Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

Ammonium as a signal for physiological and morphological responses in plants

(2017) Ying Liu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Interacting TCP and NLP transcription factors control plant responses to nitrate availability

(2017) Peizhu Guan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms

(2016) Allison Gaudinier et al.   Annual Review of Plant Biology

“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

Long-distance nitrate signaling displays cytokinin dependent and independent branches

(2016) Sandrine Ruffel et al.   Journal of Integrative Plant Biology

Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis

(2016) Ulrike Bechtold et al.   PLANT 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

NIN-like protein 8 is a master regulator of nitrate-promoted seed germination in Arabidopsis

(2016) Dawei Yan et al.   Nature Communications

Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces

(2015) Anne Krapp   CURRENT OPINION IN PLANT BIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Cytokinin response factor 4 (CRF4) is induced by cold and involved in freezing tolerance

(2015) Paul J. Zwack et al.   PLANT CELL REPORTS

Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis

(2015) Yupeng Li et al.   TRENDS IN PLANT SCIENCE

AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip

(2015) Anna Medici et al.   Nature Communications

The Primary Nitrate Response: a multifaceted signalling pathway

(2014) Anna Medici et al.   JOURNAL OF EXPERIMENTAL BOTANY

Photorespiration and nitrate assimilation: a major intersection between plant carbon and nitrogen

(2014) Arnold J. Bloom   PHOTOSYNTHESIS RESEARCH

The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression

(2014) Alberto Coego et al.   PLANT JOURNAL

Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response ofArabidopsis thalianaroots

(2014) José M. Alvarez et al.   PLANT JOURNAL

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

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments

(2014) Javier Canales et al.   Frontiers in Plant Science

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

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

LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies

(2013) Mingyi Wang et al.   PLoS One

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

(2013) Chloé Marchive et al.   Nature Communications

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

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

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Uptake, allocation and signaling of nitrate

(2012) Ya-Yun Wang et al.   TRENDS IN PLANT SCIENCE

Rapid, Organ-Specific Transcriptional Responses to Light Regulate Photomorphogenic Development in Dicot Seedlings

(2011) Y. Li et al.   PLANT PHYSIOLOGY

Nitrogen economics of root foraging: Transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand

(2011) S. Ruffel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

Members of the LBD Family of Transcription Factors Repress Anthocyanin Synthesis and Affect Additional Nitrogen Responses in Arabidopsis

(2009) G. Rubin et al.   PLANT CELL

VirtualPlant: A Software Platform to Support Systems Biology Research

(2009) M. S. Katari et al.   PLANT PHYSIOLOGY

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

(2008) R. A. Gutierrez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA