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

Mathematical modelling ofWOX5- andCLE40-mediated columella stem cell homeostasis inArabidopsis

(2015) Sarah Richards et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetic control of distal stem cell fate within root and embryonic meristems

(2015) B. C. W. Crawford et al.   SCIENCE

Transcriptional control of tissue formation throughout root development

(2015) M. A. Moreno-Risueno et al.   SCIENCE

Fast Bayesian inference for gene regulatory networks using ScanBMA

(2014) William Young et al.   BMC Systems Biology

WOX5 Suppresses CYCLIN D Activity to Establish Quiescence at the Center of the Root Stem Cell Niche

(2014) Celine Forzani et al.   CURRENT BIOLOGY

Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module

(2014) Josep Vilarrasa-Blasi et al.   DEVELOPMENTAL CELL

An Arabidopsis gene regulatory network for secondary cell wall synthesis

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

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

Novel functional roles for PERIANTHIA and SEUSS during floral organ identity specification, floral meristem termination, and gynoecial development

(2014) April N. Wynn et al.   Frontiers in Plant Science

A bHLH Complex Controls Embryonic Vascular Tissue Establishment and Indeterminate Growth in Arabidopsis

(2013) Bert De Rybel et al.   DEVELOPMENTAL CELL

A Bistable Circuit Involving SCARECROW-RETINOBLASTOMA Integrates Cues to Inform Asymmetric Stem Cell Division

(2012) Alfredo Cruz-Ramírez et al.   CELL

A PHABULOSA/Cytokinin Feedback Loop Controls Root Growth in Arabidopsis

(2012) Raffaele Dello Ioio et al.   CURRENT BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcriptomic Characterization of a Synergistic Genetic Interaction during Carpel Margin Meristem Development in Arabidopsis thaliana

(2011) April N. Wynn et al.   PLoS One

The bZIP Transcription Factor PERIANTHIA: A Multifunctional Hub for Meristem Control

(2011) Annette T. Maier et al.   Frontiers in Plant Science

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

(2010) Annelie Carlsbecker et al.   NATURE

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

(2010) R. Sozzani et al.   NATURE

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data

(2010) Andrea Rau et al.   Statistical Applications in Genetics and Molecular Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A Signaling Module Controlling the Stem Cell Niche in Arabidopsis Root Meristems

(2009) Yvonne Stahl et al.   CURRENT BIOLOGY

Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression

(2009) A. T. Maier et al.   DEVELOPMENT

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

(2009) Daniel Marbach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

High-Resolution Whole-Mount Imaging of Three-Dimensional Tissue Organization and Gene Expression Enables the Study of Phloem Development and Structure in Arabidopsis

(2008) E. Truernit et al.   PLANT CELL