Publications

Uncovering the "ZIP code" for bZIP dimers reveals novel motifs, regulatory rules and one billion years of cis-element evolution

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. For example, …

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine

The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors …

Potentials of single-cell genomics in deciphering cellular phenotype

Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate …

Major orchestration of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine

The stilbenoid pathway is responsible for the production of resveratrol and its derivatives in grapevine. A few transcription factors …

Improving plant gene regulatory network inference by integrative analysis of multi-omics and high resolution datasets

Gene regulatory networks (GRNs) model the interactions between gene expression regulators and their targets that mediate a myriad of …

Big Data to the Bench: Transcriptome Analysis for Undergraduates.

Next-generation sequencing (NGS)-based methods are revolutionizing biology. Their prevalence requires biologists to be increasingly …

Piecing together cis-regulatory networks: insights from epigenomics studies in plants

5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. …

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens

Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these …

Mapping genome-wide transcription-factor binding sites using DAP-seq

To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity …

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing …

A transcription factor hierarchy defines an environmental stress response network

Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive …

Mapping transcription factor interactome networks using HaloTag protein arrays

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an …

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can …

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome …

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light

Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant …

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

The gaseous plant hormone ethylene regulates a multitude of growth and developmental processes. How the numerous growth control …

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

Signaling and regulatory networks are essential for cells to control processes such as growth, differentiation, and response to …

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in …

Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas

Ethylene gas is essential for many developmental processes and stress responses in plants. ETHYLENE INSENSITIVE2 (EIN2), an NRAMP-like …

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular …

Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple “-Omics” Datasets

Signaling and transcription are tightly integrated processes that underlie many cellular responses to the environment. A network of …

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

Cellular signaling and regulatory networks underlie fundamental biological processes such as growth, differentiation, and response to …