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 https://sites.google.com/site/mhmanoj/

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 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 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 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.

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 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 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).

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.

Jordan Altshul graduated from UC Santa Cruz in 2019 with a B.S. in Neuroscience. She joined the Ecker Lab in April 2020 as a Research Assistant. She helps prepare the methylation libraries for the single cell pipeline.?

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.?

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

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

Stephen Gonzalez is an undergraduate student at UCSD and lab technician in the Ecker Lab since September 2019. Currently, he is using transcriptomics and differential expression analysis to assist in studying how plant genomes respond to abiotic stress.

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.

I joined the Ecker lab in December 2020 as a bioinformatics analyst. Here I am focused in understanding the role of DNA methylation patterns and their effects in blood and neuronal cells. Prior to joining the Ecker lab, I was a post-doctoral fellow with Dr. Andre Nussenzweig at National Institutes of Health, Bethesda. Here I was studying the causes and effects of genomic instability, DNA damage and their subsequent effects. I received my PhD from Texas A&M University, College Station with Dr. Aniruddha Datta. Here I was working on modeling gene regulatory networks under a Boolean and Bayesian framework and their temporal evolution.

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 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.

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 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.

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.