Ecker Lab > Personnel
Lab Members
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Junshi Yazaki |
Junshi Yazaki earned his Ph.D. at the University of Niigata, Japan, investigating the structures and functions of nutrition stress induced protein in mycobacterium. He then started rice genomics studies with whole genome EST mapping, full-length cDNA collections and transcriptome profiling at National Institute of Agrobiological Sciences and Institute of Society for Techno-Innovation of Agriculture, Forestry and Fisheries both in Tsukuba, Japan. Junshi joined the Ecker lab in 2005 with a research interest focusing on Systems biology using genomics strategies. As a first project in the lab, Junshi developed DNA methylome profiling integrated with transcriptome map in Arabidopsis - the first of its kind for any organism, using whole genome tiling array technologies in 2006 as collaboration with the Jacobsen lab. Currently Junshi is working towards generating the first high-confidence binary protein-protein interaction network map using Arabidopsis ORF clone collections. In collaboration with the lab of Dr. Marc Vidal at CCSB, two orthogonal screen-based approaches, a matrix-based Y2H strategy and protein microarray technology, are being employed toward creating such a resource. He aims to integrate all these “omics” data including methylome, transcriptome and interactome for system-level approaches in biology, and to target the important trait loci for agriculture. |
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Hong Qiao |
Hong Qiao, She received her PhD from Institute of Genetics and Developmental Biology, Chinese Academy of Science (IGD). She previously studied the genetics and biochemistry mechanism of plant gametophyte self-incompatibility (SI). Currently, she is working on EIN2, the key regulator of ethylene signaling pathway. Her goal is to understand the regulatory mechanism of EIN2 in ethylene signaling pathway and hope to find the bridge of the signaling from the ER membrane to the regulate nuclear gene expression. |
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Bob Schmitz Post Doc rschmitz@salk.edu |
Bob Schmitz earned his Ph.D. at the University of Wisconsin-Madison. During his graduate training he studied an environmentally-induced epigenetic switch known as vernalization in Dr. Richard Amasino's Laboratory. Bob joined the Ecker laboratory in August of 2008 and is currently leading the Ecker lab contribution to the Arabidopsis 1,001 genomes project. In addition, he is further defining transcriptional regulatory networks in Arabidopsis using a ChIPseq approach. |
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Ronan O'Malley Post Doc omalley@salk.edu |
I study the phenotypic outcomes of induced and natural genotypic differences in Arabidopsis thaliana using various genomic tools, including large-scale reverse genetic screens and high-throughput sequencing technologies. For the past three years I have lead a project to identify two distinct T-DNA homozygous insertion lines for every gene in Arabidopsis. We are three fifths of the way complete having isolated over 30,000 mutant lines. We have begun applying this collection to genome-scale reverse genetic screens using a variety of phytohormone and conditional challenges to systematically test for functional roles for the thousands of un- or under-annotated genes in Arabidopsis. In collaboration with other members of the lab I am also working to map and analyze the genetic, epigenetic and transcriptional differences between Arabidopsis ecotypes to investigate the effect of genomic variation on natural biological variation. Finally I am working on a project to develop a methodology to use high-throughput sequencing to assist in the rapid creation of new, large T-DNA insertional collections in any plant transformable with Agrobacterium. This technology, together with detailed maps of natural genomic variation, should allow us to quickly test predictions regarding phenotypic outcomes of specific natural variations. |
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Mat Lewsey Post Doc mlewsey@salk.edu |
Mathew earned his PhD in lab of Dr J.P. Carr, University of Cambridge, studying the functions of the 2b RNA silencing suppressor protein encoded by cucumber mosaic virus. He continued his research there, investigating how plant viruses manipulate hormone signaling, and the impacts of this on antiviral defense and virus transmission. Mathew joined the lab in 2010 on a Marie Curie International Outgoing Fellowship. In collaboration with Prof. R. Solano (Centro Nacional de Biotenología, Madrid) he is currently investigating transcriptional responses to plant hormones using high-throughput sequencing techniques. |
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Mingtang Xie |
Mingtang Xie earned his Ph.D. at the University of California Riverside. During his graduate study he dissected the cytokinin function and regulation in stem-cell homeostasis using live imaging and genetic approaches. Mingtang joined the Ecker group on January 3, 2011. Currently, he is charting plant hormone signaling pathway networks using ChIP-Seq. Specifically, he is interested in deciphering the interaction between auxin and cytokinin. Ultimately, he aims to improve plants of economic importance by application of our understanding of the mechanisms of plant hormone actions. |
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Liang Song Post Doc lsong@salk.edu |
Liang Song received her Ph.D. at the Pennsylvania State University, studying microRNA biogenesis in Arabidopsis. She joined the Ecker lab in Feb. 2011. Her current research aims to elucidate the crosstalk of phytohormones in Arabidopsis seedlings. She focuses on examining the transcriptional response of the gibberellin and abscisic acid signaling pathways using high-throughput sequencing approaches. |
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Shao-shan Carol Huang Post Doc shhuang@salk.edu |
I joined the Ecker lab in November 2011. I am broadly interested in using computational approaches for integrated analysis of diverse proteomics and genomics datasets, using Arabidopsis as a model organism. I am currently investigating how different factors such as sequence preference and chromatin structure contribute to the binding of transcription factors and subsequently the regulation of target gene expression. I completed my PhD in the Computational and Systems Biology program at the Massachusetts Institute of Technology, in the lab of Prof. Ernest Fraenkel. The focus of my graduate study was the development of a computational algorithm for constructing regulatory networks from global phosphoproteomics and transcriptional profiling data. |
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Mark Zander Post Doc mzander@salk.edu |
I earned my Ph.D. in the lab of Prof. Christiane Gatz at the University of Göttingen, Germany, where I tried to understand the molecular mechanisms underlying crosstalk phenomena between different defense pathways in Arabidopsis. My research was focused on TGA transcription factors, which serve as an integration node between salicylic acid and jasmonic acid/ethylene defense signaling. I joined the Ecker lab in January 2012 to visualize cis-regulatory networks, which are operational in defense hormone responses utilizing different high-throughput sequencing approaches. |
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Jeff Nelson Graduate Student jeffnelson@ucsd.edu |
Jeff Nelson is a graduate student in the Division of Biological Sciences at the University of California, San Diego. He earned his B.S. in Biochemistry and Neurobiology at the University of Wisconsin-Madison while performing research on plant-pathogen interactions in Populus tremuloides. Upon graduating, he worked as a research assistant at the UW-Madison Hospital in the lab of Dr. Jon Odorico, studying the potential of embryonic stem cells in type I diabetes treatment. He is currently conducting research on the transcriptional networks underlying circadian rhythms in Arabidopsis. |
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Matt Schultz Graduate Student schultzmattd@gmail.com |
Matt Schultz is a graduate student in the Bioinformatics program at UCSD. He earned his BS in Genetics from UC Davis where he worked on creating a computational model to study the effects of light and the circadian clock on hypocotyl growth in Arabidopsis. Matt joined the Ecker lab in June 2010. His current projects include studying the relationship between differential expression and differential methylation in human embryonic stem cells as well as applying GWAS techniques to identify the genetic basis for phenotypes in Arabidopsis. |
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Huaming Chen Bioinformatician hchen@salk.edu | Huaming Chen is a staff bioinformatician and program developer. He administers the SIGnAL web site, as well as databases of T-DNA Express, Transcriptome, RiceGE, CRE, etc. He also develops novel web-based or desktop in-house computational applications such as ChipViewer, GCAT. |
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Rick McCosh Research Technician rmccosh@salk.edu |
Rick McCosh earned his B.S. and M.S. at Montana State University. He joined the Ecker lab in 2011 as a research technician. He is working with Bob Schmitz on the Arabidopsis 1,001 genomes project. |
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Raul Carlos Serrano Research Technician rserrano@salk.edu |
Raul Carlos Serrano is a Lab Technician who recently joined the Ecker Lab in 2011 to support Mat Lewsey, Liang Song and Mingtang Xie in investigating transcriptional responses to plant hormones using high-throughput sequencing techniques. Carlos graduated with a B.S. in Biochemistry from the University of California, San Diego. |
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Mark Urich Undergraduate Student urich@salk.edu |
Mark Urich is currently Lab Assistant I and is working toward a B.S. in General Biology from San Diego State University. He joined the Ecker lab in June of 2005 and is currently working with Bob Schmitz on recombineering Arabidopsis transcription factors for future ChIPseq experiments. |