Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

(2018) Vân Anh Huynh-Thu et al.   Scientific Reports

A Maize Gene Regulatory Network for Phenolic Metabolism

(2017) Fan Yang et al.   Molecular Plant

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data

(2017) Ji Huang et al.   PLANT PHYSIOLOGY

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Enhancing gene regulatory network inference through data integration with markov random fields

(2017) Michael Banf et al.   Scientific Reports

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

(2016) Lin Li et al.   BMC GENOMICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

CLAVATA-WUSCHEL signaling in the shoot meristem

(2016) Marc Somssich et al.   DEVELOPMENT

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

Gene regulatory network inference using fused LASSO on multiple data sets

(2016) Nooshin Omranian et al.   Scientific Reports

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

(2015) Chi-Nga Chow et al.   NUCLEIC ACIDS RESEARCH

MaizeGDB update: new tools, data and interface for the maize model organism database

(2015) Carson M. Andorf et al.   NUCLEIC ACIDS RESEARCH

RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

(2015) Junpeng Zhan et al.   PLANT CELL

Annotation of gene function in citrus using gene expression information and co-expression networks

(2014) Darren CJ Wong et al.   BMC PLANT BIOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

The Maize TFome - development of a transcription factor open reading frame collection for functional genomics

(2014) Brett Burdo et al.   PLANT JOURNAL

Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response ofArabidopsis thalianaroots

(2014) José M. Alvarez et al.   PLANT JOURNAL

Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development

(2014) Jian Chen et al.   PLANT PHYSIOLOGY

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

(2014) Jose L. Pruneda-Paz et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A comparative study of statistical methods used to identify dependencies between gene expression signals

(2013) S. de Siqueira Santos et al.   BRIEFINGS IN BIOINFORMATICS

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Topological analysis and interactive visualization of biological networks and protein structures

(2012) Nadezhda T Doncheva et al.   Nature Protocols

TCP transcription factors interact with AS2 in the repression of class-I KNOX genes in Arabidopsis thaliana

(2012) Ziyu Li et al.   PLANT JOURNAL

A High-Throughput Screening System for Arabidopsis Transcription Factors and Its Application to Med25-Dependent Transcriptional Regulation

(2011) Bin Ou et al.   Molecular Plant

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

Classification and regression trees

(2011) Wei-Yin Loh   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

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

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

BNFinder: exact and efficient method for learning Bayesian networks

(2008) B. Wilczynski et al.   BIOINFORMATICS

The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis

(2008) Stefan Schwarz et al.   PLANT MOLECULAR BIOLOGY