Publications

Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions

Gene regulatory networks (GRNs) drive organism structure and functions, so the discovery and characterization of GRNs is a major goal …
Abbas Shojaee, Shao‐shan Carol Huang
Code Dataset DOI PubMed View at journal

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC …
Miaomiao Li, Tao Yao, Wanru Lin, Will E. Hinckley, Mary Galli, Wellington Muchero, Andrea Gallavotti, Jin-Gui Chen, Shao‐shan Carol Huang
Project DOI PubMed View at journal

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, …
Miaomiao Li, Wanru Lin, Will Hinckley, Tao Yao, Wellington Muchero, Jin-Gui Chen, Shao‐shan Carol Huang
DOI bioRxiv

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 …
Luis Orduña, Miaomiao Li, David Navarro-Payá, Chen Zhang, Antonio Santiago, Pablo Romero, Živa Ramšak, Gabriele Magon, Janine Höll, Patrick Merz, Kristina Gruden, Alessandro Vannozzi, Dario Cantu, Jochen Bogs, Darren C. J. Wong, Shao‐shan Carol Huang, José Tomás Matus
DOI PubMed View at journal

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 …
Abbas Shojaee, Michelle Saavedra, Shao‐shan C. Huang
DOI PubMed View at journal

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 …
Luis Orduña, Miaomiao Li, David Navarro-Payá, Chen Zhang, Antonio Santiago, Pablo Romero, Živa Ramšak, Gabriele Magon, Janine Höll, Patrik Merz, Kristina Gruden, Alessandro Vannozzi, Dario Cantu, Jochen Bogs, Darren C. J. Wong, Shao‐shan Carol Huang, José Tomás Matus
DOI bioRxiv

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 …
Yichun Qian, Shao‐shan C. Huang
DOI View at journal

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 …
Carl Procko, Steven Morrison, Courtney Dunar, Sara Mills, Brianna Maldonado, Carlee Cockrum, Nathan Emmanuel Peters, Shao‐Shan Carol Huang, Joanne Chory
DOI PubMed View at journal

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. …
Shao‐shan C. Huang, Joseph R. Ecker
DOI PubMed View at journal

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 …
Oana Ursu, Sara J. C. Gosline, Neil Beeharry, Lauren Fink, Vikram Bhattacharjee, Shao‐shan Carol Huang, Yan Zhou, Tim Yen, Ernest Fraenkel
DOI PubMed View at journal

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 …
Anna Bartlett, Ronan C O’Malley, Shao‐shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
DOI PubMed View at journal

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 …
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O’Malley, Shao‐shan C Huang, Zhuzhu Z Zhang, Mary Galli, Joseph R Ecker
DOI PubMed View at journal

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 …
L. Song, S.-s. C. Huang, A. Wise, R. Castanon, J. R. Nery, H. Chen, M. Watanabe, J. Thomas, Z. Bar-Joseph, J. R. Ecker
DOI PubMed View at journal

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 …
Junshi Yazaki, Mary Galli, Alice Y. Kim, Kazumasa Nito, Fernando Aleman, Katherine N. Chang, Anne-Ruxandra Carvunis, Rosa Quan, Hien Nguyen, Liang Song, José M. Alvarez, Shao‐shan Carol Huang, Huaming Chen, Niroshan Ramachandran, Stefan Altmann, Rodrigo A. Gutiérrez, David E. Hill, Julian I. Schroeder, Joanne Chory, Joshua LaBaer, Marc Vidal, Pascal Braun, Joseph R. Ecker
DOI PubMed View at journal

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can …
Taiji Kawakatsu*, Shao‐shan Carol Huang*, Florian Jupe*, Eriko Sasaki*, Robert J. Schmitz, Mark A. Urich, Rosa Castanon, Joseph R. Nery, Cesar Barragan, Yupeng He, Huaming Chen, Manu Dubin, Cheng-Ruei Lee, Congmao Wang, Felix Bemm, Claude Becker, Ryan sO’Neil, Ronan C. O’Malley, Danjuma X. Quarless, The 1001 Genomes Consortium, Nicholas J. Schork, Detlef Weigel, Magnus Nordborg, Joseph R. Ecker, (* indicates co-first author)
DOI PubMed View at journal

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 …
Ronan C. O’Malley*, Shao‐shan Carol Huang*, Liang Song, Mathew G. Lewsey, Anna Bartlett, Joseph R. Nery, Mary Galli, Andrea Gallavotti, Joseph R. Ecker, (* indicates co-first author)
DOI PubMed View at journal

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 …
Ullas V. Pedmale, Shao‐shan Carol Huang, Mark Zander, Benjamin J. Cole, Jonathan Hetzel, Karin Ljung, Pedro A.B. Reis, Priya Sridevi, Kazumasa Nito, Joseph R. Nery, Joseph R. Ecker, Joanne Chory
DOI PubMed View at journal

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 …
Katherine Noelani Chang, Shan Zhong, Matthew T Weirauch, Gary Hon, Mattia Pelizzola, Hai Li, Shao‐shan Carol Huang, Robert J Schmitz, Mark A Urich, Dwight Kuo, Joseph R Nery, Hong Qiao, Ally Yang, Abdullah Jamali, Huaming Chen, Trey Ideker, Bing Ren, Ziv Bar-Joseph, Timothy R Hughes, Joseph R Ecker
DOI PubMed View at journal

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 …
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao‐Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
DOI PubMed View at journal

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 …
Shao‐shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
DOI PubMed View at journal

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 …
H. Qiao, Z. Shen, S.-s. C. Huang, R. J. Schmitz, M. A. Urich, S. P. Briggs, J. R. Ecker
DOI PubMed View at journal

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 …
N. Tuncbag, S. McCallum, S.-s. C. Huang, E. Fraenkel
DOI PubMed View at journal

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 …
Shao‐shan Carol Huang, Ernest Fraenkel
DOI PubMed View at journal

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 …
S.-s. C. Huang, E. Fraenkel
DOI PubMed View at journal