Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

Toward an empirical framework for interpreting plastid evolution

(2014) John W. Stiller   JOURNAL OF PHYCOLOGY

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Conservation of the 2-keto-3-deoxymanno-octulosonic acid (Kdo) biosynthesis pathway between plants and bacteria

(2013) Kevin M. Smyth et al.   CARBOHYDRATE RESEARCH

A Modern Descendant of Early Green Algal Phagotrophs

(2013) Shinichiro Maruyama et al.   CURRENT BIOLOGY

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

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Phagocytosis and Cytokinesis: Do Cells Use Common Tools to Cut and to Eat? Highlights on Common Themes and Differences

(2013) Chantal Deschamps et al.   TRAFFIC

Retrotransposon replication in plants

(2013) Alan H Schulman   Current Opinion in Virology

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Morphostasis in a novel eukaryote illuminates the evolutionary transition from phagotrophy to phototrophy: description of Rapaza viridis n. gen. et sp. (Euglenozoa, Euglenida)

(2012) Aika Yamaguchi et al.   BMC EVOLUTIONARY BIOLOGY

Peptidoglycan: a post-genomic analysis

(2012) Caroline Cayrou et al.   BMC MICROBIOLOGY

Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa

(2012) Thomas Cavalier-Smith   EUROPEAN JOURNAL OF PROTISTOLOGY

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants

(2012) Laura Emery et al.   Frontiers in Plant Science

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

GamA is a eukaryotic-like glucoamylase responsible for glycogen- and starch-degrading activity of Legionella pneumophila

(2011) Vroni Herrmann et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The Role of Photosynthesis and Food Uptake for the Growth of Marine Mixotrophic Dinoflagellates1

(2011) PER JUEL HANSEN   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Pathway for lipid A biosynthesis in Arabidopsis thaliana resembling that of Escherichia coli

(2011) C. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Transcriptomic Evidence That Longevity of Acquired Plastids in the Photosynthetic Slugs Elysia timida and Plakobranchus ocellatus Does Not Entail Lateral Transfer of Algal Nuclear Genes

(2010) H. Wagele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular characterization of the evolution of phagosomes

(2010) Jonathan Boulais et al.   Molecular Systems Biology

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

Turning the Table: Plants Consume Microbes as a Source of Nutrients

(2010) Chanyarat Paungfoo-Lonhienne et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endocytosis in plant–microbe interactions

(2010) Nathalie Leborgne-Castel et al.   PROTOPLASMA

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance

(2009) Christophe Bertsch et al.   Biology Direct

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Puzzle of Plastid Evolution

(2009) John M. Archibald   CURRENT BIOLOGY

Proteomic analysis of Legionella-containing phagosomes isolated from Dictyostelium

(2009) Olga Shevchuk et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Phagotrophy in the origins of photosynthesis in eukaryotes and as a complementary mode of nutrition in phototrophs: relation to Darwin's insectivorous plants

(2009) J. A. Raven et al.   JOURNAL OF EXPERIMENTAL BOTANY

Functional Role of Feline Zona Pellucida Protein 4 Trefoil Domain: A Sperm Receptor or Structural Component of the Domestic Cat Zona Pellucida?

(2009) BC Braun et al.   REPRODUCTION IN DOMESTIC ANIMALS

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

(2009) A. Z. Worden et al.   SCIENCE

Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

(2009) Gabi Kastenmüller et al.   GENOME BIOLOGY

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids

(2008) Monique Turmel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY