The Salk Insitute - Ecker Lab

	Mattia Pelizzola Post Doc mpelizzola@salk.edu	Mattia Pelizzola is a computational biologist interested in the integration of high-throughput epigenomics and transcriptional data. He received his PhD in Bioinformatics in 2006 at the University of Tourin in Italy, working on the identification of gene regulatory modules and the development of a pipeline for the automated analysis of microarray data. He moved to Yale University in 2007 as a Postdoctoral associate in the department of Biostatistics. There, he worked on the analysis of DNA methylation data for the identification of markers in human skin cancer. He joined the Ecker Lab in 2009 and is involved in the analysis of DNA methylation map in human Stem cells. He is also collaborating with other group members on the analysis of plants epigenomics data.
	Ryan Lister Post Doc lister@salk.edu	Ryan Lister earned his Ph.D. at the University of Western Australia, investigating the composition of the plant mitochondrial protein import machinery. Ryan joined the Ecker lab in August 2006 on a Human Frontier Science Program long-term fellowship, with a research interest focussing on characterization of global patterns of DNA methylation in the Arabidopsis genome. Ryan developed methodologies for using new high-throughput sequencing technologies to characterize genome-wide patterns of DNA methylation and cellular transcriptional activity, generating the first high-resolution integrated maps of the epigenome in a higher eukaryote. Currently, Ryan is using these approaches to study epigenetic natural variation in Arabidopsis accessions and epigenetic changes during human cellular differentiation.
	Liz Howell Post Doc colangelo@salk.edu	Elizabeth Howell joined the Ecker lab in 2006 after earning her Ph.D. from Dartmouth College where she studied the regulation of metal uptake in plants. She continues to work on plants in the Ecker lab, where her research focuses on the response of Arabidopsis thaliana to the hormone ethylene. She is using genetic, biochemical, and genomic approaches to characterize an ethylene insensitive mutant and to better understand ethylene signaling transduction. When she is not in the lab she is saving labs, as a volunteer with Labrador Rescuers.
	Junshi Yazaki Post Doc jyazaki@salk.edu	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.
	Hong Qiao Post Doc hqiao@salk.edu	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.
	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.
	Ronan O'Malley Postdoc 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.
	Kat Chang Graduate Student kchang@salk.edu	Kat Chang is a graduate student in the Division of Biology at the University of California, San Diego. She earned her B.S. in Biosystems Engineering at University of Hawaii, Manoa working on the bioremediation of petroleum impacted soils. She then earned her M.S. in Biological and Environmental Engineering at Cornell University researching the kinetics of cadmium transport in vacuoles pertaining to the phytoremediation of cadmium. In May 2005, Kat joined the Ecker lab. She is studying the ethylene transcriptional response mediated by the transcription factor EIN3.
	Robbie Dowen Research Collaborator rdowen@ucsd.edu	Robbie Dowen recently received his Ph.D. at the University of California, San Diego. His graduate work in the Ecker and Dixon (UCSD) laboratories focused on understanding the molecular mechanisms that underlie the plant-pathogen interaction. Robbie is interested in a class of bacterial virulence factors (type III effector proteins) that are utilized by bacterial pathogens during plant infections. He is currently using genetic, biochemical, and genomic approaches to dissect the complex and dynamic interaction between Arabidopsis and Pseudomonas syringae.
	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.
	Qian Peng Graduate Student qpeng@cs.ucsd.edu	Qian Peng is a Ph.D. candidate in the Department of Computer Science and Engineering at the University of California, San Diego. Broadly defined, her research interests are computational biology and bioinformatics. She earned her B.S. in Computer Science from Beijing University and an M.S. in Biomedical Engineering from UT-Memphis. Prior to joining UCSD, she worked as a scientific software developer for a number of years. She joined Ecker's lab as an IGERT fellow in 2006. Her research projects ranged from genome rearrangements, repeat identification for Arabidopsis, to the study of plant duplications. Her present research interest is in the area of computational epigenomics. One particular project she is working on is epitype/methylome assembly. In addition, she is interested in studying the combined effect of genomic and epigenomic variations on transcriptional activity using both combinatorial and machine learning methods.
	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.
	Mary Galli Research Technician mgalli@salk.edu	Mary Galli is a Research Technician who has been working in the Genomics Analysis Lab since 2007. She earned her B.S. and M.S. from the University of Californina, San Diego and has been actively engaged in Arabidopsis research for over 10 years. Currently Mary is working towards generating the first high-confidence binary Arabidopsis protein-protein interaction network map using a set of 12,000 Arabidopsis ORF clones. 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.
	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.

The Ecker Lab