Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling

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

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

Crop Yield Prediction Using Deep Neural Networks

(2019) Saeed Khaki et al.   Frontiers in Plant Science

A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth

(2019) Gytis Bernotas et al.   GigaScience

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

(2019) Ryan J. Spurney et al.   PLANT JOURNAL

California Almond Yield Prediction at the Orchard Level With a Machine Learning Approach

(2019) Zhou Zhang et al.   Frontiers in Plant Science

Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data

(2018) Martin Modrák et al.   BMC BIOINFORMATICS

Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network

(2018) Simon Scofield et al.   DEVELOPMENT

A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration

(2018) Momoko Ikeuchi et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index

(2018) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states

(2018) Ignasius Joanito et al.   Scientific Reports

Integrating co-expression networks with GWAS to prioritize causal genes in maize

(2018) Robert Schaefer et al.   PLANT CELL

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes

(2017) Jiye Kim et al.   Evolutionary Bioinformatics

A deep learning and novelty detection framework for rapid phenotyping in high-content screening

(2017) Christoph Sommer et al.   MOLECULAR BIOLOGY OF THE CELL

From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress

(2017) Lisa Van den Broeck et al.   Molecular Systems Biology

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

PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data

(2017) Toru Kudo et al.   PLANT AND CELL PHYSIOLOGY

RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes

(2017) Hong Lin et al.   PLANT JOURNAL

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

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

Predicting gene regulatory networks by combining spatial and temporal gene expression data inArabidopsisroot stem cells

(2017) Maria Angels de Luis Balaguer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

(2017) Xiaohuan Sun et al.   Nature Communications

Transcriptomic analysis of the regulation of stalk development in flowering Chinese cabbage (Brassica campestris) by RNA sequencing

(2017) Xinmin Huang et al.   Scientific Reports

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds

(2017) Neelam Redekar et al.   Frontiers in Plant Science

“Hit-and-Run” transcription: de novo transcription initiated by a transient bZIP1 “hit” persists after the “run”

(2016) Joan Doidy et al.   BMC GENOMICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

(2016) O.C. Martin et al.   Physics of Life Reviews

Joint genetic and network analyses identify loci associated with root growth under NaCl stress inArabidopsis thaliana

(2016) Yuriko Kobayashi et al.   PLANT CELL AND ENVIRONMENT

A transcription factor hierarchy defines an environmental stress response network

(2016) L. Song et al.   SCIENCE

Molecular mechanisms at the core of the plant circadian oscillator

(2016) Maria A Nohales et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana

(2016) Si Wu et al.   PLoS Genetics

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses

(2015) Pankaj Barah et al.   NUCLEIC ACIDS RESEARCH

A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis

(2015) Nathalie Gonzalez et al.   PLANT CELL

Gene network analysis ofArabidopsis thalianaflower development through dynamic gene perturbations

(2015) Diarmuid S. Ó'Maoiléidigh et al.   PLANT JOURNAL

FlowerNet: A Gene Expression Correlation Network for Anther and Pollen Development

(2015) Simon Pearce et al.   PLANT PHYSIOLOGY

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks

(2014) Ricardo A Chávez Montes et al.   BMC PLANT BIOLOGY

Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions

(2014) Qi Lv et al.   BMC PLANT BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

An Arabidopsis gene regulatory network for secondary cell wall synthesis

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

ArabidopsisEnsemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress

(2014) Vanessa Vermeirssen 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

Predictive ability of machine learning methods for massive crop yield prediction

(2014) Alberto Gonzalez-Sanchez et al.   SPANISH JOURNAL OF AGRICULTURAL RESEARCH

PLANEX: the plant co-expression database

(2013) Won Yim et al.   BMC PLANT BIOLOGY

Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling

(2013) Hulin Wu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

TARGET: A Transient Transformation System for Genome-Wide Transcription Factor Target Discovery

(2013) Bastiaan O.R. Bargmann et al.   Molecular Plant

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

ETHYLENE RESPONSE FACTOR6 Acts as a Central Regulator of Leaf Growth under Water-Limiting Conditions in Arabidopsis

(2013) M. Dubois et al.   PLANT PHYSIOLOGY

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

(2013) Katherine Noelani Chang et al.   eLife

Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana

(2013) Nora Bujdoso et al.   Frontiers in Plant Science

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

(2012) C. A. Penfold et al.   BIOINFORMATICS

Complexity in the Wiring and Regulation of Plant Circadian Networks

(2012) Dawn H. Nagel et al.   CURRENT BIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana

(2011) Cheng-Wei Yao et al.   BMC BIOINFORMATICS

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

(2011) W Walter Lorenz et al.   BMC GENOMICS

Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

(2011) Frank Dondelinger et al.   EUPHYTICA

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

(2011) Matthieu Vignes et al.   PLoS One

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

Identifying essential genes in bacterial metabolic networks with machine learning methods

(2010) Kitiporn Plaimas et al.   BMC Systems Biology

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

CORNET: A User-Friendly Tool for Data Mining and Integration

(2010) S. De Bodt et al.   PLANT PHYSIOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Fluorescence Activated Cell Sorting of Plant Protoplasts

(2010) Bastiaan O. R. Bargmann et al.   Jove-Journal of Visualized Experiments

Inducible gene expression systems and plant biotechnology

(2009) Giandomenico Corrado et al.   BIOTECHNOLOGY ADVANCES

From gene expression to gene regulatory networks in Arabidopsis thaliana

(2009) Chris J Needham et al.   BMC Systems Biology

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

A comparative study of different machine learning methods on microarray gene expression data

(2008) Mehdi Pirooznia et al.   BMC GENOMICS

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

(2008) Kitiporn Plaimas et al.   BMC Systems Biology