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List of works by Philip N Benfey

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture

scientific article published on 11 April 2013

A Co-opted Regulator of Lateral Root Development Controls Nodule Organogenesis in Lotus

scientific article published on 01 January 2020

A Friend in Need (of Nutrients) Is a….

scientific article

A SIMPLE Pipeline for Mapping Point Mutations.

scientific article published on 25 May 2017

A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division

scientific article

A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression

scientific article

A gene expression map of the Arabidopsis root

scientific article

A gene regulatory network for root epidermis cell differentiation in Arabidopsis

scientific article (publication date: 2012)

A high-resolution root spatiotemporal map reveals dominant expression patterns.

scientific article published in November 2007

A microfluidic device and computational platform for high-throughput live imaging of gene expression

scientific article

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

scientific article published on 07 February 2022

A stele-enriched gene regulatory network in the Arabidopsis root

scientific article

ASYMMETRIC CELL DIVISION IN PLANTS.

scientific article published on June 1999

Advanced imaging techniques for the study of plant growth and development

scientific article

An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis

scientific article

An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants

scientific article published on April 2007

Analyzing lateral root development: how to move forward

scientific article published on 6 January 2012

Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis

scientific article published on 27 November 2019

Apical-basal polarity: why plant cells don't stand on their heads.

scientific article published on 13 December 2005

Arabidopsis thaliana as a model organism in systems biology

scientific article

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root

scientific article published on 22 August 2017

Bimodular auxin response controls organogenesis in Arabidopsis

scientific article

Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement

scientific article published on 04 December 2008

Brassinosteroid gene regulatory networks at cellular resolution in the <i>Arabidopsis</i> root

scientific article published on 31 March 2023

COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation

article by François Roudier et al published June 2005 in The Plant Cell

Cell identity mediates the response of Arabidopsis roots to abiotic stress.

scientific article published on 24 April 2008

Cell identity regulators link development and stress responses in the Arabidopsis root

scientific article

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.

scientific article published on 21 April 2010

Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines

scientific article published in August 2005

Cell type‐specific transcriptional profiling: implications for metabolite profiling ⬇️

scientific article published on April 1, 2012

Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis

scientific article published on 01 November 2020

Combining expression and comparative evolutionary analysis. The COBRA gene family

scientific article

Control of Arabidopsis Root Development ⬇️

scientific article published on February 9, 2012

Control of Arabidopsis lateral root primordium boundaries by MYB36.

scientific article

Correction: Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis.

scientific article

Cortex proliferation: simple phenotype, complex regulatory mechanisms

scientific article

Detecting separate time scales in genetic expression data

scientific article (publication date: 16 June 2010)

Distinct sensitivities to phosphate deprivation suggest that RGF peptides play disparate roles in Arabidopsis thaliana root development

scientific article

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

scientific article published on 27 October 2016

Evolution, interactions, and biological networks

scientific article

Fluorescence-activated cell sorting in plant developmental biology

scientific article published in January 2010

Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem

scientific article published on 2 October 2017

From genotype to phenotype: systems biology meets natural variation

scientific article published in April 2008

Functional genomics of root growth and development in Arabidopsis

scientific article published on 29 December 2008

GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis

scientific article published on 8 February 2018

Genes and networks regulating root anatomy and architecture.

scientific article published on 20 May 2015

Genotypic recognition and spatial responses by rice roots

scientific article published on 29 January 2013

Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research

scientific article

GiA Roots: software for the high throughput analysis of plant root system architecture.

scientific article

Growth control of root architecture

scholarly article published 2012

HEC of a job regulating stem cells.

scientific article

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

scientific article published on 9 November 2016

High-Throughput, Noninvasive Imaging of Root Systems

scientific article published on 01 January 2013

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

scientific article published on 22 September 2011

High-resolution metabolic mapping of cell types in plant roots

scientific article published on 8 March 2013

High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems.

scientific article

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype ⬇️

scientific article published on March 28, 2011

Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW

scientific article published on 08 February 2019

Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays

scientific article published on 01 January 2016

Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems

scientific article published on 27 January 2010

Information processing without brains--the power of intercellular regulators in plants

scientific article published on April 2010

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

scientific article

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

scientific article published on 31 December 2010

Integrating gene flow, crop biology, and farm management in on‐farm conservation of avocado (Persea americana, Lauraceae) ⬇️

scientific article published on 01 November 2003

Integrative systems biology: an attempt to describe a simple weed

scientific article published on 23 January 2012

Intercellular communication during plant development.

scientific article published on 08 March 2011

Intercellular movement of the putative transcription factor SHR in root patterning.

scientific article

Intergenic and genic sequence lengths have opposite relationships with respect to gene expression

scientific article

Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root

scientific article

Lateral Root Initiation: The Emergence of New Primordia Following Cell Death

scientific article published on 01 February 2020

MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root

scientific article

Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment

scientific article

Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT.

scientific article published in June 2005

Mechanism and function of root circumnutation

scientific article

Mechanism and function of root circumnutation

Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus.

scientific article published on 23 February 2017

Mechanisms regulating SHORT-ROOT intercellular movement

scientific article published in October 2004

MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots

scientific article

Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root

scientific article published on 30 July 2018

Molecular analysis of the SCARECROW gene in maize reveals a common basis for radial patterning in diverse meristems.

scientific article

Network building: transcriptional circuits in the root

scientific article

Omics meet networks - using systems approaches to infer regulatory networks in plants

scientific article published on 28 December 2009

Oscillating gene expression determines competence for periodic Arabidopsis root branching

scientific article

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

scientific article

Patterning the primary root in Arabidopsis

scientific article

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

scientific article published on 17 March 2014

Phage-Resistant Bacteria Reveal a Role for Potassium in Root Colonization

scientific article published on 17 August 2021

Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future

scientific article published on 01 August 2020

Plant stem cell niches: standing the test of time

scientific article

Polarized Radicals ⬇️

scientific article published on April 11, 2013

Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer

scientific article published in September 2009

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT

scientific article published in 2022

Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips

scientific article

Quantification of transcription factor expression from Arabidopsis images

scientific article published in July 2006

Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture.

scientific article published on 11 February 2015

RGF1 controls root meristem size through ROS signalling

scientific article published on 04 December 2019

Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root.

scientific article

Reconstructing spatiotemporal gene expression data from partial observations

scientific article published on 16 July 2009

Regulation of Division and Differentiation of Plant Stem Cells

article

Root development

scientific article

Root layers: complex regulation of developmental patterning

scientific article published on 09 July 2008

Shootward and rootward: peak terminology for plant polarity

article

Signaling in and out: control of cell division and differentiation in the shoot and root.

scientific article

Signals that regulate stem cell activity during plant development

scientific article

Spatial coordination between stem cell activity and cell differentiation in the root meristem

scientific article

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.

scientific article

Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development

scientific article

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.

scientific article published on 21 October 2016

Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis

scientific article

Systems approaches to identifying gene regulatory networks in plants.

scientific article

Systems biology.

scientific article published on March 2004

The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth

scientific article

The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion

scientific article published on October 2002

The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size

scientific article published on 14 March 2019

The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.

scientific article

The auxin influx carrier LAX3 promotes lateral root emergence

article

The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots

scientific article

The protein expression landscape of the Arabidopsis root.

scientific article

Time-based patterning in development: The role of oscillating gene expression.

scientific article published on May 2011

Tissue-Specific Transcriptome Profiling in Arabidopsis Roots

scientific article published on 01 January 2017

To branch or not to branch: the role of pre-patterning in lateral root formation

scientific article

Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

scientific article published on 11 June 2016

Transcription factors and hormones: new insights into plant cell differentiation

scientific article

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots

scholarly article

Transcriptional control of tissue formation throughout root development

scientific article

Transcriptional networks controlling plant development

scientific article

Transcriptional networks in root cell fate specification

scientific article

Transcriptional profile of the Arabidopsis root quiescent center

scientific article

Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root

scientific article published in November 2010

Transcriptional switches direct plant organ formation and patterning.

scientific article published on January 2012

Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation

scientific article

Unique cell-type-specific patterns of DNA methylation in the root meristem.

scientific article

Unraveling the dynamic transcriptome

scientific article published on September 2006

Using cauliflower to find conserved non-coding regions in Arabidopsis

scientific article published on 01 June 2002

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis

scientific article published on 2 May 2006

X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture

scientific article published on 16 May 2016

managedpop: a computer simulation to project allelic diversity in managed populations with overlapping generations

scientific article published in 2002

β-Cyclocitral is a conserved root growth regulator

scientific article published on 08 May 2019

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