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Lab Members

Joe Ecker's Lab

Ronan O'Malley Ronan O'Malley
Staff Researcher
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.
Manoj Hariharan Manoj Hariharan
Staff Researcher
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.
Mingtang Xie

Mingtang Xie
Post Doc

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.

Liang Song Liang Song
Post Doc
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.
Shao-shan Carol Huang Shao-shan Carol Huang
Post Doc
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.
Mark Zander Mark Zander
Post Doc
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.
Chongyuan Luo Chongyuan Luo
Post Doc
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.
Mathew Lewsey Mat Lewsey
Research Associate
Mathew earned his PhD by studying the functions of the 2b RNA silencing suppressor protein encoded by cucumber mosaic virus in the lab of Dr J.P. Carr, University of Cambridge. 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 Ecker lab in 2010 on a Marie Curie International Outgoing Fellowship in collaboration with Prof Roberto Solano (Centro Nacional Biotecnología, Madrid). He is currently investigating hormone-regulated transcriptional networks influencing seedling growth. This research uses a combination of wet-lab and computational approaches, focusing on genomic and epigenomic techniques.
Zhuzhu Zhang Zhuzhu Zhang
Post Doc
I got my Ph.D. in Computational Biology and Bioinformatics at University of North Carolina at Chapel Hill. I studied the influence of chromatin state on transcriptional regulation and pluripotency. I am broadly interested in understanding the epigenetic variation and regulation during the differentiation and determination of cell identity, using both experimental and computational approaches. I joined Ecker lab in August 2014. I am currently investigating how different neuron types differ in their epigenomes and how those epigenetic differences contribute to their different functions.
Yupeng He Yupeng He
Graduate Student
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.
Ryan O'Neil

Ryan O’Neil
Graduate Student

Ryan O'Neil is a graduate student in the Bioinformatics program at UCSD. He earned his B.S. in Biological Engineering from Cornell University. Ryan joined the Ecker lab in August 2013. His current project compares the epigenetic aberrations of two methods of human pluripotent stem cell generation. The focus of his graduate studies is on the generation of efficient human pluripotent stem cells.
shelly trigg Shelly Trigg
Graduate Student
Shelly Trigg is a graduate student in the Biological Sciences Program at UCSD. She earned her B.S. in Biochemistry from Simmons College in Boston after which she continued post-baccalaureate research doing high throughput protein interaction screening at the Center for Cancer Systems Biology at Dana Farber Cancer Institute. Shelly joined the Ecker lab in November 2011. She is working on a project to create next generation interactome maps that can be applied to non-model organisms for understanding how cellular networks vary across cell types and give rise to a particular phenotype.
Huaming Chen Bioinformatician 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.

Recent Publications - Pubmed database