Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis

Deciphering the nature of the coral–Chromera association

(2018) Amin R Mohamed et al.   ISME Journal

Ploidy and Number of Chromosomes in the Alveolate Alga Chromera velia

(2018) Jan Vazač et al.   PROTIST

Chloroplast Glutamine Synthetase, the Key Regulator of Nitrogen Metabolism in Wheat, Performs Its Role by Fine Regulation of Enzyme Activity via Negative Cooperativity of Its Subunits

(2018) Edit Németh et al.   Frontiers in Plant Science

The Birth of Red Complex Plastids: One, Three, or Four Times?

(2018) Miroslav Oborník   TRENDS IN PARASITOLOGY

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites

(2018) Michael J. Boucher et al.   PLOS BIOLOGY

Protein Import into the Endosymbiotic Organelles of Apicomplexan Parasites

(2018) Natalia Mallo et al.   Genes

Proteomics of human mitochondria

(2017) Johan Palmfeldt et al.   MITOCHONDRION

The proteome of baker's yeast mitochondria

(2017) Humberto Gonczarowska-Jorge et al.   MITOCHONDRION

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

(2017) Richard G Dorrell et al.   eLife

Extensive gain and loss of photosystem I subunits in chromerid algae, photosynthetic relatives of apicomplexans

(2017) Roman Sobotka et al.   Scientific Reports

Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes

(2016) Gurjeet S Kohli et al.   ISME Journal

Plants grow with a little help from their organelle friends

(2016) Judith Van Dingenen et al.   JOURNAL OF EXPERIMENTAL BOTANY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Role of Charge in Protein Targeting Evolution

(2016) Sriram G. Garg et al.   TRENDS IN CELL BIOLOGY

Apicomplexan Energy Metabolism: Carbon Source Promiscuity and the Quiescence Hyperbole

(2016) Damien Jacot et al.   TRENDS IN PARASITOLOGY

Ancestral Reconstruction

(2016) Jeffrey B. Joy et al.   PLoS Computational Biology

The Organellar Genomes ofChromeraandVitrella, the Phototrophic Relatives of Apicomplexan Parasites

(2015) Miroslav Oborník et al.   Annual Review of Microbiology

Divergent Mitochondrial Respiratory Chains in Phototrophic Relatives of Apicomplexan Parasites

(2015) Pavel Flegontov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

(2015) Ansgar Gruber et al.   PLANT JOURNAL

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

(2015) Sebastian G. Gornik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

(2015) Jan Janouškovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

(2015) Michael W. Gray   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Investigation of Tricarboxylic Acid Metabolism during the Plasmodium falciparum Life Cycle

(2015) Hangjun Ke et al.   Cell Reports

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

(2015) Stepan Tymoshenko et al.   PLoS Computational Biology

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

(2015) Yong H Woo et al.   eLife

The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance

(2015) Markus Kunze et al.   Frontiers in Physiology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Chromera velia, Endosymbioses and the Rhodoplex Hypothesis—Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles, and Haptophytes (CASH Lineages)

(2014) Jörn Petersen et al.   Genome Biology and Evolution

Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants

(2014) Ryan M.R. Gawryluk et al.   Journal of Proteomics

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes

(2014) Denis V. Tikhonenkov et al.   PLoS One

Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics

(2014) A. Gupta et al.   Open Biology

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

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

(2014) Richard G. Dorrell et al.   PLoS Genetics

BCKDH: The Missing Link in Apicomplexan Mitochondrial Metabolism Is Required for Full Virulence of Toxoplasma gondii and Plasmodium berghei

(2014) Rebecca D. Oppenheim et al.   PLoS Pathogens

The Algal Past and Parasite Present of the Apicoplast

(2013) Giel G. van Dooren et al.   Annual Review of Microbiology

Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning

(2013) Rakesh Kaundal et al.   BMC BIOINFORMATICS

Colponemids Represent Multiple Ancient Alveolate Lineages

(2013) Jan Janouškovec et al.   CURRENT BIOLOGY

Evolution: Unveiling Early Alveolates

(2013) Richard G. Dorrell et al.   CURRENT BIOLOGY

Increased growth and pigment content ofChromera veliain mixotrophic culture

(2013) Christie Foster et al.   FEMS MICROBIOLOGY ECOLOGY

Hallmarks of a new era in mitochondrial biochemistry

(2013) D. J. Pagliarini et al.   GENES & DEVELOPMENT

Biosynthetic Pathway and Health Benefits of Fucoxanthin, an Algae-Specific Xanthophyll in Brown Seaweeds

(2013) Koji Mikami et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

Deciphering the Role of Aspartate and Prephenate Aminotransferase Activities in Plastid Nitrogen Metabolism

(2013) F. de la Torre et al.   PLANT PHYSIOLOGY

The rice mitochondria proteome and its response during development and to the environment

(2013) Shaobai Huang et al.   Frontiers in Plant Science

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Mitochondrial Metabolism of Glucose and Glutamine Is Required for Intracellular Growth of Toxoplasma gondii

(2012) James I. MacRae et al.   Cell Host & Microbe

Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin

(2012) Fabien Burki et al.   Genome Biology and Evolution

Proteomics Reveals Plastid- and Periplastid-Targeted Proteins in the Chlorarachniophyte Alga Bigelowiella natans

(2012) Julia F. Hopkins et al.   Genome Biology and Evolution

The glyoxalase pathway in protozoan parasites

(2012) Marta Sousa Silva et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Alveolate Mitochondrial Metabolic Evolution: Dinoflagellates Force Reassessment of the Role of Parasitism as a Driver of Change in Apicomplexans

(2012) Jillian C. Danne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites

(2012) Achchuthan Shanmugasundram et al.   NUCLEIC ACIDS RESEARCH

Chromera velia is Endosymbiotic in Larvae of the Reef Corals Acropora digitifera and A. tenuis

(2012) Vivian R. Cumbo et al.   PROTIST

The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features

(2011) Mia Terashima et al.   CURRENT GENETICS

Non-photochemical fluorescence quenching inChromera veliais enabled by fast violaxanthin de-epoxidation

(2011) Eva Kotabová et al.   FEBS LETTERS

Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia

(2011) Christian Woehle et al.   Genome Biology and Evolution

Identification of Plant-like Galactolipids inChromera velia, a Photosynthetic Relative of Malaria Parasites

(2011) Cyrille Y. Botté et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic Fate of Fumarate, a Side Product of the Purine Salvage Pathway in the Intraerythrocytic Stages ofPlasmodium falciparum

(2011) Vinay Bulusu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Tetrapyrrole Synthesis of Photosynthetic Chromerids Is Likely Homologous to the Unusual Pathway of Apicomplexan Parasites

(2011) Luděk Kořený et al.   PLANT CELL

Plastid Proteomics in Higher Plants: Current State and Future Goals

(2011) K. J. van Wijk et al.   PLANT PHYSIOLOGY

Morphology, Ultrastructure and Life Cycle of Vitrella brassicaformis n. sp., n. gen., a Novel Chromerid from the Great Barrier Reef

(2011) Miroslav Oborník et al.   PROTIST

The Mitochondrial Proteome and Human Disease

(2010) Sarah E. Calvo et al.   Annual Review of Genomics and Human Genetics

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

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

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

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

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

(2009) Torsten Blum et al.   BMC BIOINFORMATICS

The carbon and energy sources of the non-photosynthetic plastid in the malaria parasite

(2009) Liting Lim et al.   FEBS LETTERS

A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the  -Proteobacterial Mitochondrial Ancestor

(2009) A. Atteia et al.   MOLECULAR BIOLOGY AND EVOLUTION

HECTAR: A method to predict subcellular targeting in heterokonts

(2008) Bernhard Gschloessl et al.   BMC BIOINFORMATICS

Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again

(2008) Miroslav Oborník et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line

(2008) Hyuntae Yoo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A photosynthetic alveolate closely related to apicomplexan parasites

(2008) Robert B. Moore et al.   NATURE

A comprehensive analysis of Trypanosoma brucei mitochondrial proteome

(2008) Aswini K. Panigrahi et al.   PROTEOMICS

Dinoflagellates: a mitochondrial genome all at sea

(2008) Edmund A. Nash et al.   TRENDS IN GENETICS