Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Heating quinoa shoots results in yield loss by inhibiting fruit production and delaying maturity

(2020) Jose C. Tovar et al.   PLANT JOURNAL

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

(2020) Christopher A Jackson et al.   eLife

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

High temperatures alter cross-over distribution and induce male meiotic restitution in Arabidopsis thaliana

(2020) Nico De Storme et al.   Communications Biology

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Plant stem-cell organization and differentiation at single-cell resolution

(2020) James W. Satterlee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-study inference of regulatory networks for more accurate models of gene regulation

(2019) Dayanne M. Castro et al.   PLoS Computational Biology

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

(2019) Emily R. Miraldi et al.   GENOME RESEARCH

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

Towards Building a Plant Cell Atlas

(2019) Seung Y. Rhee et al.   TRENDS IN PLANT SCIENCE

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Plant behaviour in response to the environment: information processing in the solid state

(2019) Salva Duran-Nebreda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High ambient temperature leads to reduced FT expression and delayed flowering in Brassica rapa via a mechanism associated with H2A.Z dynamics

(2019) Iván del Olmo et al.   PLANT JOURNAL

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

(2019) Steffen Knauer et al.   GENOME RESEARCH

Effects of Heat Stress at Vegetative and Reproductive Stages on Spikelet Fertility

(2018) Sulaiman Cheabu et al.   Rice Science

Feeling the Heat: Searching for Plant Thermosensors

(2018) Lam Dai Vu et al.   TRENDS IN PLANT SCIENCE

Wheat yield loss attributable to heat waves, drought and water excess at the global, national and subnational scales

(2017) M Zampieri et al.   Environmental Research Letters

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

(2017) Yan Song et al.   MOLECULAR CELL

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

(2017) Anna Bartlett et al.   Nature Protocols

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

(2017) Shubhada R Kulkarni et al.   NUCLEIC ACIDS RESEARCH

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules

(2017) Kelsey A. Maher et al.   PLANT CELL

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

(2017) Mauricio A. Reynoso et al.   PLANT PHYSIOLOGY

Temperature increase reduces global yields of major crops in four independent estimates

(2017) Chuang Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Increased Night Temperature Negatively Affects Grain Yield, Biomass and Grain Number in Chilean Quinoa

(2017) Jurka Lesjak et al.   Frontiers in Plant Science

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

(2017) Amy Marshall-Colon et al.   Frontiers in Plant Science

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Popular Rice ( L.) Cultivars Show Contrasting Responses to Heat Stress at Gametogenesis and Anthesis

(2015) W. Shi et al.   CROP SCIENCE

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

Plants in silico : why, why now and what?-an integrative platform for plant systems biology research

(2015) Xin-Guang Zhu et al.   PLANT CELL AND ENVIRONMENT

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

(2015) Anne Plessis et al.   eLife

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Impact of High Night-Time and High Daytime Temperature Stress on Winter Wheat

(2014) S. Narayanan et al.   JOURNAL OF AGRONOMY AND CROP SCIENCE

An Arabidopsis gene regulatory network for secondary cell wall synthesis

(2014) M. Taylor-Teeples et al.   NATURE

Inference of Transcriptional Networks inArabidopsisthrough Conserved Noncoding Sequence Analysis

(2014) Jan Van de Velde et al.   PLANT CELL

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

(2014) A. Para et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

(2013) S. Roy et al.   GENOME RESEARCH

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Evolutionary principles of modular gene regulation in yeasts

(2013) Dawn A Thompson et al.   eLife

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT