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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members

(2014) Yuqing Xiong et al.   BMC PLANT BIOLOGY

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

(2014) Rajandeep S. Sekhon et al.   PLoS One

Discovering Functional Modules across Diverse Maize Transcriptomes Using COB, the Co-Expression Browser

(2014) Robert J. Schaefer et al.   PLoS One

Genome-Wide Identification, Evolution and Expression Analysis of mTERF Gene Family in Maize

(2014) Yanxin Zhao et al.   PLoS One

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

(2014) M. R. Woodhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Regulatory modules controlling maize inflorescence architecture

(2013) A. L. Eveland et al.   GENOME RESEARCH

Genome-wide identification, splicing, and expression analysis of the myosin gene family in maize (Zea mays)

(2013) Guifeng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Gene duplication as a major force in evolution

(2013) SANTOSHKUMAR MAGADUM et al.   JOURNAL OF GENETICS

A Developmental Transcriptional Network for Maize Defines Coexpression Modules

(2013) G. S. Downs et al.   PLANT PHYSIOLOGY

Maize Metabolic Network Construction and Transcriptome Analysis

(2013) Marcela K. Monaco et al.   Plant Genome

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

Ontogeny of the Maize Shoot Apical Meristem

(2012) E. M. Takacs et al.   PLANT CELL

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

(2011) Shao-Lun Liu et al.   Genome Biology and Evolution

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

(2011) Keiichi Mochida et al.   PLANT AND CELL PHYSIOLOGY

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

(2011) Yupeng Wang et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The collapse of gene complement following whole genome duplication

(2010) David Sankoff et al.   BMC GENOMICS

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Maintenance of duplicate genes and their functional redundancy by reduced expression

(2010) Wenfeng Qian et al.   TRENDS IN GENETICS

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Omics meet networks—using systems approaches to infer regulatory networks in plants

(2009) Miguel A Moreno-Risueno et al.   CURRENT OPINION IN PLANT BIOLOGY

Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

(2009) Cheng Zou et al.   PLoS Genetics

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS