ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks

The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem

(2013) Srilakshmi Makkena et al.   BMC PLANT BIOLOGY

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

(2012) Alfredo Cruz-Ramírez et al.   CELL

The Reconstruction of Transcriptional Networks Reveals Critical Genes with Implications for Clinical Outcome of Multiple Myeloma

(2011) L. Agnelli et al.   CLINICAL CANCER RESEARCH

A Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots

(2011) Anthony Bishopp et al.   CURRENT BIOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Auxin triggers a genetic switch

(2011) Steffen Lau et al.   NATURE CELL BIOLOGY

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

The Basic Helix-Loop-Helix Transcription Factor MYC2 Directly RepressesPLETHORAExpression during Jasmonate-Mediated Modulation of the Root Stem Cell Niche inArabidopsis

(2011) Qian Chen et al.   PLANT CELL

Disruption of LACCASE4 and 17 Results in Tissue-Specific Alterations to Lignification of Arabidopsis thaliana Stems

(2011) S. Berthet et al.   PLANT CELL

OVATE FAMILY PROTEIN4 (OFP4) interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana

(2011) Eryang Li et al.   PLANT JOURNAL

The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems

(2011) Carmen Dorca-Fornell et al.   PLANT JOURNAL

VASCULAR-RELATED NAC-DOMAIN 7 directly regulates the expression of a broad range of genes for xylem vessel formation

(2011) Masatoshi Yamaguchi et al.   PLANT JOURNAL

Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT

(2011) Hiromi Ogasawara et al.   PLANT MOLECULAR BIOLOGY

Genome-Wide Direct Target Analysis Reveals a Role for SHORT-ROOT in Root Vascular Patterning through Cytokinin Homeostasis

(2011) H. Cui et al.   PLANT PHYSIOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Mutation of the chitinase-like protein-encoding AtCTL2 gene enhances lignin accumulation in dark-grown Arabidopsis seedlings

(2010) Md Aktar Hossain et al.   JOURNAL OF PLANT PHYSIOLOGY

Global Analysis of Direct Targets of Secondary Wall NAC Master Switches in Arabidopsis

(2010) Ruiqin Zhong et al.   Molecular Plant

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

(2010) R. Sozzani et al.   NATURE

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

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

ArabidopsisVASCULAR-RELATED NAC-DOMAIN6 Directly Regulates the Genes That Govern Programmed Cell Death and Secondary Wall Formation during Xylem Differentiation

(2010) Kyoko Ohashi-Ito et al.   PLANT CELL

VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation inArabidopsis

(2010) Masatoshi Yamaguchi et al.   PLANT CELL

LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems

(2010) Silke Schulze et al.   PLANT JOURNAL

Transcriptional reprogramming regulated by WRKY18 and WRKY40 facilitates powdery mildew infection of Arabidopsis

(2010) Shree P. Pandey et al.   PLANT JOURNAL

A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana

(2010) Xiaofei Yu et al.   PLANT JOURNAL

Arabidopsis Homologs of the Petunia HAIRY MERISTEM Gene Are Required for Maintenance of Shoot and Root Indeterminacy

(2010) E. M. Engstrom et al.   PLANT PHYSIOLOGY

TRICHOME BIREFRINGENCE and Its Homolog AT5G01360 Encode Plant-Specific DUF231 Proteins Required for Cellulose Biosynthesis in Arabidopsis

(2010) V. Bischoff et al.   PLANT PHYSIOLOGY

VASCULAR-RELATED NAC-DOMAIN6 and VASCULAR-RELATED NAC-DOMAIN7 Effectively Induce Transdifferentiation into Xylem Vessel Elements under Control of an Induction System

(2010) M. Yamaguchi et al.   PLANT PHYSIOLOGY

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Spatio-temporal sequence of cross-regulatory events in root meristem growth

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

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells

(2009) K. Basso et al.   BLOOD

Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves

(2009) T. J. Donner et al.   DEVELOPMENT

MYB83 Is a Direct Target of SND1 and Acts Redundantly with MYB46 in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis

(2009) R. L. McCarthy et al.   PLANT AND CELL PHYSIOLOGY

Identifying New Components Participating in the Secondary Cell Wall Formation of Vessel Elements in Zinnia and Arabidopsis

(2009) S. Endo et al.   PLANT CELL

Brassinosteroid signaling and auxin transport are required to establish the periodic pattern of Arabidopsis shoot vascular bundles

(2009) M. Ibanes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann et al.   BIOINFORMATICS

Flowering as a Condition for Xylem Expansion in Arabidopsis Hypocotyl and Root

(2008) Richard Sibout et al.   CURRENT BIOLOGY

Evolutionary plasticity of genetic interaction networks

(2008) Julia Tischler et al.   NATURE GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis

(2008) R. Zhong et al.   PLANT CELL

Cysteine proteases XCP1 and XCP2 aid micro-autolysis within the intact central vacuole during xylogenesis in Arabidopsis roots

(2008) Utku Avci et al.   PLANT JOURNAL

VASCULAR-RELATED NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots

(2008) Masatoshi Yamaguchi et al.   PLANT JOURNAL

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

(2008) Kimberly L. Gallagher et al.   PLANT JOURNAL

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

A Genetic Framework for the Control of Cell Division and Differentiation in the Root Meristem

(2008) R. D. Ioio et al.   SCIENCE

Transcription factor AtTCP14 regulates embryonic growth potential during seed germination inArabidopsis thaliana

(2007) Kiyoshi Tatematsu et al.   PLANT JOURNAL