People



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.

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.

Jianjun (Jim) Guo (Postdoc) I was drawn to plant molecular biology by my aspiration to understand and discover how living organisms operate at the molecular level. Driven by this aspiration, I did my Ph.D. with Dr. Jin-Gui Chen at University of British Columbia, Canada, where I studied the function of a small gene family RACK1 (Receptor for activated C-protein kinase 1) in abscisic acid-mediated stress signaling in Arabidopsis thaliana. Upon graduation, I obtained a two-year post-doctoral fellowship from NSERC (Natural Sciences and Engineering Research Council of Canada). I spent my first year in Dr. Jen Sheen’s group at Harvard University, where I focused on using transient expression system to probe the molecular function of genes involved in KIN10-mediated stress and energy signaling pathway. Seeing the potential of bioinformatics and statistics in deciphering the molecular network that directs plant traits, I did my second year of the NSERC fellowship in Dr. Gerald A Tuskan’s group at Oak Ridge National Laboratory (ORNL). At ORNL, I learned how to use genome wide association study to identify genes associated with increased biofuel production in Populus trichocarpa and characterized the function of these genes using protoplast transient expression system.

I was attracted to Prof. Rhee’s group by her reputation in developing and implementing computational tools to effectively guide the functional characterization of genes and networks. Her group offers me a great opportunity to explore approaches to effectively bridge computational biology and experimental biology, plus a pleasant and stimulating working environment. Currently, I am interested in combining the genetic association and network-guided association methods to identify novel genes/pathways involved in plant adaptation to abiotic stress conditions, and characterizing their mode of function using genetic, molecular and cellular biological approaches.

I have been an indoor person outside of my research life, enjoying the muscle sore after a workout. I have been spending much more time outdoors since I came to Palo Alto. I can’t resist the temptation of the delightful weather. The good news is: there is no lack of outdoor places to explore in California!

Hye-In Nam (Research Assistant) 

Caryn Johansen (Research Assistant) I received my B.S. from Humboldt State University in Cellular and Molecular Biology with a minor in chemistry in May 2012. In 2009, I had the opportunity to work on metabolic engineering of cyanobacteria to create biofuels in Ruanbao Zhou’s lab at the South Dakota State University. This internship piqued my interest in metabolic engineering and has helped shape my interest in biotechnology as a tool for addressing social and economic issues. My interest in plant genetics began in college after writing a research paper on Ug99, a particularly threatening strain of wheat rust. It opened my eyes to the risk that pathogens and abiotic stresses have on world food supply. Plants, as sessile organisms, have intricate response mechanisms and my interest in how plants can interpret and respond to their environment led me to Sue Rhee’s lab. The research I do in her lab on how Arabidopsis response to abiotic stress is invigorating and challenging, and I hope to expand on this topic in graduate school.

I have always been inspired by my experiences outdoors, especially from growing up in the Jemez Mountains of New Mexico. Now, I feel lucky to live in California, where fresh fruits and vegetables are abundant and the landscape is calling for adventure. Outside of work, I enjoy hiking, rock climbing, biking, running, ultimate frisbee, gardening DIY projects and origami. I’m currently teaching myself to play the ukulele, the to chagrin of my housemates.

Jue Fan (Postdoc) I got my B. Sc from University of Science and Technology of China (USTC) and a Ph.D in Computational Chemistry from Clark Univeristy. My Ph.D. work in Dr. Sharon Huo's group focused on studying the structural properties of biomolecules using computational tools. The folding of individual proteins could have a large impact on the  organism as a whole, and understanding protein folding may facilitate drug design to target misfolded proteins associated with deseases. We use graphs to represent the complicated networks of protein conformational changes.

Along with the interests in structural biology, I am always curious about a broader and more general field of bioinformatics. To learn biology and master bioinformatic approaches, I joined Dr. Sue Rhee's lab in May 2013. This is a perfect place for me to seek more knowledge and skills in the area, because everyone in this group has a very unique background, ranging from experimentalists, computational biologists, and computer scientists. My project in Dr. Rhee's lab is to prioritize candidate quantitative trait genes (QTGs) of a C4 model plant Setaria by integrating different levels and types of evidences into consideration. I also work on analyzing transcriptomic and genomic differences of two ecotypes of Arabidopsis thaliana that have adapted different strategies to deal with salt stress.

I am a curious person and I'd like to explore anything unknown. In my spare time, I love to travel, both in cities and national parks. I also like to read novels and watch sports.

 

Chuan Wang (postdoc) I got my B.Sc. in Biology from China Agricultural University, I worked on sequence alignment algorithms towards the goal of obtaining better fold recognition and alignment accuracy. I have also been developing methods for identifying new members of protein families using structural alignments (e.g. WD40-containing proteins).

I joined Sue Rhee's group in October 2012. I am developing better methods for predicting transporters and their detailed functions, so that we can include them for reconstructing metabolic networks.

I study, I work, and I play a lot. Karaoke is my favorite and I am really a good singer. I also dance, and play badminton. I have been travelling through places and trying so many different things since I met my wife Lan and waved computer games good bye in 2006. I love her and my family.

Michael Banf (Postdoc) During my Ph.D., I enjoyed reading about a wide variety of fields in science and stumbled upon Genetics. As a computer scientist with a background in Electrical Engineering, I became increasingly fascinated about how information is encoded in the DNA and the circuit-like genetic pathways and networks in biological systems. I started asking questions about how machine learning and mathematical modeling can contribute to the analysis of the regulation of these complex mechanisms. In finishing my Ph.D. project on auditory image understanding for the visually impaired, I started searching for a postdoctoral position in the area of computational systems biology and came across the Rhee lab.

The lab is engaged in systematically elucidating the regulation of metabolic and signaling pathways in plants using experimental as well as computational approaches, which allows me to start my research on developing computational models of transcriptional gene regulation in these pathways and collaborate with experienced biologists. The focus on plants is a great research opportunity, because little is known about the regulatory mechanisms, in comparison to animals and microbes, although plants provide the essentials to allow life on Earth.

Apart from the scientific stuff, I love to read inspiring biographies or the works by great analytical thinkers, such as J. Polkinghorne, C.S. Lewis or B. Pascal, on some of life’s tough questions. To clear my head, I enjoy training Krav Maga, playing the piano, watching movies or Brazilian Jiu-Jitsu and listening to music… especially Hans Zimmer soundtracks.

  Bernard Hauser (Visiting Professor, University of Florida, USA)
  In-Seob Han (Visiting Professor, Ulsan University, Korea)

Group Photo, Summer of 2013

 From left: Sue Rhee, Hey-In Nam, Lessley Peterson, Jim Guo, Catherine Doyle, Lan Jiang, Flavia Bossi, Chuan Wang, Caryn Johansen, Lee Chae, Taehyong Kim, Meng Xu, Jue Fan, Kate Dreher, Peifen Zhang, Ricardo Nilo Poyanco