Structural and Functional Analyses of Hub MicroRNAs in an Integrated Gene Regulatory Network of Arabidopsis

MicroRNAs and Their Regulatory Roles in Plant–Environment Interactions

(2019) Xianwei Song et al.   Annual Review of Plant Biology

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

(2019) Matthew D. Brooks et al.   Nature Communications

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

(2018) Dijun Chen et al.   Nature Communications

Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms

(2016) Allison Gaudinier et al.   Annual Review of Plant Biology

Genome wide predictions of miRNA regulation by transcription factors

(2016) Matthew Ruffalo et al.   BIOINFORMATICS

A miR-34a-Numb Feedforward Loop Triggered by Inflammation Regulates Asymmetric Stem Cell Division in Intestine and Colon Cancer

(2016) Pengcheng Bu et al.   Cell Stem Cell

Repression of MYBL2 by Both microRNA858a and HY5 Leads to the Activation of Anthocyanin Biosynthetic Pathway in Arabidopsis

(2016) Yulong Wang et al.   Molecular Plant

FAR-RED ELONGATED HYPOCOTYL3activatesSEPALLATA2but inhibitsCLAVATA3to regulate meristem determinacy and maintenance inArabidopsis

(2016) Dongming Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A transcription factor hierarchy defines an environmental stress response network

(2016) L. Song et al.   SCIENCE

AnArabidopsisTranscriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors

(2015) Jinpu Jin et al.   MOLECULAR BIOLOGY AND EVOLUTION

StarScan: a web server for scanning small RNA targets from degradome sequencing data

(2015) Shun Liu et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Transcription Factor NAC016 Promotes Drought Stress Responses by RepressingAREB1Transcription through a Trifurcate Feed-Forward Regulatory Loop Involving NAP

(2015) Yasuhito Sakuraba et al.   PLANT CELL

MYBD employed by HY5 increases anthocyanin accumulation via repression ofMYBL2in Arabidopsis

(2015) Nguyen Hoai Nguyen et al.   PLANT JOURNAL

An Arabidopsis gene regulatory network for secondary cell wall synthesis

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

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

(2014) K. S. Heyndrickx et al.   PLANT CELL

MicroRNA408 Is Critical for theHY5-SPL7Gene Network That Mediates the Coordinated Response to Light and Copper

(2014) Huiyong Zhang et al.   PLANT CELL

Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay

(2014) Q. Liu et al.   PLANT CELL

Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis

(2013) Xin Zhao et al.   GENOMICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

SQUAMOSA promoter binding protein-like7regulated microRNA408 is required for vegetative development in Arabidopsis

(2013) Huiyong Zhang et al.   PLANT JOURNAL

New insights into the regulation of anthocyanin biosynthesis in fruits

(2013) Laura Jaakola   TRENDS IN PLANT SCIENCE

Comparative Analysis of MicroRNA Promoters in Arabidopsis and Rice

(2013) Xin Zhao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Regulation of Brassinosteroid Biosynthesis and InactivationF

(2012) Baolin Zhao et al.   Journal of Integrative Plant Biology

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis

(2012) Xiaozeng Yang et al.   PLANT JOURNAL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

MicroRNA-regulated feed forward loop network

(2011) Ezra E.W. Cohen et al.   CELL CYCLE

Brassinosteroid Enhances Jasmonate-Induced Anthocyanin Accumulation in Arabidopsis Seedlings

(2011) Zhihong Peng et al.   Journal of Integrative Plant Biology

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

MicroRNA networks and developmental plasticity in plants

(2011) Ignacio Rubio-Somoza et al.   TRENDS IN PLANT SCIENCE

MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems

(2010) H. Herranz et al.   GENES & DEVELOPMENT

Genome-wide mapping of the HY5-mediated genenetworks in Arabidopsis that involve both transcriptional and post-transcriptional regulation

(2010) Huiyong Zhang et al.   PLANT JOURNAL

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis

(2009) J. Zhou et al.   PLANT CELL

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs

(2008) Xueping Yu et al.   NUCLEIC ACIDS RESEARCH

MYBL2 is a new regulator of flavonoid biosynthesis inArabidopsis thaliana

(2008) Christian Dubos et al.   PLANT JOURNAL

AtMYBL2, a protein with a single MYB domain, acts as a negative regulator of anthocyanin biosynthesis in Arabidopsis

(2008) Kyoko Matsui et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY