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 underpin terrestrial ecosystems and feed us, but also bestow renewable energy and essential medicines. Plants also sequester a significant proportion of the world’s carbon. Therefore, to meet today’s societal challenges, we need 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.

The following are the five wings of our current research program, often done in collaborations with other labs.

I. Metabolic engineering: We combine computational modeling, genetics, genomics, biochemistry, synthetic biology, and bioinformatics to model genome-scale metabolic networks of cells, organ systems, and organisms to understand, predict, and engineer metabolic traits. Examples of systems we study include source-sink relationships within a plant to maximize biomass production under suboptimal conditions, plant-pathogen relationships to identify the sources of metabolic dependency, and microbe-microbe interactions within a microbial community in the fruit fly gut. We also use omics data to decipher the rules of transcriptional regulation of metabolism and have discovered novel epigenetic and transcription factor-mediated regulatory mechanisms. Finally, we combine computational and synthetic biology methods to discover new biosynthetic pathways that synthesize natural products in plants.

II. Neuroscience: Twenty percent of American adults have experienced a mental health issue. Yet, despite decades of research we still have a limited understanding of how the mind works. One of our projects, called NeuroPlant, aims to address this gap by leveraging chemicals made in plants as tools to manipulate and decipher neuronal pathways. Our strategy is to develop methods to screen the effects of natural products on neural activity and behavior. We will focus on compounds synthesized by medicinal plants, as these chemical libraries are enriched for their efficacy through evolution and human selection. Our principal experimental system is C. elegans, which is uniquely suited for this project due to its rapid growth, its genetic and optical accessibility, and its wealth of genomic resources. After screening in worms, we will test our lead compounds in human cells. Another direction we want to take with this branch of research is to combine chemical ecology and evolutionary biology to understand how animal brains evolved to recognize plants and how plants evolved to protect themselves against herbivores through invention of chemicals that control animal behavior.

III. Sustainability: Global warming is changing the habitability of many places for many species on Earth. Plants occupy the largest portion of the land surface and understanding thermo-adaptation in plants is critical and timely for global sustainability, food security and species conservation. This is a new focus for collaboration between molecular biologists and ecologists. In the 1970s, Carnegie scientists studying Tidestromia oblongifolia in Death Valley discovered that it is highly adapted to high temperatures and has optimal photosynthetic rate at 47ºC that is comparable to crop plants in their most favorable conditions. The molecular basis of this remarkable thermo-adaptation of photosynthesis remains largely uninvestigated. To decipher the mechanisms of thermo-adaptation of T. oblongifolia, we have assembled an interdisciplinary team with expertise in ecophysiology, genomics, biochemistry and computational modeling of photosynthesis. We have successfully recreated Death Valley conditions in our customized growth chambers and are conducting physiological measurements of two T. oblongifolia ecotypes (Death Valley (max temp~50C) and Dos Palmas (max temp~42C) along with three ecotypes of a related Amaranth species called Amaranthus hypochondriacus, which is an ancient crop from the Incas that has a high potential for future agriculture.

IV. Data-driven discovery: Over 25-75% of protein-encoding genes in all sequenced genomes are not similar to anything with known molecular functions. We develop approaches to systematically characterize these ‘unknown’ genes. This part of our research program is the riskiest, but we are learning the newest biology from this approach. One example is a novel gene that we call CHIQUITA1, which is a negative growth regulator that attenuates cell division rates early in development. In the absence of the protein, cell division is accelerated during early development; organs switch from proliferation to differentiation earlier than the wild type, consigning the mutant plants to become dwarf at maturity. This is a holy-grail trait --early vigor combined with late onset dwarfism-- that farmers have been looking for since the Green Revolution. Another example is a gene we named FLOE1 (after the second movement of Philip Glass’s Glassworks), which acts as a water sensor and regulates seed germination. Upon exposure to water, the protein changes its physical nature from a glassy state to liquid droplets, which we believe changes the viscosity of the cell cytoplasm, thereby allowing metabolic activities and the germination process to start. We are currently translating these discoveries into oil crops and sorghum. Considering that these are the first two genes of the ‘unknown’ genes we have been characterizing, I am confident that this dark matter of the genome in plants is a gold mine for the riskphilic, creative, and optimistic.

V. Plant Cell Atlas: To supercharge our ability to understand how plants work, we need to quantitatively understand the dynamic molecular organization of plant cells and their functions. For this, we need a solid infrastructure that can incorporate and codify the theoretical and empirical data of plant cells, a task too big to tackle for a single group. Therefore, we want to create a community that includes scientists from plant biology, data science, AI, imaging, proteomics, single cell profiling and nanotechnology to lay the groundwork for creating a comprehensive understanding of the dynamic molecular organization of the plant cell, an initiative we are calling the Plant Cell Atlas (PCA). We have successfully kickstarted the PCA community building activities this spring with three digital workshops on the vision, technologies and broader impacts of the PCA. Because of COVID-19, our original plan for an in person gathering of 70 scientists, mostly senior faculty, turned into three virtual workshops, each of which drew 140+ scientists (70% early career) participating from around the world.

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

Jul

2021

How seeds know it’s a good time to germinate

By Carnegie HQ

Palo Alto, CA— Dehydrated plant seeds can lay dormant for long periods—over 1,000 years in some species—before the availability of water can trigger germination. This protects the embryonic plant inside from a variety of environmental stresses until ...

Jun

2021

Carnegie postdoc wins fellowship to study plants’ adaptation to climate change

By Carnegie HQ

Palo Alto, CA— Carnegie’s Megan Ruffley was awarded a prestigious Plant Genome Postdoctoral Research Fellowship in Biology from the National Science Foundation to study the genetics underpinning a plant’s ability to adapt to a changing climate. ...

Aug

2020

DOE awards biofuel research team including Carnegie plant biologists

By Carnegie HQ

Palo Alto, CA— Carnegie’s Sue Rhee and Moises Exposito-Alonso are leading members of an initiative to identify genes related to stress tolerance in the mustard plant field pennycress. Theirs was one of seven biofuel research projects awarded a total ...

Aug

2019

Carnegie-led initiative receives major DOE biofuels research grant

By Carnegie HQ

Palo Alto, CA— Carnegie plant biologists Sue Rhee and David Ehrhardt will lead one of 25 teams awarded a total of $64 million this week by the U.S. Department of Energy to pursue genomic research of potential biofuel crops. “This research will help ...

More News

Tweets

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

Seung Yon (Sue) Rhee is a Senior Staff Member of Plant Biology Department at Carnegie Institution for Science. Her group strives to uncover the molecular mechanisms underlying adaptive traits in the face of heat, drought, nutrient limitation, and pests. Dr. Rhee’s group studies a variety of plants including models, orphan crops, medicinal and desert plants. More recently their work has involved studying a model nematode C. elegans, fungal pathogens, and piezophilic bacteria. Her 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. Her group is also interested in developing translational research programs involving biomass maximization under drought in bioenergy crops. Dr. Rhee received her B.A. in biology from Swarthmore College and a Ph.D. in biology from Stanford University. She has been an investigator at the Plant Biology Department of Carnegie Institution for Science since 1999.

Lab Website

Recent Publications

Affiliation

Affiliation:

DPB Faculty

Labs:

Rhee Lab

Research Programs:

Pathway Metabolic Network

Download:

Rhee_CV_2021619-public.pdf

Teaching

2020

Fundamentals and Frontiers in Plant Biology

Stanford University

Winter 2020: BIO229/BIO129

BIO129/229: Fundamentals and Frontiers in Plant Biology

Quarter/Year: Winter 2020 Tues/Thurs 12-1:20 pm Grading: Satisfactory/No Credit

This course can serve as an elective course for Biology PhD candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.

Location: STLC room 105 Number of Units: 3

Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor.

Enrollment Cap: 20

Prerequisites: For graduate students, no prerequisites. For undergraduates, at least two of the following Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), and ongoing research in a Stanford or Carnegie plant biology laboratory.

Auditing: TGA graduate students can audit lecture classes on Tuesdays

Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genomics, genetics, biotic and abiotic interactions, cell and development, and systems and synthetic biology.

Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers.

Class activities: Each week will compose of one lecture and one paper discussion class. The discussion class is structured like a journal club, where teams of students will lead discussions on various sections of the paper. Students will write a 1 page critique of the paper and submit before class. Carnegie Winter Quarter Seminar Series will include speakers from the papers or topics of discussion and students will have an opportunity to meet with the speakers. There may be 1-2 field trips.

Grading: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments.

Topics (*Module Coordinator):

Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Walbot*, Evans, Exposito-Alonso)

Module 2 (Weeks 4-5): Plant Cell and Developmental Biology (Bergmann*, Ehrhardt)

Module 3 (Weeks 6-8): Biotic and Abiotic Interactions (Long*, Grossman, Wang)

Module 4 (Weeks 9-10): Plant Systems and Synthetic Biology (Rhee*, Bhaya)

Date	Module	Instructors (Teaching)	Topic/Papers/Learning Goals
Jan 7 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Introduction of plant macro- and micro- evolution from geological times to the anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Jan 9 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Classic paper that contributed to the modern synthesis of evolution: Clausen J, Keck DD, Hiesey WM. Regional Differentiation in Plant Species. Am Nat. 1941;75: 231–250. Available: http://www.jstor.org/stable/2457513 Frontier paper addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038. https://doi.org/10.7554/eLife.41038
Jan 10 4-5 pm	Carnegie Seminar		Host: Moises Exposito-Alonso Speaker: Dan Jacobson
Jan 14 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] haploid induction and CRISPR editing via pollen in plant breeding.
Jan 16 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Genetics of self-incompatibility: Background paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) Thanat Chookajorn, Aardra Kachroo, Daniel R. Ripoll, Andrew G. Clark, and June B.Nasrallah. PNAS 101: 911-917. https://doi.org/10.1073/pnas.2637116100 Discussion paper: S-Locus F-Box proteins are solely responsible for S-RNase-based self-incompatibility of Petunia Pollen (2018) Linhan Sun, Justin S. Williams, Shu Li, Lihua Wu, Wasi A. Khatri, Patrick G. Stone, Matthew D. Keebaugh, and Teh-hui Kao. The Plant Cell 30: 2959-2972. DOI: https://doi.org/10.1105/tpc.18.00615
Jan 17 4-5 pm	Carnegie Seminar
Jan 21 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Epigenetic regulation of gene expression in the context of plant development and heritable gene silencing
Jan 23 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	One classic paper to read and one recent paper for discussion Classic Paper: First demonstration of imprinting of an individual gene in any organism, showing that parent-of-origin, rather than gene dosage, is responsible for expression differences of R-r in maize endosperm. J.L. Kermicle (1970) DEPENDENCE OF THE R-MOTTLED ALEURONE PHENOTYPE IN MAIZE ON MODE OF SEXUAL TRANSMISSION. Genetics 66:69-85. https://www.genetics.org/content/66/1/69.long Recent Papers: Movement of small RNAs from the vegetative cell to sperm cells in pollen for transposon silencing. G. Martinez, K. Panda, C. Kohler, and R.K. Slotkin (2016) Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants 2:1-8. https://www.nature.com/articles/nplants201630 Demethylation in the endosperm is correlated with demethylation in the central cell. Park et al. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS 113:15138-15143 https://www.pnas.org/content/113/52/15138
Jan 24 4-5 pm			Host: Ginny Walbot Speaker: Tim Kelliher
Jan 28 12-1:20pm	Mod 2	Bergmann, Ehrhardt	The creation of plant bodies with an emphasis on defining features of plant development such as modularity, meristematic growth, and morphogenesis without cellular movement.
Jan 30 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Several classic (short!) papers using microsurgery to define organ positions, https://www-nature-com.laneproxy.stanford.edu/articles/167651a0 https://www-nature-com.stanford.idm.oclc.org/articles/171224b0.pdf A decades-later revisit of these surgeries https://dev-biologists-org.stanford.idm.oclc.org/content/develop/132/1/15.full.pdf and a recent paper identifying the molecules and mechanisms that are responsible for the positional information. https://elifesciences.org/articles/27421
Jan 31 4-5 pm	Carnegie seminar		Host: Dominique Bergmann Speaker: Courtney Hollender
Feb 4 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Principles of growth and morphogenesis in cells constrained by cell walls. Topics include biophysics of cells under high turgor pressure, organization of cell wall biosynthesis and yielding, establishment of asymmetries in cell growth.
Feb 6 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Classic paper: Green P.B. (1962) Mechanism for plant cellular morphogenesis. Science 138: 1404-1405. Recent Paper: Oda Y. Fukuda H. (2012) Initiation of cell wall pattern by a Rho- and microtubule-driven symmetry breaking. Science 337: 1333-1336.
Feb 7 4-5 pm
Feb 11 12-1:20pm	Mod 3	Long, Grossman, Wang	Overview of plant-microbe interactions. Major topics: recognition, bacterial signals and plant responses; genes for symbiosis with bacteria and fungi; different levels of plant defense against pathogens.
Feb 13 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic paper: Lerouge, P. et al (1990) Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal. Nature 344: 781-784. https://www.nature.com/articles/344781a0.pdf Recent paper: Teulet, A. et al (2019) The rhizobial type III effector ErnA confers the ability to form nodules in legumes. Proc. Nat. Acad. Sci. 116: 21758-21768. https://www.pnas.org/content/pnas/116/43/21758.full.pdf
Feb 14 4-5 pm	Carnegie seminar		Host suggestion: Sharon Long Speaker suggestion: Ksenia Krasileva
Feb 18 12-1:20pm	Mod 3	Long, Grossman, Wang	Basic aspects of photosynthetic metabolism; from the fixation of inorganic carbon to the generation of reactive oxygen species.
Feb 20 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic Papers: Photosynthesis. (2016) Johnson MP. Essays Biochem. Oct 31;60(3):255-273. Review. PubMed PMID: 27784776; PubMed Central PMCID: PMC5264509. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264509/pdf/bse0600255.pdf Efficient photosynthesis in dynamic light environments: a chloroplast's perspective. (2019) Kaiser E, Correa Galvis V, Armbruster U. Biochem J. 2019 Oct 15;476(19):2725-2741. doi: 10.1042/BCJ20190134. PubMed PMID: 31654058. https://portlandpress.com/biochemj/article-lookup/doi/10.1042/BCJ20190134 Recent paper: Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. (2016) Kromdijk J, Głowacka K, Leonelli L, Gabilly ST, Iwai M, Niyogi KK, Long SP. Science Nov 18;354(6314):857-861. PubMed PMID: 27856901. https://science.sciencemag.org/content/354/6314/857/tab-pdf
Feb 21 4-5 pm	Carnegie Seminar		Host suggestion: Arthur Grossman Speaker suggestion: Kris Niyogi
Feb 25 12-1:20pm	Mod 3	Long, Grossman, Wang	Developmental plasticity and acclimation to the environment, the underlying cell signaling and regulatory systems, protein networks and proteomics.
Feb 27 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic paper: (1) Park et al., Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science. 2009 May 22;324(5930):1068-71. PMID: 19407142 https://science.sciencemag.org/content/324/5930/1068/tab-pdf (2) Pandey et al., Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis. Cell. 2009 Jan 9;136(1):136-48. PMID: 19135895 https://www.ncbi.nlm.nih.gov/pubmed/19135895 Recent paper: Vaidya et al., Dynamic control of plant water use using designed ABA receptor agonists Science 366, eaaw8848 (2019) 25 October 2019. PMID: 31649167
Feb 28 4-5 pm	Carnegie Seminar
Mar 3 12-1:20pm	Mod 4	Rhee, Bhaya	Overview of plant systems biology with topics including biological networks, cell and tissue modeling, and comparison of traditional plant physiology with systems biology
Mar 5 12-1:20pm	Mod 4	Rhee, Bhaya	Classic papers: Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).https://science.sciencemag.org/content/298/5594/824 Just-in-time transcription program in metabolic pathways. (2004) Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Nat Genet.May;36(5):486-91. Epub 2004 Apr 25. PubMed PMID: 15107854. https://www.nature.com/articles/ng1348.pdf Recent paper: Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. (2018) Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499. doi: 10.1073/pnas.1721487115. Epub 2018 May 16. PubMed PMID: 29769331; PubMed Central PMCID: PMC6016767. https://www.pnas.org/content/pnas/115/25/6494.full.pdf
Mar 6 4-5 pm	Carnegie Seminar
Mar 10 12-1:20pm	Mod 4	Rhee, Bhaya	Principles of synthetic biology; a discussion of successes and challenges. How has synthetic biology been used in plant engineering?
Mar 12 12-1:20pm	Mod 4	Rhee, Bhaya	Classic paper: Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K, Zhao D, Voigt CA. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109. Epub 2012 Apr 16. PMID: 22509035 Recent paper: Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology. Proc Natl Acad Sci U S A. 2018 Sep 4E8509-E8517. doi: 10.1073/pnas.1804992115. Epub 2018 Jul 30.
Mar 13 4-5 pm	Carnegie Seminar

Career Exploration and Planning

Stanford University

Spring 2020: BIO380

BIO 380: Career Exploration and Planning

Dr. Sue Rhee (srhee@carnegiescience.edu)

Senior Staff Scientist, Carnegie Institution for Science

Associate Professor by Courtesy, Biology Department, Stanford University

Format: Discussion

Enrollment Cap: 20

Quarter/Year: Spring 2020

Prerequisite: Grad students in Life Sciences PhD programs

Grading: Satisfactory/No Credit

Number of Units: 1

Meeting Time: Thursdays 4:30-6:20 pm Location: Carnegie Seminar Room

Course Assistants:

Benjamin Jin (bjin@carnegiescience.edu)
Emily Fryer (efryer@carnegiescience.edu)

Description

Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions; have the opportunity to take various self-assessments for characterizing their personalities and identify fitting professions; discuss various career options with a life sciences PhD; and ultimately learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to life sciences PhD students in year 3 or beyond. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305 (https://dpb.carnegiescience.edu/about/contact).

Requirements

Students are expected to attend all class meetings, actively contribute to group discussions, and give a short group presentation on the final class meeting.

Schedule

April 02 — Introductions and Class Logistics, myIDP Assessment

Introduction to the structure and context of the course: we will go over requirements and expectations, complete a preliminary survey, and engage in small groups to get to know each other and discuss career opportunities in the life sciences. What are our personal and professional dreams, how do we find an overlap between the two? We will conduct the myIDP assessment in class.

Homework: Take the Myers-Briggs Type Indicator Test, to be independently completed by Tuesday, April 7th, 5 pm PST.

April 09 — Discussion of Myers-Briggs Type Indicator Test Results (guest lecture by MJ Mangiarelli of Stanford BioSci Careers)

The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.

Homework: Take the CliftonStrengths test by Gallup, to be independently completed by Tuesday, April 14th, 5 pm PST.

April 16 — Discussion of CliftonStrengths Test Results (guest lecture by Marlene Scherer Stern of Stanford BioSci Careers)

The CliftonStrengths test is designed to highlight the user’s character strengths, which can be used to assess what roles would be best in both utilizing and developing such strengths. We will be discovering our individual strengths and how these can contribute to success in our future careers, while understanding how they are only a part of our unique personalities. Stanford’s BioSci Careers will help with evaluating the results.

April 23 — Self-Assessment Decompression and Career Planning Lecture

Post-MBTI/CliftonStrengths test discussion in small groups to put the results in the context of career choices. There will also be a lecture on career planning, regarding key concepts and tools that are useful in professional development, with small group discussions to follow. Final Presentation projects will be assigned and expectations will be discussed.

April 30 — Career Panel I: “Business”

Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations. Carnegie will provide a reception after the panel to continue discussions and networking.

Kirk Clark	Executive Director, Novartis Institutes for BioMedical Research
Pamela Marrone	CEO and Founder, Marrone Bio Innovations
Jayaranjan Anthonypillai	Founder/CEO, Berkeley BioLabs; Co-Founder/Managing Partner, Focus Academy LLC
Mowgli Holms	Co-founder and CEO, Phylos Biosciences

May 7 — Career Panel II: “Academic Research”

Pleuni Pennings	Assistant Professor, San Francisco State University
Miriam Goodman	Professor, Molecular and Cellular Physiology, Stanford University
Jennifer Mortimer	Staff Scientist, Berkeley Lab; Director of Plant Systems Biology, JBEI
Rebecca Albright	Assistant Curator, California Academy of Sciences

May 14 — Career Panel III: “Scientific Journalism, Administration, Law, Philanthropy”

Amy Adams	Director of Long Range Vision Communications, Stanford University
James Keddie	Senior Patent Agent, Bozicevic, Field & Francis LLP
Rieko Yajima	Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Milan Karol	Senior Development Officer, Carnegie Institution for Science

May 21 — Career Panels Decompression and Preparation for Final Presentations

Group discussions to follow the career panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses. We will also do some brainstorming exercises called 30 circles and mind-maps, and draft a personal mission statement. Small group discussions on the draft mission statements.

May 28 — Student Final Presentations

Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus. Staff from BioSci Careers will be present to provide feedback.

Notices

Disability Access

Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email (oae-contactus@stanford.edu), or phone (650-723-1066).

Honor Code

Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.

Career Panel Participants

Career Panel I (April 30th, 2020): Business

Kirk Clark

Executive Director, Novartis Institutes for BioMedical Research

Dr. Clark received his PhD in Biochemistry at Kansas State University. After training in protein crystallography as a postdoc at The Rockefeller University, he joined the Swiss pharmaceutical company Ciba-Geigy to establish in-house protein crystallography capabilities in New Jersey. Upon the Ciba-Giegy/Sandoz merger to form the Novartis Institutes for Biomedical Research, Dr. Clark has taken on increasing responsibilities locally and globally within the company, including heading their Protein Structure “home” in Cambridge, co-chairing the Drug Prototype project sub-portfolio, and participating in both the global Chemical Biology & Therapeutics and Protein Sciences global leadership teams. He currently serves as the Director of Novartis’ Protein Sciences group.

Pamela Marrone

CEO and Founder, Marrone Bio Innovations

Dr. Marrone received her PhD in Entomology from North Carolina State University. She has built her career towards the discovery and development of environmentally-responsible bio-based products for pest management and plant health. Originally working as the group leader of Monsanto’s Insect Biology group, she branched out and started her first company, Entotech, Inc., where she screened over 50,000 microorganisms for naturally-produced insecticidal products. Dr. Marrone subsequently started another company, AgraQuest, which developed a line of naturally-derived pest management products from similarly-robust screens of microorganisms. In 2006, she left AgraQuest to found her current company, Marrone Bio Innovations (MBI). MBI has produced award-winning bio-based products for use in many agricultural markets and is additionally marketing products for invasive zebra and quagga mussel control. Dr. Marrone also serves as a board member of a number of associations and companies, such as the Association for Women in Science, the Foundation for Food and Ag Research, and the startups Pheronym and AgShift. In addition, she is a Trustee of Cornell University.

Jayaranjan (J) Anthonypillai

Founder and CEO, Berkeley BioLabs; Co-Founder and Managing Partner, Focus Academy LLC

J is a scientist and entrepreneur devoted to facilitating healthy and productive biotech startup cultures. He has a background in developing, validating, and scaling technologies, and has worked in clinical, clean-tech, biotech, and agri-tech sectors. Leveraging his experience and background in biology and lipid chemistry, he has developed novel technologies for overcoming product development, process development, and engineering challenges. Through his creations, Berkeley Biolabs and Focus Academy, he has helped seed and grow over 50 companies in the biotech sector. Berkeley Biolabs is an incubator lab while Focus Academy serves as a ‘Soft Landing’ for international biotech startups in the Bay Area. As an entrepreneur and mentor for several startups, J’s emphasis is often on product/market fit as the main driver of R&D effort and strategy.

Mowgli Holmes

Co-founder and CEO, Phylos Biosciences

Dr. Holmes earned his PhD in Microbiology and Immunology from Columbia University, and works on applying biotechnological skills towards the development of the contemporary cannabis industry. His company, Phylos Biosciences, provides genetic and sex testing services for marijuana growers, and additionally maintains an evolutionary database of different cannabis strains from thousands of varieties from over eighty countries. They also work to provide discounted services to support small-scale local growers. Holmes is the founding board member of the Cannabis Safety Institute and the Open Cannabis Project, and serves as Chair of the Oregon State Cannabis Research Task Force.

Career Panel II (May 7th, 2020): Academia

Pleuni Pennings

Assistant Professor, San Francisco State University

Dr. Pennings received her PhD in Evolutionary Biology at the University of Munich in Germany. Throughout her time in academia, she has engaged in a plethora of projects across the scales of life, from work on ant population genetics, to her current work as an Assistant Professor at SFSU studying the evolution of Human Immunodeficiency Virus drug resistance. In addition to research, she has devoted herself to science education, starting her own consulting agency to promote science communication and education in Amsterdam, and coordinating the Munich Graduate Program for Evolution, Ecology, and Systematics.

Miriam Goodman

Professor, Molecular and Cellular Physiology, Stanford University

Dr. Goodman earned a PhD from the University of Chicago in Neurobiology. Her academic career has revolved around elucidating the biological mechanisms of sensation, from her dissertation research on the ion channels necessary for hearing, to the analysis of ion channel biophysics and touch sensing as a postdoctoral fellow at Columbia University. Currently, her work at the Stanford University School of Medicine includes using C. elegans as a model to better understand touch and pain sensation, and the mechanisms in which sensory neurons are protected from damage.

Jennifer Mortimer

Staff Scientist, Berkeley Lab and Director of Plant Systems Biology, JBEI

Dr. Mortimer received her PhD in Plant Science from the University of Cambridge, as well as a Masters of Research in Bioinformatics from the University of Exeter. After attaining her degrees, she worked as a Research Associate for several years, studying a number of topics regarding Arabidopsis physiology. Her research has focused on the synthesis, transport, and use of polysaccharides for plant cell wall formation and engineering. Currently she heads a lab that utilizes numerous different model plants to investigate these questions, and serves as Director of Plant Systems Biology at the Joint BioEnergy Institute (JBEI) at the Lawrence Berkeley National Lab, where she investigates how to make biofuels and biochemicals from plant biomass.

Rebecca Albright

Assistant Curator, California Academy of Sciences

Dr. Albright got her PhD from the University of Miami in Marine Biology and Fisheries. Her work has been devoted to in-depth research on the impacts of environmental changes upon coral reef ecosystem health. She has worked as a postdoc at both the Australian Institute of Marine Science and the Carnegie Institution for Science’s Global Ecology Department, studying coral reef biogeochemistry and carbonate chemistry, as well as the effects of ocean acidification upon these processes. Currently as a curator at the California Academy of Sciences in San Francisco, Dr. Albright works on creating a coral culturing facility.

Career Panel III (May 14th, 2020): Scientific Journalism, Administration, Law, Philanthropy

Amy Adams

Director of Long Range Vision Communications, Stanford University

Adams received her MS from Cornell University in genetics and development, as well as a certification from UC Santa Cruz in science communications. Her experiences with news and feature writing regarding a range of scientific topics include freelance writing and editing for a number of notable publications and websites, such as Science, Natural History, and CBSHealthWatch.com; science writing for the Stanford University School of Medicine; communications manager for the California Institute for Regenerative Medicine; and finally back to Stanford, where she has worked as the Director of Science Communications and currently serves as Director of Long Range Vision Communications.

James Keddie

Senior Patent Agent, Bozicevic, Field & Francis LLP

Dr. Keddie received his PhD in Plant Molecular Biology from the John Innes Institute in Norwich, UK. Though he began his post-doctoral career as a fellow in several plant biology labs, including the Carnegie Institution for Science’s Plant Biology Department, studying a range of topics from plant disease resistance to development to gene expression, he began work with intellectual property as a Senior Scientist and IP Manager at Mendel Biotechnology, Inc. Dr. Keddie currently serves as a Senior Patent Agent at Bozicevic, Field & Francis LLP, where his expertise in all aspects of patent prosecution are used to provide biotech-focused clients with patent drafting and prosecution services.

Rieko Yajima

Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University

Dr. Yajima received her PhD in Chemical Biology from Penn State University. Her interests lie at the intersections of science, policy, and design. Dr. Yajima’s postdoctoral work as a Science & Design Research Scholar at Stanford University’s Center for Design Research investigated how design practices can catalyze scientific research and innovation; additionally, she has been an Associate Program Director at the American Association for the Advancement of Science in Washington, DC, and served as a science policy fellow at the National Academy of Sciences. She currently works on human-centered drug discovery research and translational medicine as a Director at Stanford’s SPARK Translational Research Program while also serving as a member of the Global Young Academy, an organization for young scientists to lead intersectional dialogue to diversify global decision-making.

Milan Karol

Senior Development Officer, Carnegie Institution for Science

Mr. Karol received an MS in Library and Information Science from the University of Illinois at Urbana-Champaign. Throughout his career, he has become an experienced development officer and fundraiser in various environments, from working as a Sales Representative for a company in the software industry, to working as a Development Officer at two liberal arts colleges, to raising philanthropic dollars for medical research at Johns Hopkins Medicine. Currently, he is the Senior Development Officer for the Carnegie Institution for Science, building relationships and working with donors and philanthropists to achieve institutional goals.

2019

Career Exploration and Planning

Stanford University

Spring 2019: BIO380

Description: Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions, discuss various career options with a PhD in life sciences, and learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to PhD students in Biosciences programs. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305.

Requirements: Students are expected to attend all class meetings, actively contribute to group discussions, and to give a short group presentation on the final class meeting.

Schedule

April 4 — Introductions

Introduction to the structure and context of the course, as well as an excellent opportunity for participants to get to know one another. We will go over requirements and expectations of the course, complete a preliminary survey, and engage in small group activities discussing career opportunities in the life sciences, personal/professional dreams, and how to find an overlap between the two.

April 11 — Myers-Briggs Type Indicator Test

The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Staff from Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.

April 18 — Career Panel I: “Policy, Administration, and Scientific Journalism”

Policy: Mary Maxon, Ph.D. Associate Laboratory Director, Biosciences Labs at UC Berkeley
Govt Program Management: Devaki Bhaya, Ph.D. Adjunct Staff Scientist, Carnegie Institute for Science, Department of Plant Biology
Science Writing: Amy Adams, M.S. Director of Science Communications, Stanford University
Academic Administration: Rieko Yajima, Ph.D. Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University

April 25 — Career Panel I Decompression

Group discussions to follow the “Policy, Administration, and Scientific Journalism” panel. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.

May 2 — Introduction to Final Presentations/Career Planning Lecture

Final Presentation projects will be assigned and expectations will be discussed. In addition, there will be a lecture on career planning to introduce students to key concepts and tools that are useful in professional development, with group discussions to follow.

May 9 — Career Panel II: “Business”

Venture Capital: James Zhang, Ph.D. Chief Strategy Officer, Centrillion Technologies Inc., and Partner, GRC Fund
Patent Law: James Keddie, Ph.D. Senior Patent Agent, Bozicevic, Field & Francis LLP
Industry: Lee Chae, Ph.D. Co-Founder and CTO, Brightseed
Entrepreneurship: Fred Hempel, Ph.D. Co-Owner of Baia Nicchia Farm and Artisan Seeds
Industry administration: Malavika Kannuswamy, M.S. Associate Director, Portfolio Planning and Program Management, Denali Therapeutics

May 16 — Career Panel III: “Research”

Academic Research: Ashby Morisson, Ph.D. Associate Professor of Biology, Stanford University
NGO Research: Rebecca Shaw, Ph.D. Senior Vice President and Chief Scientist, World Wildlife Fund
Government Research: John Vogel, Ph.D. Staff Scientist, Joint Genome Institute, and Adjunct Professor, UC Berkeley Department of Plant and Microbial Biology
Teaching: Jesse Miller, Ph.D. Lecturer, Stanford University

May 23 — Career Panels II & III Decompression

Group discussions to follow the “Business” and “Research” panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.

May 30 — Student Final Presentations

Notices

Disability Access: Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email (oae-contactus@stanford.edu), or phone (650-723-1066).

Honor Code: Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.

Scientific Writing Workshop

Carnegie Institution for Science, Department of Plant Biology

Summer 2019

Carnegie Scientific Writing Workshop Syllabus

Overview: To become a successful scientist, we must write well and effectively communicate our work to a broad audience. Nevertheless, many of us do not receive official training on the fundamentals of scientific writing, and as a result struggle to highlight the significance of our work. This summer, we are offering an intensive scientific writing workshop to help you set up a writing routine, improve your writing, and gain the tools and confidence you need to become a leader in your field. * In-class exercises and lessons will be adapted from Anne E.Greene’s book titled Writing Science in Plain English.

Schedule and Location: The Carnegie scientific writing workshop is a 10-week series starting June 28th, 2019. Meetings will be held in the Carnegie Institution for Science’s Plant Biology Department Seminar Room (260 Panama Street, Stanford, CA, Building 600) on Fridays from 3-5pm.

Topics:

Week 1 (6/28): Introduction to creating a compelling narrative

Discuss the overview, goals and expectations of the writing workshop
Form scientific writing groups based off of writing experience and document type
Setup electronic folders for submitting writing material
Discuss how to tell your scientific story
- Identifying your audience
- Informal vs. formal register
- Determining your tone
- Defining subjects and action verbs
- Using active vs. passive voice
- Benefits of short vs. long words
- Simplifying noun strings
- Defining technical terms
- Concise writing
- Using transition statements
- Affirmative vs. negative statements
In-class writing exercises

Homework for next class: Create a scientific storyboard

Week 2 (7/12): Workshop Scientific Storyboard

Present scientific storyboards in writing groups
Discuss Background and Significance
- Identifying the scope and structure
- Incorporating new vs. old information
- Highlighting deficiencies in current knowledge and understanding
- Justifying your project
- Using parallel writing structures
In-class exercises

Homework for next class: write up a draft of your background and significance section

Week 3 (7/19): Workshop Background and Significance Sections

Review the Background and Significance section for two people in each writing group
Discuss designing paragraphs
- Identifying the issue
- Development phase
- Conclusion sentences
- Coming to the point
In-class exercises

Week 4 (7/26): Workshop remaining Background and Significance Sections

Review the Background and Significance section for remaining people in each writing group
Discuss different ways to arrange paragraphs
- Chronological order
- Broad ideas to narrow ideas
- Least important to integral information
- Problem to solution
- Compare and contrast
- Transition statements associated with different paragraph styles
In-class exercises

Homework for next class: write up a draft of your Results and Approach

Week 5 (8/9) Workshop Results and Approach

Review the results and approach section for two people in each writing group
Discuss useful tips for making figures and figure legends
- Identify your message
- Writing strong captions
- Writing stand alone text
- Data visualization
In-class exercise

Week 6 (8/16): Discuss Authorship, Publishing, and Reviewing/ Wine tasting

Using a few case scenarios, we will discuss topics relevant for publication

Discuss available authorship guidelines from journals and scientific societies
Discuss the process of publishing and reviewing

Week 7 (8/23): Workshop remaining Results and Approach

Review the results and approach section for remaining people in each writing group
Discuss how to organize a discussion and impact

Homework for next class: write up a draft of your discussion and impact

Week 8 (8/30): Workshop Discussion and Impact sections

Review the discussion and impact section for all people in each writing group
Discuss how to write an abstract

Homework for next class: write an abstract

Week 9 (9/6): Workshop Abstract sections

Review the abstract sections of all writing group members.
Introduce how to write a cover letter

Homework for next class: write a cover letter

Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript

Review the cover letters for all members in the writing group
Discuss how to review a manuscript

Calendar

Websites

Main Lab Projects

Collaborative Projects

Lab Members

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 (Postdoctoral Fellow)
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.
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!
Maxwell Eckelbarger (Research Assistant)
My name is Maxwell Eckelbarger, and this year I am a sophomore at Stanford University studying a self-designed major called Botanical Engineering. I am from Spencerville Indiana and grew up on a farm and in the forests, and this instilled in me a love for nature and plants. I want to study how plants and other biological vectors can be used to fix environmental issues and repair Earth's ecosystems and make modern life more sustainable. I am most interested in cold sensation and toxin processing in plants' secondary metabolism as of recent. I am also an art minor and pursuing a notation in science communication, and am passionate about communicating science to the public through images.
Emily Fryer (Research Assistant)
I received my B.S. in Biology concentrating in Ecology, along with a minor in Computing from San Francisco State University in Fall 2018. During my undergrad I was a member of the CoDE (Coding to Understand Disease Evolution) lab where I was introduced to the principles of population genetics and computational biology. My research focused on utilizing computational methods to understand the fitness costs associated with drug resistance mutations in HIV. In addition I've had the opportunity to dabble in front-end web development, data mining and topic modeling to understand sentiment on social media. My passions have always been rooted in the world of plants, their ecology and coevolution with other organisms. I am excited to be a member of the Rhee lab where I will apply computational methods to understanding metabolic processes in plants. My ultimate goal is to pursue a PhD and am interested in understanding the effect of varying ploidy levels on evolution. In my spare time I enjoy hiking, baseball, cooking and grazing my way through the culinary savanna of the the Bay Area.
Danny Ginzburg (Research Assistant)
I was born and raised in Chicago. I did my undergrad at Northwestern where I studied Earth Sciences and Environmental Policy. I then worked as a sustainability data analyst for 2 years before moving to Israel to get my masters degree in agricultural sciences at Hebrew University's Faculty of Agriculture. I completed my graduate research at the Israel Ministry of Agriculture studying the 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.
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.
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.
Justin Krupp (Bioinformatics Research Assistant)
I graduated from UCSC with a bachelor's in bioinformatics back in June, 2019. While I was in school, I worked part-time for the UCSC Genomics Institute, developing the Human Cell Atlas data storage system. I wrote tests, implemented continuous integration infrastructure into a few repositories, and designed coding examples to show consumers how to use the Human Cell Atlas API. Outside of work, I was involved in several extracurricular activities, including the UCSC Bioinformatics Club (which I co-founded along with several other classmates). The club turned out to be a smashing success, and we were able to both spread interest in the field as well as help our underclassmen excel in their studies.

My interests don't stop at bioinformatics, either. I took three years of Japanese during my undergraduate career, and even acted in a multilingual theater performance. Beyond that, I taught myself piano and have been playing since freshman year in high school. I'm also a massive nerd when it comes to tabletop games, and I always enjoy a long, 3-4 hour match of commander in Magic: The Gathering.
Elena Lazarus (Research Assistant)
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.
Olivia MacDonald (Research Assistant)
I graduated from UC Berkeley in 2019 with a bachelor’s degree in Molecular and Cell Biology and a minor in Forestry and Natural Resource Management. My love for plant biology was cultivated through my undergraduate research at the UC Berkeley Plant Gene Expression Center in the Hake Lab that culminated in a post-graduate summer fellowship. After graduation, I took a leap into a field completely unfamiliar to me- merging cutting edge biochemistry with machine learning- as a Research Lab Technician at Google Accelerated Science. I am excited for the next step in my career as a research assistant in the Rhee Lab, where I hope to build on my past experiences and contribute to meaningful research in plant biology. In the future, I aspire to obtain my PhD and dedicate my career to elucidating information about plant systems and their responses to disease, drought, and stress - especially in the context of climate change. Outside of work, I enjoy sailing on the San Francisco Bay, backpacking, and tending to my ever growing jungle of houseplants.
Karine Prado (Postdoctoral Fellow)
I received my PhD from the University of Montpellier (France) where I studied the molecular and cellular mechanisms controlling the hydraulic properties of Arabidopsis thaliana rosette in response to environmental stresses. Then I joined the University of Edinburgh (UK) as a postdoctoral research associate. I studied the contribution of non-transcriptional mechanisms to biological timekeeping of the pico-alga Ostreococcus tauri that has become a new relevant model for plant Systems Biology. Then I studied how light and thermo-sensitive phytochrome photoreceptors regulate chloroplast RNA processing and photosynthesis.

At the Carnegie Institution, I am going to study mechanisms of thermoadaptation of a desert extremophile C4 plant. The long term goal of this project is to improve crops and to address relevant challenges in response to worldwide climate changes.

When I am not working in lab, I like hiking, dancing, swimming, reading and watching movies.
Selena Rice (Biocurator)
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.
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.
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!
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.
Bo Xue (Research Assistant)
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 information from data has always been interesting to me and after working at the Chinese Academy of Science on 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 project, mainly the Plant Metabolic Network. Which includes developing computational pipelines and visualization of our databases. If I'm not working, you'll probably find me trying to catch a movie. I love the theater going experience.
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.

Publications

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.

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 In press. bioRxiv 2020.08.07.242172; doi: https://doi.org/10.1101/2020.08.07.242172
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. bioRxiv: doi: https://doi.org/10.1101/2020.04.27.063495 [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. bioRxiv: doi: https://doi.org/10.1101/2020.02.03.931444 [full text]
Zhao K and Rhee SY* (2019) Epigenomic Landscape of Arabidopsis thaliana Metabolism Reveals Bivalent Chromatin on Specialized Metabolic Genes. bioRxiv 589036; doi: https://doi.org/10.1101/589036 Under revision.
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]

Selected recent reviews and perspectives

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]
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]
Rhee SY and Mutwil M* (2014) Towards revealing the functions of all genes in plants. Trends in Plant Science 19(4):212-221. [pdf]

***ALL PEER REVIEWED PUBLICATIONS (* corresponding author)***

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 (2021) Plant Single-Cell Solutions for Energy and the Environment. Communications Biology Accepted.

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* (2020) Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress. Cell In press. bioRxiv 2020.08.07.242172; doi: https://doi.org/10.1101/2020.08.07.242172

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. bioRxiv: doi: https://doi.org/10.1101/2020.04.27.063495 [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. bioRxiv: doi: https://doi.org/10.1101/2020.02.03.931444 Genes|Genomes|Genetics 10(7): 2411–2421

Zhao K and Rhee SY* (2019) Epigenomic Landscape of Arabidopsis thaliana Metabolism Reveals Bivalent Chromatin on Specialized Metabolic Genes. bioRxiv 589036; doi: https://doi.org/10.1101/589036 Under revision.

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

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
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

Software

This page lists and makes available the programs we have developed in our lab.

Title	Description	Software
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	A machine learning algorithm to prioritize causal genes in quantitative trait loci. [README]	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

Join Us

We always look forward to adding new members to the team as openings become available. If you are interested in joining our group, please feel free to send an email to Sue Rhee. We encourage and welcome students and postdocs 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:

Scientific Coordinator

Computational Biology Postdoctoral Position to Model Metabolic Networks of C4 Photosynthesis Plants under Drought and Heat

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 are accepted between Jan 1 to March 31. Applicants can send a cover letter and CV to Dr. Sue Rhee (srhee at carnegiescience.edu) Interviews are conducted during April and decisions are made by April 30 and notified during the first week of May. 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 Aug where the interns show off their work and the entire Carnegie and Stanford plant community is invited.

Expectations

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

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

Diversity Pledge

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:

Educating yourself about racial justice and systemic discrimination against marginalized communities.
Participating in the Diversify Plant Science Initiative from ASPB.
Listening to and uplifting voices from these communities even when they challenge your assumptions and make you uncomfortable.
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).
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).
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):
- Fellowship for the Future by 500 Women Scientists
- Black Girls Code
- SACNAS

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.

I COMMIT TO THESE ACTIONS

Art Gallery

Talks

Talks:

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
- Dr. Michael Freeling is a professor of biology at University of California at Berkeley. Here he talks about how he started his career in science and the fascinating and wonderful paths and discoveries he made along the way. Currently, he is actively engaged in using plant comparative genomics to test evolutionary hypotheses, and often focuses on conserved noncoding sequences.
Living Legends: Charley Yanofsky, 2010
- Dr. Charley Yanofsky, professor emeritus of biology at Stanford, talks about his illustrious career in science. The combined use of genetics, biochemistry and molecular biology led his group to elucidate the beautiful and elegant pathway of making an essential amino acid, trypophan. Along the way, he has made some seminal, Nobel-prize worthy discoveries such as the experimental proof of the one gene-one protein hypothesis, in vivo confirmation of the genetic code and discovery of transcriptional attenuation. He has influenced hundreds of world-class scientists directly through training and thousands of students through teaching and hopefully millions of aspiring scientists through this video.

Movies

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Lab Tabs

Research Interests: 2002 | 2005 | 2009 | 2012

Research Interests (JANUARY 2019)

On training…

Senior Staff Scientist

Profile

2020

2019

Scientific Writing Workshop

Carnegie Scientific Writing Workshop Syllabus

Week 1 (6/28): Introduction to creating a compelling narrative

Week 2 (7/12): Workshop Scientific Storyboard

Week 3 (7/19): Workshop Background and Significance Sections

Week 4 (7/26): Workshop remaining Background and Significance Sections

Week 5 (8/9) Workshop Results and Approach

Week 6 (8/16): Discuss Authorship, Publishing, and Reviewing/ Wine tasting

Week 7 (8/23): Workshop remaining Results and Approach

Week 8 (8/30): Workshop Discussion and Impact sections

Week 9 (9/6): Workshop Abstract sections

Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript

Main Lab Projects

Collaborative Projects

Selected recent references

Selected recent reviews and perspectives

ALL PEER REVIEWED PUBLICATIONS (* corresponding author)

Book chapters and other publications

POPULAR SCIENCE ESSAYS

Databases and Bioinformatics Tools

Collaborative Projects

Outreach in the Rhee Lab

outreach projects

***ALL PEER REVIEWED PUBLICATIONS (* corresponding author)***