Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana

Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?

(2017) Anna-Lisa Paul et al.   PLoS One

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

(2017) Wenbin Mei et al.   Frontiers in Plant Science

The effect of spaceflight on the gravity-sensing auxin gradient of roots: GFP reporter gene microscopy on orbit

(2016) Robert J Ferl et al.   NPJ Microgravity

Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development

(2015) T. Kwon et al.   AMERICAN JOURNAL OF BOTANY

Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

(2015) Sergei Filichkin et al.   CURRENT OPINION IN PLANT BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions inBrachypodium distachyon

(2015) Kranthi K. Mandadi et al.   PLANT CELL

Insect herbivory elicits genome-wide alternative splicing responses inNicotiana attenuata

(2015) Zhihao Ling et al.   PLANT JOURNAL

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

(2015) Shawn R. Thatcher et al.   PLANT PHYSIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype

(2014) Nicola Vitulo et al.   BMC PLANT BIOLOGY

Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight

(2013) Anna-Lisa Paul et al.   BMC PLANT BIOLOGY

Spaceflight Transcriptomes: Unique Responses to a Novel Environment

(2012) Anna-Lisa Paul et al.   ASTROBIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Plant growth strategies are remodeled by spaceflight

(2012) Anna-Lisa Paul et al.   BMC PLANT BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS