Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

(2018) Pierre-François Perroud et al.   PLANT JOURNAL

Dispersal biophysics and adaptive significance of dimorphic diaspores in the annual Aethionema arabicum (Brassicaceae)

(2018) Waheed Arshad et al.   NEW PHYTOLOGIST

Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae

(2017) Per K I Wilhelmsson et al.   Genome Biology and Evolution

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

(2017) Wojciech Antosz et al.   PLANT CELL

TAF15b, involved in the autonomous pathway for flowering, represses transcription of FLOWERING LOCUS C

(2017) Hyunjoo Eom et al.   PLANT JOURNAL

NYEs/SGRs-mediated chlorophyll degradation is critical for detoxification during seed maturation in Arabidopsis

(2017) Zhongpeng Li et al.   PLANT JOURNAL

Extensive translational regulation during seed germination revealed by polysomal profiling

(2016) Bing Bai et al.   NEW PHYTOLOGIST

Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum

(2016) Teresa Lenser et al.   PLANT PHYSIOLOGY

Seed maturation: Simplification of control networks in plants

(2016) Martine Devic et al.   PLANT SCIENCE

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits

(2015) Yaqiong Wang et al.   NEW PHYTOLOGIST

Staying Alive: Molecular Aspects of Seed Longevity

(2015) Naoto Sano et al.   PLANT AND CELL PHYSIOLOGY

Regulation of mRNA translation controls seed germination and is critical for seedling vigor

(2015) Marc Galland et al.   Frontiers in Plant Science

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 Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

(2014) Ramesh Yelagandula et al.   CELL

A histone methyltransferase inhibits seed germination by increasingPIF1 mRNA expression in imbibed seeds

(2014) Nayoung Lee et al.   PLANT JOURNAL

The chromatin landscape of the mossPhyscomitrella patensand its dynamics during development and drought stress

(2014) Thomas Widiez et al.   PLANT JOURNAL

Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals

(2014) Steven Footitt et al.   PLANT JOURNAL

Specialization of Oleosins in Oil Body Dynamics during Seed Development in Arabidopsis Seeds

(2014) M. Miquel et al.   PLANT PHYSIOLOGY

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

(2014) Zong Hong Zhang et al.   PLoS One

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

(2013) Elsa Góngora-Castillo et al.   NATURAL PRODUCT REPORTS

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

HISTONE DEACETYLASE19 Interacts with HSL1 and Participates in the Repression of Seed Maturation Genes inArabidopsisSeedlings

(2013) Yi Zhou et al.   PLANT CELL

Mutations in HISTONE ACETYLTRANSFERASE1 affect sugar response and gene expression in Arabidopsis

(2013) Timothy J. Heisel et al.   Frontiers in Plant Science

Histone H2A variants in nucleosomes and chromatin: more or less stable?

(2012) C. Bonisch et al.   NUCLEIC ACIDS RESEARCH

Molecular mechanisms of seed dormancy

(2012) KAI GRAEBER et al.   PLANT CELL AND ENVIRONMENT

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

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

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study

(2011) Kai Graeber et al.   PLANT CELL

Beyond gibberellins and abscisic acid: how ethylene and jasmonates control seed germination

(2011) Ada Linkies et al.   PLANT CELL REPORTS

Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in Arabidopsis

(2011) D. Xiang et al.   PLANT PHYSIOLOGY

Identification of the Arabidopsis REDUCED DORMANCY 2 Gene Uncovers a Role for the Polymerase Associated Factor 1 Complex in Seed Dormancy

(2011) Yongxiu Liu et al.   PLoS One

Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation

(2011) M. van Zanten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

(2010) A. Bräutigam et al.   PLANT BIOLOGY

Stored and neosynthesized mRNA in Arabidopsis seeds: effects of cycloheximide and controlled deterioration treatment on the resumption of transcription during imbibition

(2010) Mitsuhiro Kimura et al.   PLANT MOLECULAR BIOLOGY

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

(2010) B. H. Le et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physiological and developmental regulation of seed oil production

(2010) Sébastien Baud et al.   PROGRESS IN LIPID RESEARCH

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

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

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

(2009) J. G. Gibbons et al.   MOLECULAR BIOLOGY AND EVOLUTION

Role of WRINKLED1 in the transcriptional regulation of glycolytic and fatty acid biosynthetic genes in Arabidopsis

(2009) Sébastien Baud et al.   PLANT JOURNAL

The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2

(2009) Ihab B. Lolas et al.   PLANT JOURNAL

LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana

(2008) Michaela Hundertmark et al.   BMC GENOMICS

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Seed Dehydration and the Establishment of Desiccation Tolerance During Seed Maturation is Altered in the Arabidopsis thaliana Mutant atem6-1

(2008) A. J. Manfre et al.   PLANT AND CELL PHYSIOLOGY