Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity

(2014) Lu Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-Nucleotide Resolution Mapping of the Gossypium raimondii Transcriptome Reveals a New Mechanism for Alternative Splicing of Introns

(2014) Qin Li et al.   Molecular Plant

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

Genome-Wide Landscape of Alternative Splicing Events in Brachypodium distachyon

(2013) B. Walters et al.   DNA RESEARCH

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

(2013) X. Lu et al.   PLANT PHYSIOLOGY

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants

(2013) Mohammed Nuruzzaman et al.   Frontiers in Microbiology

Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

(2012) Piyanuch Piyatrakul et al.   BMC PLANT BIOLOGY

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

(2012) Rachel S. Meyer et al.   NEW PHYTOLOGIST

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

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Vitamin B6: Killing two birds with one stone?

(2010) Sutton Mooney et al.   PHYTOCHEMISTRY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

The molecular basis for stress-induced acquisition of somatic embryogenesis

(2009) Omid Karami et al.   MOLECULAR BIOLOGY REPORTS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

(2008) Gerben van Ooijen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE