Lab Members

Joseph Ecker

Principal Investigator


Manoj Hariharan

Staff Scientist

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:

  1. 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
  2. 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,
  3. analyzing transcriptomic changes in the brain during development of schizophrenia model of mouse which is relevant to understand long-term effects of neuropsychiatric disorders,
  4. 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


Robert Henley

Postdoctoral Fellow

Robert Henley received his Ph.D degree at Northeastern University with Dr. Meni Wanunu. During his graduate studies he helped develop new next-generation sequencing techniques and improve existing ones. Robert joined the Ecker Lab in 2017. He is interested in studying how DNA methylation defines cell types and how the spatial context of these cell types drives tissue level behaviors.

Travis Lee

Postdoctoral Fellow

Travis Lee received his Ph.D. at the University of California, Riverside with Dr. Julia Bailey-Serres. During his graduate studies he investigated the genome-wide effects of hypoxia on gene regulation spanning epigenetic through translational regulation. Travis joined the Ecker lab in July 2018. He is interested in studying stimulus driven epigenetic and transcriptional regulation in single cells. Currently he is adapting and developing methods to profile several outputs of gene regulation in single cells of Arabidopsis.
Tatsuya Nobori

Tatsuya Nobori

Postdoctoral Fellow

Tatsuya Nobori received his Ph.D degree at the Max-Planck Institute in Cologne, Germany, with Dr. Kenichi Tsuda. During his graduate studies, he established methods for transcriptome and proteome profiling of bacteria in plants, and investigated how plant immunity affects pathogens and the microbiota. Tatsuya joined the Ecker lab in May 2019. He is employing single cell (epi)genomics to study host-microbe interactions.

Wei Tian

Postdoctoral Fellow

Wei Tian received his Ph.D from University of Illinois at Chicago, where he studied computational biology with Dr Jie Liang. During his graduate studies, he developed new methods for predicting structures and calculating thermodymaical properties of beta barrel membrane proteins. He also worked on computational geometry and topology and systems biology. He joined the Ecker Lab in September 2019. He is working on bioinformatics analysis of single cell sequencing data to investigate the spatiotemporal dynamics of epigenetics of brains.
Qin An

Qin An

Postdoctoral Fellow

Qin An received his Ph.D. degree from the University of California, Los Angeles, with Dr. Guoping Fan. His research was focusing on bioinformatics data analysis and algorithm development for different types of single-cell sequencing data. Using these approaches, he studied various kinds of biological questions, including the neurogenesis in retinal organoids, trophoblast differentiation in embryos, and epigenetic regulation of regeneration in the peripheral nervous system. Qin joined Ecker’s lab in Sep 2020. Currently, he is studying the epigenomic dynamics within different neuron subtypes during early neuronal development, and their relevance to neurodevelopmental disorders.

Natanella Illouz-Eliaz

Postdoctoral Fellow

Natanella Illouz-Eliaz was born in the northern part of Israel, near the Lebanese boarder. She received her PhD degree in plant sciences from the Hebrew University of Jerusalem. In her work towards her PhD degree, Natanella studied the mechanism by which the gibberellin (GA) receptors regulate tomato plant development and response to water-deficit stress. Natanella joined the Ecker lab, September 2020, and is interested in exploring abiotic stress-response mechanisms at the plant single-cell level.

Joseph Swift

Postdoctoral Fellow

Joseph Swift received his Ph.D from New York University, where he studied the systems biology of nutrient signaling in the lab of Prof. Gloria Coruzzi. Joseph joined the Ecker lab in March 2019. He is investigating how plant tissues signal and integrate abiotic signals, with particular focus on drought responses. He’s also interested in understanding the roles different plant hormones play in mediating such responses.

Bang-An Wang

Postdoctoral Fellow

Bang-An Wang received his Ph.D. degree in Biochemistry and Cell Biology at Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, in the lab of Prof. Guo-liang Xu. He intensively worked with the DNA methylation involved in germ cell and embryo development. Bang-An joined Ecker lab in October 2016. He is interested in exploring dynamic epigenetic regulation during brain development. Currently he is developing tools to edit DNA methylation to uncover the functional roles of the regulatory elements located at DMRs (Differentially methylated regions).

Mark Zander

Postdoctoral Fellow

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.

Zhuzhu Zhang

Postdoctoral Fellow

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.

Anna Bartlett

Research Assistant

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.

Cesar Barragan

Research Assistant

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

Rosa Castanon

Research Assistant

I prepare all the different types of libraries we sequence from projects like Encode, 1001 genomes, TDNAseq, DAPseq, Brain development.

Renee Garza

Research Assistant

In October of 2014, Renee joined the Ecker lab. She works on the next generation Arabidopsis protein interactome project.

Joe Nery

Research Assistant

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.

Peter Berube

Graduate Student

Peter Berube is a graduate student in the Biological Science Program at UCSD. He earned his B.S. in Biochemistry from Boston College in 2017 and worked on understanding cell fate transitions during cellular reprogramming. He joined Ecker lab in August 2020. His interests include understanding the cellular diversity in the brain using single-cell genomics techniques and how epigenetic and genetic variation contribute to disease.

Hanqing Liu

Graduate Student

Hanqing Liu is a graduate student in the Biological Science Program at UCSD. He earned his B.S. in Biotechnology from Zhejiang University in China and was a MD student in the same university for one year before he decided to pursue a scientific career. He jointed Ecker lab in April 2018. He is working on using several single cell transcriptomic and epigenomic sequencing technologies to study the spatiotemporal diversity of whole mouse brain.
Simon Niu

Shengyong Niu

Graduate Student


Ryan O’Neil

Graduate Student

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.

Jingtian Zhou

Graduate Student

Jingtian Zhou is a Ph.D. candidate in Bioinformatics and Systems Biology program at UCSD. He received his B.S. from Tsinghua University in 2016 and joined the Ecker lab in summer 2017. He is working on integrative analysis of multi-modality single-cell data to understand the neural cell-types, connectivities, and the dynamics of gene regulation during brain development.

Bruce Jow

Lab Tech

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


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.
Undergraduate Students

Clement Shen

Lab Assistant

Yusuke Koga

Lab Assistant

Ecker lab alumni

Alonso, Jose

Williams Neal Reynolds Distinguished Professor of Plant Biology and Genetics
University Faculty Scholar
North Carolina State University

Bell, Callum

National Center for Genome Resources

Borevitz, Justin

Associate Professor
University of Chicago

Chang, Katherine

Staff Scientist
Illumina, San Diego

Chao, Qimin

Group Leader
Morphotek, Inc.

Dal-Bianco, Maximiller

Univ. Federal de Viçosa, Brazil

Dewar, Ken

Associate Professor
Department of Human Genetics
McGill University

Dowen, Robbie

Postdoctoral Fellow
Department of Molecular Biology
Massachusetts General Hospital/Harvard

Dunn, Patrick

Celera Genomics

Galli, Mary

Research Assistant III
Gallavotti Lab, The Waksman Institute for Microbiology at Rutgers University

Gregory, Brian

Associate Professor and Graduate Chair
Department of Biology
University of Pennsylvania

Guo, Hongwei

Peking University

Guzman, Plinio

Departamento de Ingenieria Genetica – Unidad Irapuato, Centro de Investigacion y de Estudios Avanzados del Insituto Politecnico Nacional, Mexico

He, Yupeng

Guardant Health
Sr. Bioinformatics Scientist

Hirayama, Takashi

Huang, Shao-shan Carol

Assistant Professor
New York University

Ishiguro, Sumie

Assistant Professor
Nagoya University

Johnson, Phoebe

Jupe, Florian

Product Design Lead
Plant Health and Genomics
Chesterfield, Missouri

Kawakatsu, Taiji

Principal researcher
National Institute of Agrobiological Sciences, Japan

Kieber, Joseph

University of North Carolina, Chapel Hill

Kurihara, Yukio

RIKEN Plant Science Center
Plant Functional Genomics Research Group (E820)

Lewsey, Mat

Senior Lecturer
Centre for AgriBioscience,
La Trobe University, Bundoora, VIC 3086, Australia

Li, Hai

Head of Cellular Assays at High Throughput Screening Center
Associate Research Scientist
Columbia University

Lim, Jun

Associate Professor
Department of Bioscience and Biotechnology, Konkuk University
Seoul, Korea

Liljegren, Sarah

Assistant Professor
University of Mississippi

Lister, Ryan

Winthrop Professor
Plant Energy Biology, ARC Centre of Excellence
The University of Western Australia

Luo, Chongyuan

Assistant Professor
Department of Human Genetics

Lurin, Claire

Vice Director
INRA, Evry, France

Matallana Redondo, Emilia

Assistant Professor
University of Valencia, Spain

McCosh, Rick

University of West Virginia

McGrath, Robert

Center for Technology Transfer
University of Pennsylvania

Nehring, Ramlah

Vice President of Corporate Development at Foundation Medicine
Cambridge, Massachusetts

Nelson, Jeff

Postdoctoral Fellow
University of Wisconsin – Madison

Nourizadeh, Saeid

Current position unknown

O’Malley, Ronan

Group Lead of Sequencing Technologies
Joint Genome Institute, Lawrence Berkeley Laboratory

Pelizzola, Mattia

IEO, European Institute of Oncology

Peng, Qian

Research Associate
Nicolas Schork Lab
Scripps Translational Science Institute

Sandoval, Justin

Lab Tech

Schultz, Matt

Staff Scientist
Human Longevity, Inc.

Raz, Vered

Assistant Professor
Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands

Roman, Gregg

Associate Professor
University of Houston

Rothenberg, Madge

Director of Foundation and Corporate Programs, Bryn Mawr College

Schmitz, Bob

Assistant Professor
University of Georgia

Shiba, Hiroshi

Assistant Professor
Nara University, Japan

Singer, Tatjana

Manager of Collaborations
Omniome, Inc.

Solano, Roberto

Dept. Genética Molecular de Plantas
Centro Nacional de Biotecnologia-CSIC

Song, Haili

Research Assistant

Song, Liang

Assistant Professor
University of British Columbia

Stepanova, Anna

Assistant Professor
North Carolina State University

Sundaresan, Ambika

Sr. Bioinformatics Scientist
San Diego, CA

Tan, Pengcheng

UCLA Bioinformatics Program

Trigg, Shelly

Postdoctoral Fellow
University of Washington

Wang, Kevin (Long-Chi)

Assistant Professor
Academia Sinica, Taipei, Taiwan

Xie, Mingtang


Yazaki, Junshi

Angeline Rivkin