennia, humanity has used medicinal plants and plant-based compounds to treat a variety of neurological ailments including epilepsy, mania, migraines, and bipolar disorder. Now a team of researchers from Carnegie and Stanford ...

Lab PI

Sue Rhee

Senior Staff Scientist

Plant Biology

Carnegie Institution for Science

srhee@carnegiescience.edu
650-739-4251
Office:
260 Panama Street
Stanford, CA 94305, US

Profile

Bio

Where do you come from?

I find two things magical: plants and movies. My love of plants started when I wrote a little story about a tree that grew next to the apartment building we lived in Seoul when I was 12. We lived on the sixth floor and my room had a window next to the tree whose canopy was the same height. I was amazed that a tree could grow so tall amidst the concrete towers in the high-rise jungle and wrote an imaginary biography of the tree and its thousands of dancing leaves. My story got a national award and I thought I was destined to become a writer. Little did I know that my little world would be uprooted and transplanted across the globe within a year. A new life in the US where I no longer had control over the language dissolved my dream of becoming a writer. Little did I know that I would eventually end up studying and writing about the mysteries of plants for a living!

What was your first experience with research?

The smell of ether singularly captures my memory of science and research in high school and college. We had a little room behind the biology classroom of Dr. Kowalski’s at Yorktown High, where we conducted genetics experiments with the fruit fly. We would knock them out with ether so that we could count their eye colors and learn about the magical ratio of Mendelian segregation. At Swarthmore college, in the fancy Howard Hughes laboratory of Dr. Mark Jacobs, we wanted to identify protein kinase C from plants and purified the protein from rat brains (one of the most abundant sources of PKC) to establish the biochemical assays. Trips to the Psychology department for the source of PKC were angst-ridden as we ‘took care’ of the rats by knocking them out with ether in a large aluminum garbage can on the roof and surgically removed their brains with rusted guillotine and scissors. These were ‘exciting’ times but also solidified my distaste for doing experiments with animals.

How did you choose graduate school?

A new life in the beautiful San Francisco bay area got started when I came for an interview to do graduate work at Stanford. Learning about the cutting-edge research at Stanford was thrilling, but what really made me decide to settle here were the lovely dinners hosted by plant biologists Drs. Ginny Walbot and Sharon Long. Ginny grilled a whole salmon on her deck and we sat around a picnic table overlooking her gorgeous garden of native plants in full bloom. Sharon and Hal McGee (a science food writer with a cult following) made a wonderful meal and we talked about science and food around the table for hours. In my eyes, they were the Meryl Streeps and Katharine Hepburns of science.

How did you choose a graduate project and lab?

A lot of soul searching goes on during a graduate program. I probably hold a record in not settling into a laboratory to perform graduate work. After doing 4 rotations in various labs, I was still uncertain about where to do my Ph.D. work, and I was gearing up to do yet another rotation when Ginny interjected and encouraged me to talk with a plant biologist, Dr. Chris Somerville, who was coming to Carnegie (a non-profit research institute whose plant biology department was located on campus) as the new director. He was gracious enough to meet me during one of his visits to Stanford and we sat in the white plastic picnic chairs outside the seminar room. Before I realized, we had talked for over two hours, sharing our ideas, perspectives, and science, and I was certain that he was the ideal mentor I was looking for. Although I had to wait another year until his lab moved to Carnegie and didn’t get started with my Ph.D. research until my third year into graduate school, it was a wonderful experience and Chris remains as one of my favorite scientists and friends of all time.

What was your path after getting a Ph.D.?

A lot of soul searching goes on after getting a Ph.D. While I enjoyed the intense period of digging deep into the mysteries of how pollen cell wall formed and unformed into the wee hours of the night, I wasn’t sure whether this was the life I wanted to pursue for the rest of my life. My curiosity knew no bounds, yet what I could do to attack these bouts of curiosities remained frustratingly limiting. So I decided to leave science and turned my attention to the other magical medium, filmmaking. I developed a project with a dear friend from college, Nan Bress, who had just finished a masters program in documentary filmmaking at Stanford. We wanted to make a series of short documentaries about career paths and choices with a degree in science. We pursued our project for two years with a lot of zeal and heart but couldn’t raise enough funds to realize our goals. While I was pursuing this path, I took on a part-time job as a database curator at the Genetics department at Stanford. The database, AtDB, held genetic information about Arabidopsis, the plant I studied as a graduate student. I shared the office with postdocs from Dr. David Botstein’s lab where new genomics technologies were being developed. With the human and Arabidopsis genome sequencing projects well underway and the Internet becoming a household name, I could almost taste the beginning of a new era in biology and I wanted to be a part of it!

I was in the right place at the right time. The Arabidopsis community, which amassed its critical mass, thanks to dynamic leaders like Chris Somerville and Elliot Meyerowitz, wanted a brand new database to hold all of Arabidopsis data that was about to explode. I was part of one of the teams that submitted a proposal to this call and we were successful in getting it. We got the news on my 30^th birthday and because I was second in charge (the person who was going to run the project had just taken a job at industry a month before), this project essentially landed on my lap. With a team of about 10 people I put together back at Carnegie, we created the next generation Arabidopsis database called The Arabidopsis Information Resource (TAIR).

This is my 20^th year at Stanford 18^th year at Carnegie. Since I (re)-started at Carnegie as a staff associate building TAIR and other biological databases in 1999, I was promoted to a staff scientist in 2005 at which time I passed on the baton of running TAIR to Dr. Eva Huala. Since 2005, I have been revamping my scientific program to understand how plants exhibit complex traits like drought and salt tolerance by elucidating the underlying genome-wide networks of proteins and metabolites. We want to identify all of the unknown processes and functions in plants using methods and concepts from computer science, evolution, and genetics and connect the dots in a way that we can explain the complex behavior of plants mechanistically, quantitatively, and predictably.

Affiliation

Carnegie Affiliation:

DPB Employees

DPB Affiliation:

DPB Faculty

Labs:

Rhee Lab

Research Programs:

Pathway Metabolic Network

Download:

Rhee_CV.pdf

Calendar

Lab Members

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)
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.
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.
Bo Xue (Research Assistant)
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.

Publications

Selected recent references

Papers from our group are highly cited with a current H-Index (as of Aug 2018) of 49 on Google Scholar (See ciation page). Some of our papers are listed below.

Schlapfer P, Zhang P, Chuan W, Kim T, Chae L, Dreher K, Nilo-Poyanco R, Arvind Chavali, and Rhee SY (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiology 173(4):2041-2059. [pdf][correction]
Bossi F, Fan J, Xiao J, Chandra L, Shen M, Dorone Y, Wagner D, and Rhee SY (2017) Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC Genomics 18(1):480 [pdf]
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. [pdf]
Chae L, Kim T, Dreher K, and Rhee SY. Genomic signatures of specialized metabolism in plants. (2014) Science 344:510-513. [pdf] [supplemental info]
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, Frommer WB (2014) Border control – a membrane-linked interactome of Arabidopsis. (2014) Science 344:711-716. [pdf] [supplemental info]

Selected recent reviews and perspectives

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. [pdf]
Friesner et al. (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiology 175(4):1499-1509. [pdf]
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. [Online]
Xu M and Rhee SY (2014) Becoming data-savvy in a big data world. Trends in Plant Science 19(10):619-22. [pdf]
Rhee SY and Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science 19(4):212-221. [pdf]

Book chapters

1. Rhee SY and Flanders, DJ. (2000) Web-based bioinformatic tools for Arabidopsis researchers. In Arabidopsis: A Practical Approach. 2000 pp. 225-265. Zoe Wilson ed., Oxford University Press, UK.

2. Berardini TA and Rhee SY (2004) Arabidopsis thaliana: Characteristics and Annotation of a Model Genome. Encyclopedia of Plant & Crop Science. Marcel Dekker, Inc. 47-50.

3. 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.

4. 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.

5. 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

6. Ilic K, Stevens PF, Kellogg EA, 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.

Papers

7. Ruan ZS, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, Maloney, PC. (1992) Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. Journal of Biological Chemistry 267(15):10537-43.

8. Preuss D, Rhee SY, Davis RW. (1994) Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes. Science. 1994 Jun 3;264(5164):1458-60.

9. Rhee SY, Somerville CR. (1994) Flat-Surface Grafting in Arabidopsis thaliana Plant Molecular Biology Reporter. 13:118-123.

10. Rhee SY, 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(1):79-88.

11. Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, Rounsley SD. (1998) Genome maps 9. Arabidopsis thaliana. Wall chart. Science. 282(5389):663-7.

12. Rhee SY, Weng S, Bongard-Pierce DK, Garcia-Hernandez M, Malekian A, Flanders, DJ, Cherry JM. (1999) Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. Nucleic Acids Research. 27(1):79-84.

13. Rhee, SY (2000) Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. Plant Physiology. 124(4):1460-4.

14. 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.

15. The Gene Ontology Consortium (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Research. 11(8):1425-1433.

16. Rhee, SY (2001) Extending the Frontiers of Plant Biology: Large scale biology, bioinformatics, and information management. Plant Biotechnology Institute Bulletin May:10-12.

17. 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.

18. 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, S, Tacklind, J, Weems, D, Wu, Y, Xu, I, Yoo, D, Yoon, J (2002) TAIR: A Resource for Integrated Arabidopsis Data. Functional and Integrated Genomics. 2(6):239-253.

19. Clarke, BC, Lambrecht, M and Rhee, SY (2003) Assessing the utility of Arabidopsis genomic information for interpreting wheat EST sequences. Functional and Integrated Genomics. 3(1):33-38.

20. 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, 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.

21. Mueller, LA., Zhang, P., Rhee SY (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 132(2):453-60.

22. Rhee SY, Osborne, E, Poindexter, P, 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.

23. 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, White R; Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research. 32 Database issue:D258-61.

24. 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.

25. Rhee, SY (2004) Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiology. 134(2):543-7

26. Bard, JL and Rhee, SY (2004) Ontologies in biology: design, applicatioins and future challenges. Nature Review Genetics 5(3):213-22.

27. 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. The Plant Journal. 37(6):914-39.

28. 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.

29. 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.

30. 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.

31. 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.

32. 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. The Plant Journal. 39(6):905-19.

33. 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, Kell, DB. (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology. 22(12):1601-6.

34. 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.

35. Bard, J, Rhee SY, Ashburner, M (2005) An ontology for cell types. Genome Biology. 6:R21

36. 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.

37. 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.

38. Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70

39. Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. 138(1):1-3.

40. 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, Zapata F. (2005) Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Functional and Integrated Genomics. 6:388-397.

41. 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): 527–539.

42. Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp P (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research. 34(Database issue):D511-6.

43. Gene Ontology Consortium (2006) The Gene Ontology Project in 2006. Nucleic Acids Research. 34(Database issue):D322-6

44. Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee SY, Wagner U, Hennig L. (2006) MIAME/Plant – adding value to plant microarrray experiments. Plant Methods. 2:1

45. Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360

46. 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.

47. 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.

48. Stein LD, Beavis WD, Gessler DD, Huala E, Lawrence CJ, Main D, Mueller LA, Rhee SY, Rokhsar DS (2006) Save our data! Scientist. 20(4):24-25.

49. Ilic K, Kellogg E, Jaiswal P, Zapata F, Stevens P, Vincent L, Pujar A, Avraham S, Reiser L, McCouch SR, Sachs S, Schaeffer M, Rhee SY, Ware D and Stein L. (2006) Plant Structure Ontology: A Unified Vocabulary for Flowering Plants. Plant Physiology. 143(2):587-99

50. The Gene Ontology Consortium (2007) The Gene Ontology project in 2008. Nucleic Acids Research. doi: 10.1093/nar/gkm883

51. 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. (2007) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research. doi:10.1093/nar/gkm900

52. Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics. 3(3):195-201.

53. 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

54. 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. The Plant Journal. 53(4):610-35

55. 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.

56. 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.

57. 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, Rhee SY (2008) The future of biocuration. Nature. 455:47-50.

58. 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.

59. 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

60. Reference Genome Group of the Gene Onology Consortium (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLOS Computational Biology. 5(7): e1000431.

61. 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.

62. 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, Dickerson JA (2010) PlantMetabolomics.org: A web portal for Plant Metabolomics Experiments. Plant Physiology. 152(4): 1807-16.

63. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, 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.

64. 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 Physiology. 1(24):1-14.

65. 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.

66. Hwang S, RheeSY, 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.

67. Chae L, Lee I, Shin J, Rhee SY (2012) Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology. 15:177-184. [pdf]

68. Quanbeck, SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Preeti Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, HuhmanDV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES and Nikolau BJ (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.

69. 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.

70. 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. The Plant Cell. 24(10):3859-75. [pdf]

71. Rhee SY and Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science. 19(4):198-199. [pdf]

72. 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):149-15. [pdf]

73. Rhee SY (2014) Interview with Seung Yon (Sue) Rhee. Trends in Plant Science. 19(4):212-221. [pdf]

74. Chae L, Kim T, Dreher K, and Rhee SY. Genomic signatures of specialized metabolism in plants. (2014) Science. 344:510-513. [pdf] [supplemental info]

75. 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, Frommer WB (2014) Border control – a membrane-linked interactome of Arabidopsis. (2014) Science. 344:711-716. [pdf] [supplemental info]

76. Xu M and Rhee SY (2014) Data analysis in plant biology. Trends in Plant Science. 19(10):619–622.

77. Peng J, Uygun S, Kim T, Wang Y, Rhee SY, and Chen J (2015) NetSim: A novel tool for measuring functional similarities using Gene Ontology and gene co-function networks. BMC Bioinformatics. 16(1):44.

78. 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) Unraveling the relationship between genotype and metabotype in Arabidopsis thaliana. Plant Physiology. 167(4):1685-98.

79. 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.

80. de Klein N, Magnani E, and Rhee SY (2015) microProtein Prediction Program (miP3): a software for predicting microProteins and their target transcription factors. International Journal of Genomics. Article ID 734147. 1-4.

81. 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.

82. 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.

83. 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.

84. Banf M, Rhee SY (2016) Computational inference of gene regulatory networks: approaches, limitations and opportunities. BBA Gene Regulatory Mechanisms. S1874-9399(16)30188-2.

85. Walsh JR, Schaeffer ML, Zhang P, 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(1):129.

86. 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.

87. Banf M, Rhee SY. (2017) Enhancing gene regulatory network inference through data integration with markov random fields. Nature Scientific Reports. 7:41174.

88. 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

89. Chavali A, Rhee SY. (2017) Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Briefings in Bioinformatics. bbx020. doi: 10.1093/bib/bbx020.

90. Schlapfer P, Zhang P, Chuan W, Kim T, Chae L, Dreher K, Nilo-Poyanco R, Arvind Chavali, and Rhee SY (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiology. 173(4):2041-2059.

91. 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.

92. 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 Physiology. 175(4):1499-1509.

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Websites

Databases and Bioinformatics Tools

AraNet
Gene Functional Associations
Gene Ontology Consortium
Ontologies
Plant Metabolic Network
Genome-scale databases of metabolic enzymes, compounds, and pathways in plants
The Arabidopsis Information Resource
Model Organism Database

Collaborative Projects

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
Setaria for Biofuels
Genetic architecture of drought tolerance in grasses

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