Modelling transcriptional networks in leaf senescence

Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs

(2013) Alexandra Pokhilko et al.   BMC Systems Biology

ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription

(2013) Mamoona Rauf et al.   EMBO REPORTS

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves

(2013) Richard Hickman et al.   PLANT JOURNAL

The Single-Stranded DNA-Binding Protein WHIRLY1 Represses WRKY53 Expression and Delays Leaf Senescence in a Developmental Stage-Dependent Manner in Arabidopsis

(2013) Y. Miao et al.   PLANT PHYSIOLOGY

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

(2013) Takeshi Hase et al.   PLoS Computational Biology

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

(2012) C. A. Penfold et al.   BIOINFORMATICS

The Complex Regulation of Senescence

(2012) Andreas M. Fischer   CRITICAL REVIEWS IN PLANT SCIENCES

Gene Network Analysis and Functional Studies of Senescence-associated Genes Reveal Novel Regulators of Arabidopsis Leaf SenescenceF

(2012) Zhonghai Li et al.   Journal of Integrative Plant Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

(2012) O. Windram et al.   PLANT CELL

Towards systems biological understanding of leaf senescence

(2012) Yongfeng Guo   PLANT MOLECULAR BIOLOGY

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

(2012) C. Smaczniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WRKY22 transcription factor mediates dark-induced leaf senescence in Arabidopsis

(2011) Xiang Zhou et al.   MOLECULES AND CELLS

TheArabidopsisNAC Transcription Factor VNI2 Integrates Abscisic Acid Signals into Leaf Senescence via theCOR/RDGenes

(2011) So-Dam Yang et al.   PLANT CELL

High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation

(2011) E. Breeze et al.   PLANT CELL

The impact of light intensity on shade-induced leaf senescence

(2011) BASTIAAN BROUWER et al.   PLANT CELL AND ENVIRONMENT

Directed Partial Correlation: Inferring Large-Scale Gene Regulatory Network through Induced Topology Disruptions

(2011) Yinyin Yuan et al.   PLoS One

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

The RAV1 transcription factor positively regulates leaf senescence in Arabidopsis

(2010) Hye Ryun Woo et al.   JOURNAL OF EXPERIMENTAL BOTANY

LSD: a leaf senescence database

(2010) X. Liu et al.   NUCLEIC ACIDS RESEARCH

The R-R-Type MYB-Like Transcription Factor, AtMYBL, is Involved in Promoting Leaf Senescence and Modulates an Abiotic Stress Response in Arabidopsis

(2010) Xia Zhang et al.   PLANT AND CELL PHYSIOLOGY

A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence

(2010) Salma Balazadeh 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

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

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

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Overexpression of the Rap2.4f transcriptional factor in Arabidopsis promotes leaf senescence

(2010) Heng Xu et al.   Science China-Life Sciences

Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana

(2009) S. J. Kiddle et al.   BIOINFORMATICS

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

(2009) Tarmo Äijö et al.   BIOINFORMATICS

Granger causality vs. dynamic Bayesian network inference: a comparative study

(2009) Cunlu Zou et al.   BMC BIOINFORMATICS

A MATLAB toolbox for Granger causal connectivity analysis

(2009) Anil K. Seth   JOURNAL OF NEUROSCIENCE METHODS

GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis

(2009) M. T. Waters et al.   PLANT CELL

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Trifurcate Feed-Forward Regulation of Age-Dependent Cell Death Involving miR164 in Arabidopsis

(2009) J. H. Kim et al.   SCIENCE

Transcriptome analysis of Medicago truncatula leaf senescence: similarities and differences in metabolic and transcriptional regulations as compared with Arabidopsis , nodule senescence and nitric oxide signalling

(2008) Roberto De Michele et al.   NEW PHYTOLOGIST

A novel upstream regulator ofWRKY53transcription during leaf senescence inArabidopsis thaliana

(2008) Y. Miao et al.   PLANT BIOLOGY

Identification of early senescence-associated genes in rice flag leaves

(2008) Li Liu et al.   PLANT MOLECULAR BIOLOGY

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis

(2008) V. Srinivasasainagendra et al.   PLANT PHYSIOLOGY

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