Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the ChlorarachniophyteBigelowiella natans

Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species

(2016) Shigekatsu Suzuki et al.   JOURNAL OF PLANT RESEARCH

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Prospective function of FtsZ proteins in the secondary plastid of chlorarachniophyte algae

(2015) Yoshihisa Hirakawa et al.   BMC PLANT BIOLOGY

Endosymbiosis and Eukaryotic Cell Evolution

(2015) John M. Archibald   CURRENT BIOLOGY

Dealing with light: The widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms

(2015) Antonio Emidio Fortunato et al.   JOURNAL OF PLANT PHYSIOLOGY

Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses

(2015) Guillaume Blanc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

(2015) Blake T. Hovde et al.   PLoS Genetics

Clocks in Algae

(2014) Zeenat B. Noordally et al.   BIOCHEMISTRY

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

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae

(2014) Goro Tanifuji et al.   BMC GENOMICS

Overexpression of Molecular Chaperone Genes in Nucleomorph Genomes

(2014) Yoshihisa Hirakawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Diurnal Logic of the Expression of the Chloroplast Genome in Chlamydomonas reinhardtii

(2014) Adam D. Idoine et al.   PLoS One

The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution

(2013) Patrick J. Keeling   Annual Review of Plant Biology

Zeitlupe Senses Blue-Light Fluence To Mediate Circadian Timing in Arabidopsis thaliana

(2013) Ashutosh Pudasaini et al.   BIOCHEMISTRY

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

Complexity in the Wiring and Regulation of Plant Circadian Networks

(2012) Dawn H. Nagel et al.   CURRENT BIOLOGY

External Light Conditions and Internal Cell Cycle Phases Coordinate Accumulation of Chloroplast and Mitochondrial Transcripts in the Red Alga Cyanidioschyzon merolae

(2012) Y. Kanesaki et al.   DNA RESEARCH

Expression of the Nucleus-Encoded Chloroplast Division Genes and Proteins Regulated by the Algal Cell Cycle

(2012) S.-y. Miyagishima et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

(2012) D. C. Price et al.   SCIENCE

Double loss-of-function mutation in EARLY FLOWERING 3 and CRYPTOCHROME 2 genes delays flowering under continuous light but accelerates it under long days and short days: an important role for Arabidopsis CRY2 to accelerate flowering time in continuous light

(2011) Rim Nefissi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga

(2011) Yoshihisa Hirakawa et al.   MOLECULAR MICROBIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Light inputs shape the Arabidopsis circadian system

(2011) Bénédicte Wenden et al.   PLANT JOURNAL

The cell cycle, including the mitotic cycle and organelle division cycles, as revealed by cytological observations

(2011) Y. Imoto et al.   Microscopy

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles

(2010) Annabelle Monnier et al.   BMC GENOMICS

Characterization of Periplastidal Compartment–Targeting Signals in Chlorarachniophytes

(2010) Yoshihisa Hirakawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

(2009) Gregg A Helt et al.   BMC BIOINFORMATICS

Periodic Gene Expression Patterns during the Highly Synchronized Cell Nucleus and Organelle Division Cycles in the Unicellular Red Alga Cyanidioschyzon merolae

(2009) T. Fujiwara et al.   DNA RESEARCH

Protein targeting into secondary plastids of chlorarachniophytes

(2009) Y. Hirakawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics of Photosynthesis

(2008) Stephan Eberhard et al.   Annual Review of Genetics

Plastid Evolution

(2008) Sven B. Gould et al.   Annual Review of Plant Biology

Nucleus-Encoded Periplastid-Targeted EFL in Chlorarachniophytes

(2008) G. H. Gile et al.   MOLECULAR BIOLOGY AND EVOLUTION

Physiological and Transcriptomic Evidence for a Close Coupling between Chloroplast Ontogeny and Cell Cycle Progression in the Pennate Diatom Seminavis robusta

(2008) J. Gillard et al.   PLANT PHYSIOLOGY