Ecker lab
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 PhD 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

Shuai Fu

Postdoctoral Fellow

I’m a postdoctoral fellow at the Ecker lab since December 2023, I did my Ph.D. work with Dr. Tony Wynshaw-Boris at Case Western Reserve University. During my graduate studies, I leveraged CRISPR/Cas9 genome editing and human induced pluripotent stem cells(hiPSC) models to study the disease mechanism of autism spectrum disorder (ASD). I discovered that ASD genetic background and a PTEN variant contribute to dysregulated cortical neurogenesis. I also co-developed a lineage tracing system in cortical organoids, revealing how an ASD-specific WNT pathway variant affects neuronal production in specific lineages.

Currently, I’m at the Ecker lab, focusing on developing and optimizing epigenetic editing tools using hiPSC models.


Travis Lee

Postdoctoral Fellow

Travis Lee received his PhD 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 PhD 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 PhD 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.

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.

Wubin Ding

Postdoctoral Fellow

Wubin is a computational biologist specializing in epigenetics, with a particular emphasis on computational epigenetics, software and algorithm development, machine learning, and single-cell data analysis. He earned his Ph.D. from East China Normal University, where his research focused on identifying DNA methylation biomarkers for pan-cancer diagnosis and prognosis. Additionally, he built a DNA methylation interactive visualization database as part of his thesis work.

Following his doctoral studies, Wubin pursued a two-year postdoctoral training in Dr. Wanding Zhou’s lab at the University of Pennsylvania and Children’s Hospital of Philadelphia. During this time, he worked on software development, specifically analyzing DNA methylation array and WGBS data. He actively contributed to the development of SeSAMe, an R package designed for DNA methylation array data processing and analysis. Moreover, he developed PyComplexHeatmap, a Python package for generating complex heatmaps.

In May 2023, Wubin joined the Ecker lab to further expand his research in the field of single-cell epigenomics. Within the Ecker lab, his research primarily focuses on single-cell data analysis, software and algorithm development, and machine learning. With his expertise in computational biology and dedication to advancing epigenetic research, Wubin aims to contribute significantly to the understanding of epigenetic mechanisms at the single-cell level.

Joseph Swift

Postdoctoral Fellow

Joseph Swift received his PhD 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.

James Walker

Postdoctoral Fellow

James (aka Jimmy) is from England and received his PhD degree in Biological Sciences at the John Innes Centre, UK. His work focuses on developmentally regulated DNA methylation and its relationship to gene expression in plants. He has discovered key methylation reprogramming events that are essential for development in the male germline of both Arabidopsis and the basal land plant Marchantia polymorpha, establishing the existence of functional 4mC DNA methylation in the latter. This was a particularly unexpected finding as 4mC had not previously been detected within eukaryotes! Jimmy joined the Ecker lab in January 2022 and is exploring long read sequencing technologies as well as single cell techniques to advance our understanding of developmental epigenetics within an evolutionary context.

Wenliang Wang

Postdoctoral Fellow

Wenliang received his PhD in botany from Wuhan University in China. He spent most of his time in the joint program with BGI, where he did a lot of work on plant and animal genomic studies, including de novo genome assembly, genome annotation and comparative evolutionary analysis. In his thesis work, Wenliang focused on the evolution of polyploid genomes using Brassica species as a model. After graduation, Wenliang did a two-year postdoc in Dr. Golnaz Vahedi’s lab at the University of Pennsylvania, where he studied chromatin regulation in T cells, switching from genomic to epigenomic studies. He developed a method to jointly profile chromatin accessibility and CAR-T integration sites, and found the regulatory function of TCF-1 on the 3D genome during T cell development in the Vahedi lab. He joined the Ecker lab in July 2021 to expand his understanding of the epigenome. In the Ecker lab, he focused on the perturbation of the methylome by external stimulus (including virus, vaccine, bacteria and exercise), and the reaction of different cell types to these stimulus.

Bang-An Wang

Postdoctoral Fellow

Bang-An Wang received his PhD 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).

Jordan Altshul

Research Assistant

Jordan Altshul received her BS in Neuroscience from UC Santa Cruz in June 2019. She worked in the Ecker Lab from March 2020 until September 2021, and after a brief hiatus, has been back since September 2022. She helps prepare the libraries for the single-cell methylation pipeline.


Anna Bartlett

Research Assistant

I am a staff research assistant. I joined the Ecker 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 on various projects in the lab such as TDNA-Seq and DAP-Seq. Currently I’m running and managing the single cell methylation pipeline for our ever-growing number of projects looking at methylomes, transcriptomes, and chromatin contacts of multiple 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.

Derek Chan

Research Assistant

I graduated from UCSD in 2023 with a B.S. in Bioengineering. I joined the Ecker lab shortly after as a Research Assistant. I currently prepare libraries for the single cell methylation pipeline.

Chumo Chen

Research Assistant

I joined the Ecker lab in 2023 after receiving my B.S. in Molecular and Cell Biology at UCSD. I primarily contribute to the construction of a single-cell resolution atlas of the human brain (BICAN). I handle nuclei isolation and sorting for various single-cell sequencing libraries (transcriptome, methylome and chromatin conformation), and spatial transcriptomic imaging for mammal samples. I also maintain the lab’s Sony flow cytometer.

Renee Garza

Research Assistant

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

Tanvi Jain

Research Assistant

I am a junior majoring in Bioinformatics at UCSD, and have been a part of the Ecker Lab since 2023 Feb. My focus is on the 1001 genomes project for single cell transcriptomics analysis in arabidopsis thaliana. My role as lab technician involves working at both the bench doing sciRNA-seq library prep and computational work for scRNA-seq analysis and development of pipelines for processing, integration, QC, and analysis.

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.

William Owens

Research Assistant

I joined the Ecker lab in early 2023 after finishing my undergraduate studies. I am mainly focused on running the MERFISH pipeline and operating the MERSCOPEs in the lab producing transcriptomic and other imaging data for the BICAN whole brain cell atlas as well as other projects. I have been able to develop my skills in research, exploring epigenetic and organizational aspects of the brain and engaging my curiosity toward a better understanding of the brain and behavior.

Alaina Petrella

Research Assistant

I graduated from University of Portland in 2021 with a B/S. in general biology. After graduation I worked at a biotech company in the Bay Area until February 2023 when I joined the Ecker Lab as a research assistant where I help prepare the libraries for the single-cell methylation pipeline.

Andrea Saldaña Acerbo

Research Assistant

I graduated from the University of San Diego with a BA in Behavioral Neuroscience and have been working as a research assistant in Ecker lab since September 2023. Most of my work consists of spatial transcriptomics for the NIH BRAIN Initiative Cell Atlas Network (BICAN) project and prepping nuclei for the snm3C-seq libraries. I take a special interest and enjoy learning about genetics and neurological disorders.

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.

Yue (May) Wu

Graduate Student

May is a graduate student from UCSD biological sciences. She received her B.S. in Genetics and Genomics from the University of Wisconsin-Madison in 2021. May has been working in the Ecker GAL lab since 2022 and is now studying genetic and epigenetic regulations in diseased human brains.


Qiurui Rachel Zeng

Graduate Student

Qiurui Rachel Zeng is a graduate student in the Biological Science Program at UC San Diego. She received her BA in Biomedical Science at Shanghai Jiao Tong University in June 2020. She joined the Ecker Lab in May 2022 and is now studying age-related epigenetic patterns in the mouse brain using single cell epigenetic sequencing technologies.


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.

Natalie Schenker-Ahmed

Project Manager

I am the project manager of the Center for Multiomic Human Brain Cell Atlas. I joined the Ecker lab and this project in Fall 2022. I earned my PhD in Biological Anthropology from UCSD in 2007. Throughout my research career, I have sought to integrate multiple modalities at multiple scales to achieve greater understanding. During the first part of my career, this primarily meant investigating anatomy at the gross level and merging that information with microstructural data drawn from microscope analysis. Through this work, I developed expertise in both MR imaging and brightfield microscopy, both of which served as the foundation for my investigations into non-human primate neuroanatomy, human neuroanatomy, and later oncological diagnosis. Subsequently, I participated in research that sought to integrate even more diverse data, ranging from diagnostic imaging to genotyping, and including clinical phenotypic information. The current project also seeks to integrate across multiple scales, ranging from 3-dimensional imaging of the brain to single-cell transcriptomics. In this setting, I use my expertise in neuroanatomy combined with my experience working in diverse settings to facilitate and manage the project.

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
No posts found…

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

Australian National University (ANU)

Chang, Katherine

Alliances and Partnerships Manager at Illumina

Chao, Qimin

Morphotek, Inc.

Dal-Bianco, Maximiller

Univ. Federal de Viçosa, Brazil

Dewar, Ken

Associate Professor
Department of Human Genetics
McGill University

Dowen, Robbie

Assistant Professor
UNC Department of Biology

Dunn, Patrick

Celera Genomics

Galli, Mary

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

Gonzalez, Stephen

Research Assistant

Gregory, Brian

Associate Professor and Graduate Chair
Department of Biology
University of Pennsylvania

Guo, Hongwei

Hongwei Guo-Professor
SUSTech, China

Guzman, Plinio

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

He, Yupeng

Bioinformatics, Guardant Health

Henley, Robert

Pleasanton, CA

Hirayama, Takashi

Huang, Shao-shan Carol

Assistant Professor
New York University

Ishiguro, Sumie

Assistant Professor
Nagoya University

Johnson, Phoebe

Jupe, Florian

Bayer Crop Science, St. Louis MO

Kawakatsu, Taiji

Principal researcher
National Institute of Agrobiological Sciences, Japan

Kenworthy, Mia

Weill Cornell Medical College
New York City

Kieber, Joseph

University of North Carolina, Chapel Hill

Kim, Christopher

Senior Global Market Development Manager
Thermo Fisher Scientific

Kurihara, Yukio

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

Lewsey, Mat

Associate Professor
Centre for AgriBioscience, La Trobe University, Australia

Li, Hai

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

Liljegren, Sarah

Associate Professor
Department of Biology, The University of Mississippi

Lim, Jun

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

Lister, Ryan

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

Liu, Hanqing

Junior Fellow
Harvard University

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

 Sr. Associate Vice Provost for Technology Management
Drexel Applied Innovation

Nehring, Ramlah

Vice President of Corporate Development at Foundation Medicine
Cambridge, Massachusetts

Nelson, Jeff

Assistant Faculty Associate
University of Wisconsin, Madison

Niu, Shengyong

Graduate Student

Nourizadeh, Saeid

Current position unknown

O’Malley, Ronan

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

Pelizzola, Mattia

Center for Genomic Science, Milano

Peng, Qian

Assistant Professor of MCN
Scripps Research

Qiao, Hong

Assistant Professor
UT Austin

Raz, Vered

Associate Professor
Leiden University Medical Center, The Netherlands

Rivkin, Angeline

Medical Student
The University of Illinois at Chicago

Rivkin, Angeline

Medical Student
University of Illinois at Chicago

Roman, Gregg

Associate Professor
University of Houston

Rothenberg, Madge

Impact, Philadelphia, PA

Schmitz, Bob

University of Georgia

Schultz, Matt

Team Lead
Invitae, San Francisco, CA

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

Department of Integrative Biology
University of Texas at Austin

Song, Liang

Assistant Professor
University of British Columbia

Stepanova, Anna

Associate Professor
North Carolina State University

Sundaresan, Ambika

Sr. Bioinformatics Scientist
San Diego, CA

Tan, Pengcheng

UCLA Bioinformatics Program

Trigg, Shelly

Research Scientist
Gloucester Marine Genomics Institute

Valadon, Cynthia

Wang, Kevin (Long-Chi)

Assistant Professor
Academia Sinica, Taipei, Taiwan

Xie, Mingtang


Yazaki, Junshi

Yeon, Sung

PhD Student
Yale University

Yoshida, Hitoshi

Institute of Agrobiological Sciences, NARO

Zander, Mark

Waksman Institute
Rutgers University

Zhang, Zhuzhu

Assistant Professor of Human Genetics
University of Chicago

Zhou, Jingtian

Science Fellow
Arc Institute


Hsu, Jonathan

Biology Major

Luong, Raymond

Biology Major

Melome , Jan

Biology Major

Romero, Omar

Biology Major

Sy, Candace

Biology Major


Chan, Belinda

University of Pennsylvania, Graduated
Yale Medical Schoo

Forstner, Jennifer

Harvard Law School

Hall, David

Biology Dept. Independent Study Student
University of Pennsylvania

Hildebityl, Caroline

M.D./Ph.D. Program
Jefferson Medical School

Kamen, Walter

Wharton School
University of Pennsylvania

Kohl, Jonathan

Biology Dept. Independent Study Student
University of Pennsylvania

Lubarsky, Barry

Biochemistry Major. Independent Study Student.
Thouron Fellow
Cambridge University

Ph.D. Candidate, Department of Developmental Biology
Stanford University

Madden, Kevin

HHMI Fellow in the Biology Graduate Program
Yale University

Mizugechi, Richard

Tulane Medical School
University of Pennsylvania

Ragattei, James

DuPont Co

Refaeli, Yosef


Reuter, Lynn

Graduate Program in Psychology
Princeton University

Richardson, Thomas

University of Pennsylvania

Rosen, Ira

Rutgers University
Ph.D. Program