Divergent gene expression networks underlie morphological diversity of abscission zones in grasses

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

(2018) Sandra Odonkor et al.   Frontiers in Plant Science

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

(2018) Jeffery M. Saarela et al.   PeerJ

QuantSeq 3′ mRNA sequencing for RNA quantification

(2018) Pamela Moll et al.   NATURE METHODS

Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology inSetaria viridis

(2017) Jiani Yang et al.   PLANT CELL

KNOX Protein OSH15 Induces Grain Shattering by Repressing Lignin Biosynthesis Genes

(2017) Jinmi Yoon et al.   PLANT PHYSIOLOGY

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Abscission zone development in Setaria viridis and its domesticated relative, Setaria italica

(2016) John G. Hodge et al.   AMERICAN JOURNAL OF BOTANY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Evolution of the Grain Dispersal System in Barley

(2015) Mohammad Pourkheirandish et al.   CELL

A worldwide phylogenetic classification of the Poaceae (Gramineae)

(2015) Robert J. SORENG et al.   Journal of Systematics and Evolution

Morphological diversity and genetic regulation of inflorescence abscission zones in grasses

(2014) Andrew N. Doust et al.   AMERICAN JOURNAL OF BOTANY

Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives

(2014) Daniel J. Layton et al.   AMERICAN JOURNAL OF BOTANY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The BEL1-type homeobox geneSH5induces seed shattering by enhancing abscission-zone development and inhibiting lignin biosynthesis

(2014) Jinmi Yoon et al.   PLANT JOURNAL

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

(2014) A. N. Doust et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation of fruit dehiscence pathways betweenLepidium campestreandArabidopsis thalianasheds light on the regulation ofINDEHISCENT

(2013) Teresa Lenser et al.   PLANT JOURNAL

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1

(2012) Y. Zhou et al.   PLANT CELL

Functional analyses of AGAMOUS family members in Nicotiana benthamiana clarify the evolution of early and late roles of C-function genes in eudicots

(2012) Chloé Fourquin et al.   PLANT JOURNAL

Evidence that an evolutionary transition from dehiscent to indehiscent fruits inLepidium(Brassicaceae) was caused by a change in the control of valve margin identity genes

(2012) Andreas Mühlhausen et al.   PLANT JOURNAL

Understanding the basis of a novel fruit type in Brassicaceae: conservation and deviation in expression patterns of six genes

(2012) Mariano Avino et al.   EvoDevo

A novel role for the floral homeotic gene APETALA2 during Arabidopsis fruit development

(2011) J. J. Ripoll et al.   DEVELOPMENT

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Molecular evolution of shattering loci in U.S. weedy rice

(2010) CARRIE S. THURBER et al.   MOLECULAR ECOLOGY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

MADS-box gene expression and implications for developmental origins of the grass spikelet

(2009) Jill C. Preston et al.   AMERICAN JOURNAL OF BOTANY

Inactivation of the CTD phosphatase-like geneOsCPL1enhances the development of the abscission layer and seed shattering in rice

(2009) Hyeonso Ji et al.   PLANT JOURNAL

Evolution of the Turtle Body Plan by the Folding and Creation of New Muscle Connections

(2009) H. Nagashima et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS