RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges

RNA Sequencing: Platform Selection, Experimental Design, and Data Interpretation

(2018) Yongjun Chu et al.   Nucleic Acid Therapeutics

Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate

(2017) Xinguo Shi et al.   ISME Journal

De novo assembly and characterization of the transcriptome of the newly described dinoflagellate Ansanella granifera : Spotlight on flagellum-associated genes

(2017) Se Hyeon Jang et al.   Marine Genomics

Whole Transcriptomic Analysis Provides Insights into Molecular Mechanisms for Toxin Biosynthesis in a Toxic Dinoflagellate Alexandrium catenella (ACHK-T)

(2017) et al.   Toxins

Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes

(2017) Sarah L. Gierz et al.   Frontiers in Plant Science

Multiplexed gene control reveals rapid mRNA turnover

(2017) Antoine Baudrimont et al.   Science Advances

Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

(2016) Ruoyu Guo et al.   BMC GENOMICS

Sex, Scavengers, and Chaperones: Transcriptome Secrets of DivergentSymbiodiniumThermal Tolerances

(2016) Rachel A. Levin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya

(2016) Yameng Lu et al.   MOLECULAR ECOLOGY

Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion

(2016) Joshua T. Cooper et al.   Frontiers in Microbiology

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes

(2015) Jan M Meyer et al.   BMC GENOMICS

Metatranscriptome profiling reveals versatile N-nutrient utilization, CO2 limitation, oxidative stress, and active toxin production in an Alexandrium fundyense bloom

(2015) Yunyun Zhuang et al.   HARMFUL ALGAE

Considerations for the use of transcriptomics in identifying the 'genes that matter' for environmental adaptation

(2015) T. G. Evans   JOURNAL OF EXPERIMENTAL BIOLOGY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Identification of microRNAs in the Toxigenic Dinoflagellate Alexandrium catenella by High-Throughput Illumina Sequencing and Bioinformatic Analysis

(2015) Huili Geng et al.   PLoS One

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation

(2015) Zhenfeng Liu et al.   Frontiers in Microbiology

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis

(2014) Darcie E Ryan et al.   BMC GENOMICS

Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform

(2014) Shu Zhang et al.   GENE

Transcriptome sequencing reveals single domain Type I-like polyketide synthases in the toxic dinoflagellate Gambierdiscus polynesiensis

(2014) R. Pawlowiez et al.   HARMFUL ALGAE

Unfolding the secrets of coral–algal symbiosis

(2014) Nedeljka Rosic et al.   ISME Journal

Marine dinoflagellate proteomics: Current status and future perspectives

(2014) Da-Zhi Wang et al.   Journal of Proteomics

Comparative Transcriptome Analysis of a Toxin-Producing Dinoflagellate Alexandrium catenella and Its Non-Toxic Mutant

(2014) Yong Zhang et al.   Marine Drugs

Lineage-Specific Transcriptional Profiles of Symbiodinium spp. Unaltered by Heat Stress in a Coral Host

(2014) Daniel J. Barshis et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA-Seq Technology and Its Application in Fish Transcriptomics

(2014) Xi Qian et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum

(2013) Amanda K Gibson et al.   BMC GENOMICS

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

(2013) Sebastian Baumgarten et al.   BMC GENOMICS

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinoflagellate Alexandrium Tamarense

(2013) Dahai Gao et al.   Evolutionary Bioinformatics

Caspase-like activity during aging and cell death in the toxic dinoflagellate Karenia brevis

(2013) Jillian G. Johnson et al.   HARMFUL ALGAE

Global Analysis of mRNA Half-Lives and de novo Transcription in a Dinoflagellate, Karenia brevis

(2013) Jeanine S. Morey et al.   PLoS One

Strategies for transcriptome analysis in nonmodel plants

(2012) Judson A. Ward et al.   AMERICAN JOURNAL OF BOTANY

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

(2012) Till Bayer et al.   PLoS One

The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing

(2011) Chris D Lowe et al.   BMC GENOMICS

Effective gene collection from the metatranscriptome of marine microorganisms

(2011) Atsushi Ogura et al.   BMC GENOMICS

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

(2011) Jeanine S Morey et al.   BMC GENOMICS

Grazer-induced toxin formation in dinoflagellates: a transcriptomic model study

(2011) Ines Yang et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Growth- and nutrient-dependent gene expression in the toxigenic marine dinoflagellate Alexandrium minutum

(2011) Ines Yang et al.   HARMFUL ALGAE

Post-transcriptional Regulation of S-Phase Genes in the Dinoflagellate, Karenia brevis

(2011) STEPHANIE A. BRUNELLE et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

New Approach Using the Real-Time PCR Method for Estimation of the Toxic Marine Dinoflagellate Ostreopsis cf. ovata in Marine Environment

(2011) Federico Perini et al.   PLoS One

Discovery of Nuclear-Encoded Genes for the Neurotoxin Saxitoxin in Dinoflagellates

(2011) Anke Stüken et al.   PLoS One

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

(2011) Nina Jaeckisch et al.   PLoS One

Genomic understanding of dinoflagellates

(2011) Senjie Lin   RESEARCH IN MICROBIOLOGY

Effects of pooling RNA from samples treated with different compounds for determining class specific biomarkers and processes in toxicogenomics

(2011) Tessa E. Pronk et al.   TOXICOLOGY IN VITRO

Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum

(2010) Ines Yang et al.   BMC GENOMICS

Studying bacterial transcriptomes using RNA-seq

(2010) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Transcriptome Profiling of a Toxic Dinoflagellate Reveals a Gene-Rich Protist and a Potential Impact on Gene Expression Due to Bacterial Presence

(2010) Ahmed Moustafa et al.   PLoS One

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology

(2010) Martin J. Blythe et al.   PLoS One

A dinoflagellate exploits toxins to immobilize prey prior to ingestion

(2010) J. Sheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introns, Alternative Splicing, Spliced Leader trans-Splicing and Differential Expression of pcna and cyclin in Perkinsus marinus

(2010) Huan Zhang et al.   PROTIST

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Next generation sequencing of microbial transcriptomes: challenges and opportunities

(2009) Arnoud H.M. van Vliet   FEMS MICROBIOLOGY LETTERS

The plasticity of the mammalian transcriptome

(2009) Johan Lindberg et al.   GENOMICS

A method for extracting a high-quality RNA from Symbiodinium sp.

(2009) Nedeljka N. Rosic et al.   JOURNAL OF APPLIED PHYCOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH