Flavia Bossi (Postdoc) 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.

Lee Chae (Postdoc) I grew up in California’s San Joaquin Valley, an area dominated by agriculture and the Yosemite, Sequoia, and Kings Canyon National Parks. I believe this early landscape led naturally to my interest in studying plants. In Zheng-Hui He’s lab at San Francisco State University, I used molecular genetic techniques to investigate the effect of environmental stress on a family of genes in the plant Arabidopsis thaliana. In the doctoral program in Plant Biology at UC Berkeley, I had the good fortune of training within the Graduate Group in Computational and Genomic Biology and working with a broad range of scientists, including my advisors Sheng Luan, Steven Brenner, and Sandrine Dudoit. From these experiences, I learned how to integrate experimental, statistical, and computational approaches when addressing questions in plant biology.

At the Carnegie, I work with Sue Rhee, who has cultivated a group that also crosses disciplines in terms of experimental and computational plant biology. My work with Sue falls broadly within the fields of plant comparative and computational genomics, with a particular focus on plant metabolism. Specifically, I’m interested in the metabolic strategies that plants use to successfully complete their life cycles within their given environments, how these capacities differ among species and across environments, and what mechanisms led to the appearance of these processes within the plant evolutionary lineage.

Outside of the serious stuff, I’m currently interested in the following, although the list changes every so often: beer, bike camping, cheese, cooking, kitchen gardening, 70s country music, early-80s post-punk music, and wool shirts. I’m trying to add sewing to the list, but with mixed results so far.

Taehyong Kim (Postdoc)  When I was a 5th-grade elementary school boy, I was so absorbed in spending time on a ‘computer’ (I think that it was more like a complex calculator at that time). I have totally indulged in simple computer games and programming on a black and white monitor. Indeed, I took BASIC programming classes after-school to develop calculators, games and so on. That was my first temptation and motivation to the life of my current career.

During my Ph.D. research in the department of computer science at SUNY Buffalo, I learned that tremendous knowledge could be obtained from dynamic interactions in nature, which contains invaluable but extremely huge amount of data. In fact, with the recent success of biotechnology, massive data are created and queuing up for analysis every day. The fascinating part of computational biology is that hundreds of thousands of data could be evaluated and analyzed in a timely manner, which would not even have been imagined without the help of computational analysis. I am interested in understanding dynamic relations of living organisms using network representation of cells, proteins and metabolites. Since I joined the Rhee Lab, I have been working on the metabolic networks of Arabidopsis by knocking out genes to characterize the changes in the metabolic network and eventually infer functions of unknown genes with metabolic profiling.

For most of my spare time, I am trying to enjoy the beautiful Californian mountains, parks and beaches with great sunshine. I also like listening to music, singing songs, having beer with friends, jogging, golfing and so on.

Peifen Zhang (Director, Plant Metabolic Network)

I love the pure beauty of plants and flowers, and am amazed by the modern techniques in molecular biology in seeking out answers to the ‘what’ and ‘how’ questions. I chose to focus on plant genetics for my Ph. D. thesis and had the good fortune of training with Tom Peterson at Iowa State University. I learned how to connect the dots and make a fact-backed story. After some additional years of postdoctoral research, I no longer had the extreme but necessary patience waiting for results at the bench, nor the nerve to take the seemingly endless failures of experiments. So I moved on to the field of bio-database development and biocuration and was fortunate enough to work on the TAIR and, later, PMN projects. I enjoy, very much, the multidisciplinary environment of bio-database development and biocuration, ranging from wet-lab results, to computational predictions, to ontology development and database implementation, and overall, the operation as a whole.

Outside of work and two small kids, I am interested in observing things that are visually beautiful, architectures of houses and gardens, interior designs and more.

Kate Dreher (Curator, Plant Metabolic Network) After entering Williams College with at least five majors in mind, varying from history to math, I started down the path to further studies in plant biology based on a senior research thesis that I did with Dr. Marta Laskowski that focused on transcripts rapidly up-regulated by auxin in Arabidopsis and in response to a course that I took on developmental economics with Dr. Douglas Gollin. Their teaching helped me to realize how eager I am to help uncover the intricacies of complex biological systems, yet how concerned I am about trying to connect our scientific investigations to the resolution of real-world problems related to malnutrition and sustainable development.

After graduating from college, I got to try to combine these two interests while working at an international maize and wheat research center in Mexico called CIMMYT (Centro Internacional de Mejoramiento de Maiz y Trigo). But, after a year, I returned to the field of auxin signaling and again carried out research using our favorite mustard-like model weed in graduate school at UC Davis. I enjoyed gaining a new perspective on the important regulatory role of ubiquitin-mediated protein degradation while studying in the lab of Dr. Judy Callis.

After turning in my graduate thesis, I wanted to continue to learn about and explore new scientific discoveries without necessarily having to perform wet lab experiments. Plus, I felt excited by the prospect of trying to help make valuable sources of data more available and understandable to scientists and students around the world at the Plant Metabolic Network and at TAIR. I hope that these resources facilitate basic and applied research that will lead to more biotic-and abiotic-stress tolerant crops that can grow on more marginal soils while producing higher yields and more nutritious crops. So, whether I am entering information about an individual enzyme’s activity, trying to improve the quality of computationally predicted metabolic pathway databases for different plant species, answering questions from researchers around the world, delivering seminars at conferences, colleges, or crop improvement centers, or working with public high school teachers to bring plant metabolism into their classrooms and their students into our research labs, I am grateful to be part of our team!

Outside of curating, I try to help promote environmentally friendly practices at work and in the community, I organize Peruvian tamale lunches, I listen to lots of NPR/PRI/APM, and and I’m a sucker for salsa, swing, or other styles of dancing and word games like cryptic and standard crossword puzzles, Scramble, and Scrabble.

Meng Xu (postdoc) I got my Ph.D. from University of Science and Technology of China (USTC), where I did experimental work on protein x-ray crystallography for a year and then turned to computational research. Fascinated by the complex nature of biological networks, I compared protein-protein interaction (PPI) networks among different species to find conserved subnetworks, and investigated the coevolution between interacting proteins.

I joined Sue Rhee's lab in November 2011 to continue research on biological networks. My work with Sue includes building membrane PPI network of Arabidopsis thaliana from large-scale yeast two hybrid array data using split ubiquitin system, and finding new functional modules by probing other biological information(e.g. metabolic pathways, Gene Ontology annotations, etc.). We are also interested in correlations among different functional modules at a system level. I would like to build biological models based on computational and statistical research and test them using experimental approaches.

Usually, I don't separate work and life very clearly. But I do have hobbies after turning off my laptop. I love gardening(especially orchids like Phalaenopsis and Dendrobium), sports(swimming, jogging, table tennis) and cooking for my family (grateful my wife and son for not complaining about that).

Ricardo Nilo Poyanco (postdoc) Plants are fascinating organisms that display an enormous variability from region to region. As a child in Brazil, I became familiar with its landscape, full of huge green plants adapted to a considerable precipitation level throughout the year. Then, I came back to Chile, where I was born, and found vegetation adapted to much drier conditions, especially during the summer. Such plasticity has always been intriguing to me, and hides a potential that is still far away from being known, even though it could be helpful both to benefit humanity and to improve our relationship with our environment.

The opportunity to work in such an interesting and dynamic field arrived at the end of my undergraduate studies, with a thesis entitled “Development of Methodologies to Study the Subcellular Localization of Proteins Involved in Plant non-cellulosic Polysaccharide Biosynthesis”. Subsequently I shifted to an area related to fruit ripening, an important field for Chileans due to the importance of fruit exportation for this country. This work culminated with a graduate thesis entitled “Proteomic analysis of Prunus persica fruit softening and chilling injury” and a subsequent analysis of Vitis vinifera leaves responses to high light stress. During this work I realized the relevance of bioinformatics tools to fully exploiting the data derived from large scale analyses such as those derived from the different omics approaches. Therefore, I decided to move to a laboratory mainly devoted to this area at the beginning of the year 2012. 

Dr. Rhee’s lab combines nicely the characteristics that I was looking for: a place where several bioinformatics tools and approaches are used to construct and validate metabolic pathway network databases for plant species with a sequenced genome, an approach that will help in the understanding of the processes that make plants so plastic. In addition, it has an amazing location, Palo Alto, California, a beautiful place to live. I am enjoying my stay here, which hopefully will help me to be a good scientist and, more importantly, a better person.

Hye-In Nam (Research Assistant)

Tam Tran (Research Assistant)

Damian Priamurskiy (Intern, the Plant Metabolic Network)

Group Photo, Spring of 2012

 From left: Ricardo Nilo Poyanco, Hye-In Nam, Kate Dreher, Flavia Bossi, Peifen Zhang, Sue Rhee, Taehyong Kim, Meng Xu, Lee Chae