Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression

Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants

(2017) Dong Wang et al.   PLANT JOURNAL

Transcription of Nuclear Organellar DNA in a Model Plant System

(2014) Dong Wang et al.   Genome Biology and Evolution

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

TRANSLOCASE OF THE INNER MEMBRANE9 and 10 Are Essential for Maintaining Mitochondrial Function during Early Embryo Cell and Endosperm Free Nucleus Divisions in Arabidopsis

(2014) Y. Deng et al.   PLANT PHYSIOLOGY

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

(2013) Qian-Hao Zhu et al.   NEW PHYTOLOGIST

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

(2010) M. Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

SHORT HYPOCOTYL UNDER BLUE1 Associates with MINISEED3 and HAIKU2 Promoters in Vivo to Regulate Arabidopsis Seed Development

(2009) Y. Zhou et al.   PLANT CELL

Local maternal control of seed size by KLUH/CYP78A5-dependent growth signaling

(2009) N. M. Adamski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

An atypical soybean leucine-rich repeat receptor-like kinase, GmLRK1, may be involved in the regulation of cell elongation

(2008) Sunghan Kim et al.   PLANTA

Identifying essential genes in Arabidopsis thaliana

(2008) David Meinke et al.   TRENDS IN PLANT SCIENCE