Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response

The bHLH Transcription Factor bHLH104 Interacts with IAA-LEUCINE RESISTANT3 and Modulates Iron Homeostasis in Arabidopsis

(2015) Jie Zhang et al.   PLANT CELL

Arabidopsis WRKY57 Functions as a Node of Convergence for Jasmonic Acid- and Auxin-Mediated Signaling in Jasmonic Acid-Induced Leaf Senescence

(2014) Y. Jiang et al.   PLANT CELL

Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network

(2013) Ashish Misra et al.   BMC Systems Biology

MYB10 and MYB72 Are Required for Growth under Iron-Limiting Conditions

(2013) Christine M. Palmer et al.   PLoS Genetics

Iron Uptake, Translocation, and Regulation in Higher Plants

(2012) Takanori Kobayashi et al.   Annual Review of Plant Biology

Optimal timepoint sampling in high-throughput gene expression experiments

(2012) Bruce A. Rosa et al.   BIOINFORMATICS

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

(2012) O. Windram et al.   PLANT CELL

Arabidopsis bHLH100 and bHLH101 Control Iron Homeostasis via a FIT-Independent Pathway

(2012) Alicia B. Sivitz et al.   PLoS One

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

(2011) Jeff Nie et al.   BMC Systems Biology

Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

(2011) Anjali S. Iyer-Pascuzzi et al.   DEVELOPMENTAL CELL

Enhanced Y1H assays for Arabidopsis

(2011) Allison Gaudinier et al.   NATURE METHODS

The FRD3 Citrate Effluxer Promotes Iron Nutrition between Symplastically Disconnected Tissues throughout Arabidopsis Development

(2011) H. Roschzttardtz et al.   PLANT CELL

MicroRNAs Regulate the Timing of Embryo Maturation in Arabidopsis

(2011) M. R. Willmann et al.   PLANT PHYSIOLOGY

Reverse engineering gene regulatory network from microarray data using linear time-variant model

(2010) Mitra Kabir et al.   BMC BIOINFORMATICS

The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots

(2010) T. A. Long et al.   PLANT CELL

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

(2009) Mika Gustafsson et al.   Annals of the New York Academy of Sciences

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses

(2009) Thomas J Buckhout et al.   BMC GENOMICS

Inference of Gene Regulatory Networks Using Time-Series Data: A Survey

(2009) Chao Sima et al.   CURRENT GENOMICS

Learning Genetic Regulatory Network Connectivity from Time Series Data

(2009) Nathan A Barker et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Repression of Seed Maturation Genes by a Trihelix Transcriptional Repressor in Arabidopsis Seedlings

(2009) M.-J. Gao et al.   PLANT CELL

Conservation of Lotus and Arabidopsis Basic Helix-Loop-Helix Proteins Reveals New Players in Root Hair Development

(2009) B. Karas et al.   PLANT PHYSIOLOGY

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis

(2008) Youxi Yuan et al.   CELL RESEARCH

Inferring Gene Regulatory Networks From Expression Data by Discovering Fuzzy Dependency Relationships

(2008) P.C.H. Ma et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

(2008) J. R. Dinneny et al.   SCIENCE