Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress

Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry

(2017) Yongping Li et al.   PLANT JOURNAL

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis )

(2017) Taotao Wang et al.   PLANT JOURNAL

Generation, Annotation, and Analysis of a Large-Scale Expressed Sequence Tag Library from Arabidopsis pumila to Explore Salt-Responsive Genes

(2017) Xianzhong Huang et al.   Frontiers in Plant Science

Transcriptome analysis of hexaploid hulless oat in response to salinity stress

(2017) Bin Wu et al.   PLoS One

RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant

(2017) Hongchun Xiong et al.   Scientific Reports

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

(2016) Renesh Bedre et al.   BMC GENOMICS

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

De Novo Transcriptome Sequencing of Desert Herbaceous Achnatherum splendens (Achnatherum) Seedlings and Identification of Salt Tolerance Genes

(2016) Jiangtao Liu et al.   Genes

NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes

(2016) Andrew S. Marriott et al.   PLoS One

Plant salt tolerance: adaptations in halophytes

(2015) Timothy J. Flowers et al.   ANNALS OF BOTANY

Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance

(2015) Joann Diray-Arce et al.   BMC GENOMICS

Identification and characterization of an ABA-activated MAP kinase cascade inArabidopsis thaliana

(2015) Agyemang Danquah et al.   PLANT JOURNAL

Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues ofSalvia miltiorrhizaand tanshinone biosynthesis

(2015) Zhichao Xu et al.   PLANT JOURNAL

An abscisic acid inducible Arabidopsis MAPKKK, MAPKKK18 regulates leaf senescence via its kinase activity

(2015) Daisuke Matsuoka et al.   PLANT MOLECULAR BIOLOGY

Transcriptome Analysis of Canola (Brassica napus) under Salt Stress at the Germination Stage

(2015) Weihua Long et al.   PLoS One

Mitogen-activated protein kinase cascades in signaling plant growth and development

(2015) Juan Xu et al.   TRENDS IN PLANT SCIENCE

Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa

(2015) Lingyu Zheng et al.   Frontiers in Plant Science

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Construction of a cDNA Library from the Ephemeral Plant Olimarabidopsis pumila and Preliminary Analysis of Expressed Sequence Tags

(2015) Yun-Xia Zhao et al.   ZEITSCHRIFT FUR NATURFORSCHUNG SECTION C-A JOURNAL OF BIOSCIENCES

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress

(2014) Jian Zhang et al.   PLANT CELL REPORTS

Plant salt-tolerance mechanisms

(2014) Ulrich Deinlein et al.   TRENDS IN PLANT SCIENCE

Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna

(2013) Zhen-hua Dang et al.   BMC GENOMICS

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Physiological and molecular mechanisms of plant salt tolerance

(2013) Jin-Lin Zhang et al.   PHOTOSYNTHESIS RESEARCH

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity

(2012) David R Guevara et al.   BMC PLANT BIOLOGY

Cadmium accumulation, activities of antioxidant enzymes, and malondialdehyde (MDA) content in Pistia stratiotes L.

(2012) Yong Li et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

The salt-responsive transcriptome of Populus simonii×Populus nigra via DGE

(2012) Su Chen et al.   GENE

Salt stress or salt shock: which genes are we studying?

(2012) Yuri Shavrukov   JOURNAL OF EXPERIMENTAL BOTANY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Arabidopsis MKK4 mediates osmotic-stress response via its regulation of MPK3 activity

(2011) Sun-Ho Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hormone balance and abiotic stress tolerance in crop plants

(2011) Zvi Peleg et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Arabidopsis MKKK20 is involved in osmotic stress response via regulation of MPK6 activity

(2011) Jae-Min Kim et al.   PLANT CELL REPORTS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

HINKEL kinesin, ANP MAPKKKs and MKK6/ANQ MAPKK, which phosphorylates and activates MPK4 MAPK, constitute a pathway that is required for cytokinesis in Arabidopsis thaliana

(2010) Yuji Takahashi et al.   PLANT AND CELL PHYSIOLOGY

Species, types, distribution, and economic potential of halophytes in China

(2010) Kefu Zhao et al.   PLANT AND SOIL

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ABC transporters: the power to change

(2009) Douglas C. Rees et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of Salinity Tolerance

(2008) Rana Munns et al.   Annual Review of Plant Biology

Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants

(2008) Qi-Yun Zhou et al.   PLANT BIOTECHNOLOGY JOURNAL

ECOLOGY: Crops for a Salinized World

(2008) J. Rozema et al.   SCIENCE