Ecker Lab > Personnel
Lab Members
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Ronan O'Malley Staff Researcher 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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Manoj Hariharan Staff Researcher mhariharan@salk.edu |
I earned my PhD under the guidance of Prof. Samir Brahmachari at IGIB, Delhi. During this time, I analyzed the role of human intronic microRNAs in gene regulation, using computational approaches. In Feb 2009, I joined Mike Snyder’s lab for postdoctoral training (at Yale and Stanford Universities) where my focus was mostly on identifying the combinatorial co-association of transcription factors that regulate gene expression, as part of the ENCODE project. I was also involved in identifying the role of structural variants and SNVs in transcription factor binding sites; elucidating the role of non-coding regulatory variants – in personal genomes and population wide studies. I joined the Ecker lab in Oct 2012 to explore the role of methylation patterns in gene regulation. |
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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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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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Chongyuan Luo Post Doc cluo@salk.edu |
Chongyuan Luo received his Ph.D degree at Rutgers University under the supervision of Dr. Eric Lam. During his graduate study, he investigated the functions of chromatin modifications using epigenomic profiling and global correlative analyses. Chongyuan joined the Ecker lab in May of 2012. He is interested in studying the spatial and temporal dynamics of epigenome in plants and animals. Currently he is developing methods to enable the profiling of DNA base modifications and other epigenetic marks with minute amounts of starting cells or tissues. |
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Maximiller Dal-Bianco Visiting Post Doc mcosta@salk.edu |
Max earned his PhD at the Sao Paulo University where he studied sugarcane varieties differing in their tolerance to drought stress in the field. Max joined the Ecker lab in July of 2012 on a Science without Border Fellowship (CsF/CNPq). The focus of his research is to unravel the interactome between Arabidopsis and proteins from the geminivirus CaLCuV. The project is a collaboration with profa Elizabeth Fontes (BIOAGRO/UFV and the National Research Institute for Plant-Pest Interactions) and was assembled to fulfill the need to advance our knowledge on the molecular and functional bases of biotic interactions among plants and pathogens economically relevant. |
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Taiji Kawakatsu Post Doc tkawakatsu@salk.edu | Taiji Kawakatsu earned his Ph.D. in the lab of Prof. Nagato, University of Tokyo, studying the temporal regulatory mechanisms of leaf initiation in rice. Taiji is an investigator at National Institute of Agrobiological Sciences in Japan, studying the network of rice seed quality control with Dr. Takaiwa. Taiji joined the Ecker lab in October 2012 on a postdoctoral fellowship for research abroad from Japanese Society for the Promotion of Science, and currently investigating interaction between ethylene responses and methylome changes in Arabidopsis. |
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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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Yupeng He Graduate Student yuhe@salk.edu |
Yupeng He is a graduate student in the Bioinformatics program at UCSD. He earned his B.S. in Biology and Mathematics (minor) from Shanghai Jiaotong University where he developed an integrative approach to predict transcription factor binding sites based on a machine learning model, Conditional Random Fields. Yupeng joined the Ecker lab in September 2012. He is working on a project to identify Epigenetic signatures associated with the quality of iPS cells and he is also studying the methylome of soybeans in order to understand the heredity of DNA methylation. |
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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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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. |