Transcriptional regulation of nitrogen-associated metabolism and growth

Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks

(2017) Kun-hsiang Liu et al.   NATURE

Eutrophication will increase during the 21st century as a result of precipitation changes

(2017) E. Sinha et al.   SCIENCE

Combining dependentP-values with an empirical adaptation of Brown’s method

(2016) William Poole et al.   BIOINFORMATICS

The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators

(2016) Na Xu et al.   PLANT CELL

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root

(2016) D. Ristova et al.   Science Signaling

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root

(2016) D. Ristova et al.   Science Signaling

Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits

(2015) Daniel H Chitwood et al.   CURRENT OPINION IN PLANT BIOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

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

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

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

(2015) Anna Medici et al.   Nature Communications

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

(2015) Brad T. Townsley et al.   Frontiers in Plant Science

Multiple mechanisms of nitrate sensing by Arabidopsis nitrate transceptor NRT1.1

(2015) E. Bouguyon et al.   Nature Plants

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Nitric Oxide Sensing in Plants Is Mediated by Proteolytic Control of Group VII ERF Transcription Factors

(2014) Daniel J. Gibbs et al.   MOLECULAR CELL

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

Nitrate foraging byArabidopsisroots is mediated by the transcription factor TCP20 through the systemic signaling pathway

(2014) Peizhu Guan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Plasticity of the Arabidopsis Root System under Nutrient Deficiencies

(2013) B. D. Gruber et al.   PLANT PHYSIOLOGY

Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots

(2013) E. A. Vidal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis NIN-like transcription factors have a central role in nitrate signalling

(2013) Mineko Konishi et al.   Nature Communications

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

(2013) Chloé Marchive et al.   Nature Communications

Characterization of a NADH-Dependent Glutamate Dehydrogenase Mutant ofArabidopsisDemonstrates the Key Role of this Enzyme in Root Carbon and Nitrogen Metabolism

(2012) Jean-Xavier Fontaine et al.   PLANT CELL

Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis

(2012) C. Ma et al.   PLANT PHYSIOLOGY

Enhanced Y1H assays for Arabidopsis

(2011) Allison Gaudinier et al.   NATURE METHODS

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

(2011) John S Reece-Hoyes et al.   NATURE METHODS

A framework integrating plant growth with hormones and nutrients

(2011) Gabriel Krouk et al.   TRENDS IN PLANT SCIENCE

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

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome

(2010) Ralph Kissen et al.   BMC GENOMICS

Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis

(2010) Mariana Obertello et al.   BMC Systems Biology

Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways

(2010) Inmaculada Castro Marín et al.   PLANTA

Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach

(2009) K. Van Deun et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis

(2008) Loren Castaings et al.   PLANT JOURNAL

AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response

(2008) Heng-Cheng Hu et al.   PLANT JOURNAL

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

Cell-specific nitrogen responses mediate developmental plasticity

(2008) M. L. Gifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Receptor-Like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root

(2008) I. De Smet et al.   SCIENCE