Nutrient dose-responsive transcriptome changes driven by Michaelis–Menten kinetics underlie plant growth rates

Water impacts nutrient dose responses genome-wide to affect crop production

(2019) Joseph Swift et al.   Nature Communications

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

(2019) Matthew D. Brooks et al.   Nature Communications

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

(2018) Kranthi Varala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Declining oxygen in the global ocean and coastal waters

(2018) Denise Breitburg et al.   SCIENCE

Transcriptional regulation of nitrogen-associated metabolism and growth

(2018) Allison Gaudinier et al.   NATURE

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

“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

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

(2016) Dawei Yan et al.   Nature Communications

Overexpression of Arabidopsis NLP7 improves plant growth under both nitrogen-limiting and -sufficient conditions by enhancing nitrogen and carbon assimilation

(2016) Lin-Hui Yu et al.   Scientific Reports

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

(2015) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

When Michaelis and Menten met Holling: towards a mechanistic theory of plant nutrient foraging behaviour

(2014) Gordon G. McNickle et al.   AoB Plants

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

Multiple bHLH Proteins form Heterodimers to Mediate CRY2-Dependent Regulation of Flowering-Time in Arabidopsis

(2013) Yawen Liu et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Uptake, allocation and signaling of nitrate

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

The Original Michaelis Constant: Translation of the 1913 Michaelis–Menten Paper

(2011) Kenneth A. Johnson et al.   BIOCHEMISTRY

Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize

(2011) X. S. Yang et al.   PLANT PHYSIOLOGY

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

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Redox Regulation of the NPR1-TGA1 System of Arabidopsis thaliana by Nitric Oxide

(2010) C. Lindermayr et al.   PLANT CELL

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana

(2010) E. A. Vidal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

CHL1 Functions as a Nitrate Sensor in Plants

(2009) Cheng-Hsun Ho et al.   CELL

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

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

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

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY