RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21–24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner.  (more…)

Charting plant hormone signaling pathway networks using ChIP-Seq: Aimed at deciphering the interaction between auxin and cytokinin, based on studies in the Ecker lab, the core cytokinin transcriptional regulatory network and discovery of the auxin transcriptional responses: auxin code hypothesis. Also adapting the INTACT method into a simpler version-INTACTone in order to study transcriptional network, (more…)

Mat studies cross-regulation of gene expression by hormone signaling pathways during seedling growth. This work is as part of a team including Mark Zander, Liang Song, Carol Huang, Mingtang Xie and Ronan O’Malley. (more…)

Individual genomes harbor structural variations, such as insertions and deletions ranging from several hundred to millions of base pairs. Although most identified variations have biological impact and are of evolutionary significance, technical limitations have not allowed the study of SVs on the whole-genome or population level until very recently. (more…)

The Ecker lab is now functioning also as the “Center of Excellence in Stem Cell Genomics” along with Michael Snyder’s lab at Stanford University. Created through a $40 million award by California’s stem cell agency, the California Institute for Regenerative Medicine (CIRM), the objective is to foster collaborations between California’s stem cell researchers and genomics researchers (more…)

Understanding the exact cell-type composition in brain regions is fundamental to integrating physiological, behavioral and neurochemical data to systematically understand the brain structure and function. At present, although the major categories of cell-types present in the brain have been defined, the different subtypes within these categories, as well as their location and (more…)

Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual’s cells, with epigenetic mechanisms that could play tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. (more…)

Little is known about the dynamics of the DNA methylation landscape over the trajectory of mammalian embryogenesis. Mouse has been used as a model system to study various human diseases and human biology. In this ongoing project, our lab is focused on understanding methylation profiles across 70 samples that include six early developmental time points (more…)

Biotechnological advancements allow researchers to explore new techniques of creating pluripotent cells. These methods continue to demonstrate that the pluripotent phenotype covers a broad range of cell quality and there are many metrics to score the cells. Undergoing a reprograming event to the pluripotent state is taxing to the genome; many methods attempt a reset (more…)