Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus

Inter- and Intra-Specific Transcriptional and Phenotypic Responses of Pseudo-nitzschia under Different Nutrient Conditions

(2019) Kimberley A Lema et al.   Genome Biology and Evolution

Molecular mechanisms of temperature acclimation and adaptation in marine diatoms

(2019) Yue Liang et al.   ISME Journal

Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling

(2018) Marco Catoni et al.   NUCLEIC ACIDS RESEARCH

Assessment of genomic changes in a CRISPR/Cas9 Phaeodactylum tricornutum mutant through whole genome resequencing

(2018) Monia Teresa Russo et al.   PeerJ

Resilience by diversity: Large intraspecific differences in climate change responses of an Arctic diatom

(2017) Klara K. E. Wolf et al.   LIMNOLOGY AND OCEANOGRAPHY

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into global diatom distribution and diversity in the world’s ocean

(2016) Shruti Malviya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

(2015) F. Musacchia et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A transposable element insertion in the susceptibility gene CsaMLO8 results in hypocotyl resistance to powdery mildew in cucumber

(2015) Jeroen A. Berg et al.   BMC PLANT BIOLOGY

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

(2015) Magali Lescot et al.   ISME Journal

Light and temperature effects on bioactivity in diatoms

(2015) Richard A. Ingebrigtsen et al.   JOURNAL OF APPLIED PHYCOLOGY

Use it or lose it? Loss of grazing defenses during laboratory culture of the digestion-resistant green alga Oocystis

(2015) William R. Demott et al.   JOURNAL OF PLANKTON RESEARCH

Expression of the retrotransposonsSurcoufandBlackbeardin the marine diatomPhaeodactylum tricornutumunder thermal stress

(2015) Fadoumo Egue et al.   PHYCOLOGIA

Temperature affects the silicate morphology in a diatom

(2015) N. Javaheri et al.   Scientific Reports

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach

(2014) Deepak Nanjappa et al.   PLoS One

Diatom Cell Size, Coloniality and Motility: Trade-Offs between Temperature, Salinity and Nutrient Supply with Climate Change

(2014) Filip Svensson et al.   PLoS One

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Different transcriptional responses of heat shock protein 70/90 in the marine diatom Ditylum brightwellii exposed to metal compounds and endocrine-disrupting chemicals

(2013) R. Guo et al.   CHEMOSPHERE

Different transcriptional responses of heat shock protein 20 in the marine diatomDitylum brightwelliiexposed to metals and endocrine-disrupting chemicals

(2013) Min-Ah Lee et al.   ENVIRONMENTAL TOXICOLOGY

A reappraisal of the genusLeptocylindrus(Bacillariophyta), with the addition of three species and the erection ofTenuicylindrusgen. nov

(2013) Deepak Nanjappa et al.   JOURNAL OF PHYCOLOGY

Phenotypic Plasticity of Southern Ocean Diatoms: Key to Success in the Sea Ice Habitat?

(2013) Olivia Sackett et al.   PLoS One

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

(2013) Fabrício R. Lopes et al.   PLoS One

Heat-Stress and Light-Stress Induce Different Cellular Pathologies in the Symbiotic Dinoflagellate during Coral Bleaching

(2013) C. A. Downs et al.   PLoS One

Phenotypic plasticity of coralline algae in a High CO2world

(2013) Federica Ragazzola et al.   Ecology and Evolution

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Intraspecific variability in the response of bloom-forming marine microalgae to changed climate conditions

(2012) Anke Kremp et al.   Ecology and Evolution

RNA-Seq analysis in MeV

(2011) E. A. Howe et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Antifreeze proteins in polar sea ice diatoms: diversity and gene expression in the genus Fragilariopsis

(2010) Maddalena Bayer-Giraldi et al.   ENVIRONMENTAL MICROBIOLOGY

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles

(2010) Edda Rayko et al.   NEW PHYTOLOGIST

Identification of Components Associated with Thermal Acclimation of Photosystem II in Synechocystis sp. PCC6803

(2010) John G. Rowland et al.   PLoS One

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Transposable elements and an epigenetic basis for punctuated equilibria

(2009) David W. Zeh et al.   BIOESSAYS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

(2009) Florian Maumus et al.   BMC GENOMICS

The strain concept in phytoplankton ecology

(2009) Michael Boyd Lakeman et al.   HARMFUL ALGAE

Adaptive Evolution Involving Gene Duplication and Insertion of a Novel Ty1/copia-Like Retrotransposon in Soybean

(2009) Akira Kanazawa et al.   JOURNAL OF MOLECULAR EVOLUTION

The spaceflight environment can induce transpositional activation of multiple endogenous transposable elements in a genotype-dependent manner in rice

(2009) Likun Long et al.   JOURNAL OF PLANT PHYSIOLOGY

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

MERE1, a Low-Copy-Number Copia-Type Retroelement in Medicago truncatula Active during Tissue Culture

(2009) A. Rakocevic et al.   PLANT PHYSIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Stress-induced mobility of OPHIO1 and OPHIO2, DNA transposons of the Dutch elm disease fungi

(2007) Guillaume F. Bouvet et al.   FUNGAL GENETICS AND BIOLOGY