A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum

Signatures of Long-Term Balancing Selection in Human Genomes

(2018) Bárbara D Bitarello et al.   Genome Biology and Evolution

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

(2018) Achal Rastogi et al.   Scientific Reports

One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing

(2018) Manuel Serif et al.   Nature Communications

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana

(2018) Julie A. Koester et al.   Scientific Reports

Extreme Lewontin’s Paradox in Ubiquitous Marine Phytoplankton Species

(2018) Dmitry A Filatov   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments

(2017) Anna Godhe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms

(2017) Eric R. Moore et al.   PLoS One

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

(2017) Kerry A. Whittaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

(2017) Richard G Dorrell et al.   eLife

Population genomics of picophytoplankton unveils novel chromosome hypervariability

(2017) Romain Blanc-Mathieu et al.   Science Advances

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

(2016) Achal Rastogi et al.   BMC BIOINFORMATICS

Multisignal control of expression of the LHCX protein family in the marine diatomPhaeodactylum tricornutum

(2016) Lucilla Taddei et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetically distinct populations of a diatom co-exist during the North Atlantic spring bloom

(2016) Gang Chen et al.   LIMNOLOGY AND OCEANOGRAPHY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean

(2016) Antonio Emidio Fortunato et al.   PLANT CELL

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

A CRISPR/Cas9 system adapted for gene editing in marine algae

(2016) Marianne Nymark et al.   Scientific Reports

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

ClicO FS: an interactive web-based service of Circos: Fig. 1.

(2015) Wei-Hien Cheong et al.   BIOINFORMATICS

A Novel Protein, Ubiquitous in Marine Phytoplankton, Concentrates Iron at the Cell Surface and Facilitates Uptake

(2015) Joe Morrissey et al.   CURRENT BIOLOGY

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

(2015) Sebastian Matuszewski et al.   GENETICS

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

(2015) Magali Lescot et al.   ISME Journal

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms

(2015) Benjamin Bailleul et al.   NATURE

Timing, rates and spectra of human germline mutation

(2015) Raheleh Rahbari et al.   NATURE GENETICS

Oil Accumulation by the Oleaginous DiatomFistulifera solarisas Revealed by the Genome and Transcriptome

(2015) Tsuyoshi Tanaka et al.   PLANT CELL

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green AlgaChlamydomonas reinhardtii

(2015) Jonathan M. Flowers et al.   PLANT CELL

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

(2015) Sebastian Matuszewski et al.   GENETICS

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum

(2015) Alaguraj Veluchamy et al.   GENOME BIOLOGY

Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy

(2014) Irena Kaczmarska et al.   AMERICAN JOURNAL OF BOTANY

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

(2014) Romain Blanc-Mathieu et al.   BMC GENOMICS

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

(2014) Jason T. Huff et al.   CELL

Genetic and phenotypic intra-species variation inCandida albicans

(2014) Matthew P. Hirakawa et al.   GENOME RESEARCH

Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution

(2014) Katherine E Helliwell et al.   ISME Journal

Reduction in Carotenoid Levels in the Marine Diatom Phaeodactylum tricornutum by Artificial MicroRNAs Targeted Against the Endogenous Phytoene Synthase Gene

(2014) Simrat Kaur et al.   MARINE BIOTECHNOLOGY

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation inPhaeodactylum tricornutum

(2014) Heni Abida et al.   PLANT PHYSIOLOGY

Genetic and Microscopic Evidence for Sexual Reproduction in the Centric Diatom Skeletonema marinoi

(2014) Anna Godhe et al.   PROTIST

Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

(2014) Fayza Daboussi et al.   Nature Communications

Population Genomics of Human Adaptation

(2013) Joseph Lachance et al.   Annual Review of Ecology Evolution and Systematics

Transposable elements and microevolutionary changes in natural populations

(2013) Georgi Bonchev et al.   Molecular Ecology Resources

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

AUREOCHROME1a-Mediated Induction of the Diatom-Specific CyclindsCYC2Controls the Onset of Cell Division in Diatoms (Phaeodactylum tricornutum)

(2013) Marie J.J. Huysman et al.   PLANT CELL

Compensatory Base Changes in ITS2 Secondary Structures Correlate with the Biological Species Concept Despite Intragenomic Variability in ITS2 Sequences – A Proof of Concept

(2013) Matthias Wolf et al.   PLoS One

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

(2013) Alaguraj Veluchamy et al.   Nature Communications

Passive rafting is a powerful driver of transoceanic gene flow

(2012) R. Nikula et al.   Biology Letters

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Interactions between Diatoms and Bacteria

(2012) S. A. Amin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein

(2012) E. M. Bertrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and Functional Discussion of the Tetra-Trico-Peptide Repeat, a Protein Interaction Module

(2012) Natalie Zeytuni et al.   STRUCTURE

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

THE EFFECT OF VARIABLE FREQUENCY OF SEXUAL REPRODUCTION ON THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF A CYCLICAL PARTHENOGEN

(2011) Desiree E. Allen et al.   EVOLUTION

Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

(2011) K. E. Helliwell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

How and Why DNA Barcodes Underestimate the Diversity of Microbial Eukaryotes

(2011) Gwenael Piganeau et al.   PLoS One

Hundred years of genetic structure in a sediment revived diatom population

(2011) K. Harnstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influence of light and nitrate assimilation on the growth strategy in clonal weed Eichhornia crassipes

(2010) Weiguo Li et al.   AQUATIC ECOLOGY

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

(2010) R. Shoemaker et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light

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

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

(2010) Marie JJ Huysman et al.   GENOME BIOLOGY

Digital expression profiling of novel diatom transcripts provides insight into their biological functions

(2010) Uma Maheswari et al.   GENOME BIOLOGY

Light is a key factor in triggering sexual reproduction in the pennate diatom Haslea ostrearia

(2009) Jean-Luc Mouget et al.   FEMS MICROBIOLOGY ECOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The life of diatoms in the world's oceans

(2009) E. Virginia Armbrust   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum

(2009) Mathieu Vartanian et al.   NEW PHYTOLOGIST

Gene silencing in the marine diatom Phaeodactylum tricornutum

(2009) Valentina De Riso et al.   NUCLEIC ACIDS RESEARCH

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Update of the Diatom EST Database: a new tool for digital transcriptomics

(2008) U. Maheswari et al.   NUCLEIC ACIDS RESEARCH

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

(2008) I. J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA