Lab Members
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:
- 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.
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
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.
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).
Zhuzhu Zhang
Postdoctoral Fellow
I got my PhD 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.
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 http://www.springer.com/us/book/978149392443.
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.
Cynthia Valadon
Research Assistant
Cynthia graduated with a BS in molecular, cell, and developmental biology from UC Santa Cruz. She joined the Ecker lab in 2021 as a research assistant to help prepare libraries for the single-cell methylation pipeline.
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
Postdoctoral Fellow
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.
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.
Jingtian Zhou
Postdoctoral Fellow
Jingtian Zhou is a PhD 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
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.
Undergraduate Students
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