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.
I am a Bioinformatics researcher and I enjoy exploring the complexities of mammalian gene regulation. I joined the Ecker lab in October 2012. Here I’m focused on four major areas:
- leading the various collaborative projects focused on embryonic stem cell biology, initiated as part of the Center for Excellence in Stem Cell Genomics (CESCG) funded by the California Institute of Regenerative Medicine (CIRM). For more details, please visit Salk CESCG
- building gene regulatory networks [epigenetic and transcription factor mediated regulation] that shape early development in mouse, which is important to understand severe birth defects in humans like orofacial clefts and congenital heart defects, as part of the ENCODE phase 3 project,
- analyzing transcriptomic changes in the brain during development of schizophrenia model of mouse which is relevant to understand long-term effects of neuropsychiatric disorders,
- profiling the small RNA landscape of embryonic stem (ES) cells and their early lineages in order to elucidate their role in cellular differentiation.
Prior to joining the Ecker lab I was a postdoc at Mike Snyder’s lab at Stanford University (and Yale, since Feb 2009) where my focus was mostly on identifying the combinatorial co-association of transcription factors that regulate gene expression, as part of the ENCODE project, phase 2. I was also involved in identifying the role of non-coding regulatory variants – in personal genomes and population wide studies. I did my Ph.D under the guidance of Prof. Samir Brahmachari at the Institute of Genomics and Integrative Biology, Delhi. During this time, I analyzed the role of human intronic microRNAs in gene regulation, using computational approaches.
You can read more about my science and some non-science on my website https://sites.google.com/site/mhmanoj/
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 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.
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 earned his Ph.D. in the lab of Prof. Christiane Gatz at the University of Göttingen, Germany, where he tried to decipher the molecular mechanisms underlying crosstalk phenomena between different defense pathways in Arabidopsis. He joined the Ecker lab in January 2012. His main research focus lies on the regulatory contribution of various chromatin features on gene expression in plant hormone pathways. He is furthermore investigating the functional relationship between transcription factors and chromatin remodeling complexes utilizing different high-throughput sequencing approaches.
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.
Florian investigates population-wide large-scale structural genome variations, interlinked genomic elements and their DNA methylation landscape. This work is part of the Arabidopsis 1001 Epigenome project. To conduct these studies, Florian utilizes cutting edge technologies including PacBio SMRT sequencing, Oxford Nanopore MinION sequencing, as well as ultra-long DNA molecule maps (Bionano Genomics Irys). Important questions that are being answered during this project concentrate on how the environment shapes plant genomes and how structural variation and DNA methylation are inherited.
In a collaboration with Felix Bemm (MPI, Tuebingen) and Todd Michael (Abbott Sciences), Florian is currently involved in generating highest quality de novo reference genomes and annotations for a diversity panel of Arabidopsis thaliana accessions using above mentioned technologies.
Florian joined the Ecker lab 2015 after PhD and PostDoc in the Jones lab at The Sainsbury Laboratory in Norwich, UK. There, Florian and colleagues developed RenSeq – R gene enrichment and sequencing – a custom sequence capture strategy to identify, describe and clone the NLR/NB-LRR type plant disease resistance gene complements, using Illumina MiSeq and PacBio SMRT sequencing (doi:10.1038/nbt.3540).
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 is a PhD candidate in the Bioinformatics program at UC San Diego. He earned his B.S. in Biology and Mathematics (minor) from Shanghai Jiaotong University. Yupeng joined the Ecker lab in September 2012. His research focus on applying and developing computational tools to understand the roles of DNA methylation in gene regulation, tissue development and stem cell biology.
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.
Ryan O’Neil is a graduate student in the Bioinformatics program at UCSD. Previously, he earned his B.S. in Biological Engineering from Cornell University in 2011. Joining the Ecker lab in August 2013, Ryan classifies and investigates epigenetic aberrations of human pluripotent stem cell generation methods. The focus of his graduate studies is the generation of efficient human pluripotent stem cells.
I am a staff research assistant at the CESCG and Genomic Analysis lab. At CESCG, I handle the samples from our collaborators and track their sequencing progress. For GAL, I have been working mostly on the T-DNA genotyping project with the goal of identifying 2 T-DNA inserts in every protein coding gene. With more than 90% of genome saturation now we are using these lines for genome-wide phenotypic analysis. A protocol in how to use the SALK T-DNA resources can be found in the book “Plant Functional Genomics”. Click here for a free preview http://www.springer.com/us/book/978149392443.
I am a staff research assistant in the Ecker lab. I joined the lab in 2007 after completing my BS in Biology at UCSD. My main focus is genetics, and I’ve been able to use and grow this knowledge working on the TDNA-Seq and DAP-Seq projects (O’Malley, in process). I’m currently working with others in the lab to establish a high-throughput method of creating new insertional mutant collections, and I’m continuing to employ the DAP-Seq methodology to find variations in protein binding across Arabidopsis accessions, as well as in other species.
I prepare all the different types of libraries we sequence from projects like Encode, 1001 genomes, TDNAseq, DAPseq, Brain development.
I do the sequencing for the lab. I started running the sequencers way back when we had a Solexa 1G Genome Analyzer and a pair of Illumina GA’s.
In October of 2014, Renee joined the Ecker lab. She works on the next generation Arabidopsis protein interactome project.
I do high throughput genotyping using tecan automation for the T-DNA project as well as supporting researches with their greenhouse specific needs.
I manage all the greenhouse activities. I also help in lab duties that require highthroughput DNA extraction from plants for the T-DNA project and support researchers with their greenhouse specific needs.
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.
Associate Professor, North Carolina State University
Program Lead, National Center for Genome Resources
Associate Professor, University of Chicago
Staff Scientist, Illumina, San Diego
Group Leader, Morphotek, Inc.
Univ. Federal de Viçosa, Brazil
Principal Investigator, Genome Quebec
Department of Molecular Biology
Massachusetts General Hospital/Harvard
Research Assistant III
Gallavotti Lab, The Waksman Institute for Microbiology at Rutgers University
Assistant Professor, University of Pennsylvania
Professor, Peking University
Investigator, Departamento de Ingenieria Genetica – Unidad Irapuato, Centro de
Investigacion y de Estudios Avanzados del Insituto Politecnico Nacional, Mexico
IPSR, Okayama University
Assistant Professor, Nagoya University
Professor, University of North Carolina, Chapel Hill
RIKEN Plant Science Center
Plant Functional Genomics Research Group (E820)
Postdoctoral Fellow, Columbia University
Department of Bioscience and Biotechnology, Konkuk University
Assistant Professor, University of Mississippi
Plant Energy Biology, ARC Centre of Excellence
The University of Western Australia
Vice Director, INRA, Evry, France
Matallana Redondo, Emilia
Assistant Professor, University of Valencia, Spain
University of West Virginia
Center for Technology Transfer, University of Pennsylvania
Scientific Research Analyst, Sagient Research
University of Wisconsin – Madison
Current position unknown
IEO, European Institute of Oncology
Research Associate, Nicolas Schork Lab
Scripps Translational Science Institute
Staff Scientist, Human Longevity, Inc.
Assistant Professor, University of Texas at Austin
Department of Human and Clinical Genetics, Leiden University Medical Center,
Associate Professor, University of Houston
Director of Foundation and Corporate Programs, Bryn Mawr College
Assistant Professor, University of Georgia
Assistant Professor, Nara University, Japan
Staff Researcher, The Salk Institute
Dept. Genética Molecular de Plantas
Centro Nacional de Biotecnologia-CSIC
Assistant Professor, North Carolina State University
Staff Scientist, Illumina, San Diego
Wang, Kevin (Long-Chi)
Assistant Professor, Academia Sinica, Taipei, Taiwan
Hokuriku Research Center, National Agricultural Research Center
Principal researcher, National Institute of Agrobiological Sciences, Japan
Full list of publications: http://www.ncbi.nlm.nih.gov/pubmed/?term=ecker+jr