Research Interests (June 24, 2009): How do plants and humans decide?
Two things drive my research these days. One is a desire to uncover the mysteries of how plants process the myriad of information from their environment and reprogram their growth and development. I am fascinated with how plants decide. The other is a desire to uncover the potential for greatness in emerging scientists. I am fascinated with how humans, in particular scientists, decide.
I am trying to engage these two drivers in designing projects to foster the diverse interests of individual members of my group, ranging from evolution of pathways to mechanisms of gene regulation, and to capitalize on the diverse training backgrounds in the group, ranging from molecular biology to physics.
Naturally this network of inspiration lends itself to projects that can be described as a series of Venn diagrams where the intersections represent collaborative and integrative projects among the members. I believe that the union will help satisfy the two driving forces of my research program. Also turnover of lab members over time serves as natural check points and selective forces on the evolution of our collective knowledge and expertise.
We employ several methods in our quest: 1) combination of computational modeling and targeted experimental testing in the lab; 2) systematic collection of large-scale data needed for the modeling through collaboration with other labs; 3) robust, quantitative analysis of the data and the models.
Here are examples of the ‘intersecting’ projects in our group to illustrate the types of questions we are asking and approaches we are taking.
- The quest for novel biological processes
- Systematic discovery of the role of protein degradation in response to the environment
- Exploring the power of metabolomics in dissecting genetic interactions
- Systematic discovery of signaling pathways and complexes (Lalonde et al, 2010)
- Genome-wide gene association network (AraNet) (Lee et al, 2010)
- Network-guided reverse genetic screening (Lee et al, 2010)
- Automated metabolic network generation from a set of protein sequences (Zhang et al, 2010)
- Discovering missing links in gene expression clusters (Chen et al, 2009)
I expect that many of the current projects will leave along with the lab members to establish their own groups. I am humbled by so many intriguing, unsolved problems in plant biology and am brewing some concrete ideas about the following topics currently, which may or may not become major projects in my group in the next several years.
- Systematic discovery of novel reactions and pathways
- Determining the “key” players in functional modules
- Mechanism of cross-talk between exogenous and endogenous signals for growth and development
- Mechanism of genome-wide homeostasis against genetic and environmental variation
My group has two types of trainees: postdoctoral researchers who are in their last leg 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.
In general, my style is to give as much independence and freedom on establishing problems, outlining approaches, designing and executing experiments and interpreting results. Depending on the level of need, I help out in all of these aspects. I meet with each member weekly and we have a weekly group meeting where each person rotates in presenting their work to get feedback from the group. The individual meetings are almost always driven by the individual and he or she decides what to discuss with me and what sort of feedback they’re looking for. I almost never approach the individual to ask what is going on, but rather have an open door policy. Basically I leave people alone, but am cognizant of the scientific questions they’re asking and the problems they’re facing.
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.
As a Carnegie Scientist, I am not obliged to teach. Nonetheless, our department’s affiliation to the Biology department of Stanford encouraged me to start teaching seminar courses for incoming undergraduates. Starting spring of 2010, I am teaching a seminar called “Networks in Biology” (BIO39N). The course description is as follows:
Networks are everywhere: Friendship links on Facebook, airline routes, power grids, the Internet, the Web, highway systems. The list goes on. Biology is no exception. Food chains, protein interaction maps, metabolic pathways are examples of networks in biology. Despite their ubiquitousness, the study of networks in the real world only started about a decade ago. Exploration and exploitation of network analysis in biological systems is only at its infancy. In this course, we will explore the types of networks in biology and the approaches people are using in studying them through discussions and presentations of original research papers.
Starting spring of 2013, I will also be teaching a freshmen seminar called "Creativity in Biology". Its course description is as follows:
Can creativity learned? This course will explore how we can learn to be creative in biology. We will use steps described in 'Borrowing Brilliance' by David Kord Murray to go through the motion of coming up with a creative solution for a problem. The class will collectively choose a problem to work on as a group. Examples of overarching problems include, but not limited to, energy limitation, food security, species conservation, and climate change. Once we settle on a problem, students will work in teams to find similar problems and solutions in other fields, and construct a new solution together. Finally, students will debate positive and negative aspects of the solution in teams to refine the solution. Students will work in small groups to research and report their findings to the whole class each week. Through this process, they will gain experience in reading primary literature, innovative thinking, speaking and listening skills. The 'final' will be a group presentation of the class’s solution to 'experts', several professors and other professionals working in related fields in the bay area.
Recent references (All references)
- Hwang S, Rhee SY, Marcotte, and Lee I (2011) Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nature Protocols. 6(9):1429-1442. [pdf]
- 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. [pdf] [supplemental info]
- Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi MA, Parsa SA, Kim D-Y, Acharya BR, Stein EV, Hu H-C, Villiers F, Takeda K, Yang Y, Han YS, Schwacke R, Chiang W, Kato N, Loqué D, Assmann SM, Kwak JM, Schroeder J, Rhee SY and Frommer WB (2010) A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2. Frontiers in Plant Physiology. 1(24):1-14. [pdf]
- Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiology. 153(4):1479-91. [pdf]
- 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 [pdf]
- AraNet (gene functional associations)
- Plant Metabolic Network (metabolic pathways)
- Plant Metabolomics Consortium (metabolomics)
- Associomics Consortium (protein-protein interactions)
- The Arabidopsis Information Resource (model organism database)
- Gene Ontology Consortium (ontologies)
- Chae L, Lee I, Shin J, Rhee SY (2012) Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology. 15:177-184. [pdf]
- Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St. Pierre S, Twigger S, White O, Rhee SY (2008) The future of biocuration. Nature. 455:47-50. [pdf]
- 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. [pdf]
- 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 [pdf]
- Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360 [pdf]
- 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. [pdf]
- Bard, JL and Rhee, SY (2004) Ontologies in biology: design, applications and future challenges. Nature Review Genetics 5(3):213-22. [pdf]
- Rhee, SY (2004) Carpe Diem. Retooling the Publish or Perish Model into the Share and Survive Model. Plant Physiology. 134(2):543-7. [pdf]