Published in Genome Biol Evol on November 15, 2010
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev (2012) 2.65
The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci (2012) 2.12
Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. Genome Biol Evol (2011) 1.15
Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families. Genome Biol Evol (2012) 0.99
Three old and one new: protein import into red algal-derived plastids surrounded by four membranes. Protoplasma (2013) 0.93
Chromera velia, endosymbioses and the rhodoplex hypothesis--plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages). Genome Biol Evol (2014) 0.91
Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryot Cell (2013) 0.89
Distribution of the SELMA translocon in secondary plastids of red algal origin and predicted uncoupling of ubiquitin-dependent translocation from degradation. Eukaryot Cell (2012) 0.88
Genomic perspectives on the birth and spread of plastids. Proc Natl Acad Sci U S A (2015) 0.86
Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga. Eukaryot Cell (2012) 0.84
Evidence for glycoprotein transport into complex plastids. Proc Natl Acad Sci U S A (2013) 0.82
Protein sorting in complex plastids. Biochim Biophys Acta (2012) 0.82
Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis. BMC Genomics (2014) 0.81
Glycoprotein import: a common feature of complex plastids? Plant Signal Behav (2013) 0.75
Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. BMC Evol Biol (2016) 0.75
Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes. Genome Biol Evol (2015) 0.75
Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement. PLoS One (2016) 0.75
Review: origin of complex algae by secondary endosymbiosis: a journey through time. Protoplasma (2017) 0.75
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol (2008) 38.22
Application of phylogenetic networks in evolutionary studies. Mol Biol Evol (2005) 31.72
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97
Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol (2003) 8.51
ERAD: the long road to destruction. Nat Cell Biol (2005) 7.46
Fast statistical alignment. PLoS Comput Biol (2009) 5.92
Plastid evolution. Annu Rev Plant Biol (2008) 3.39
Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science (2009) 3.31
The highly reduced genome of an enslaved algal nucleus. Nature (2001) 3.31
The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol (2008) 2.94
Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol (2007) 2.91
Phylogenomics reshuffles the eukaryotic supergroups. PLoS One (2007) 2.67
The origin and establishment of the plastid in algae and plants. Annu Rev Genet (2007) 2.32
Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol (2007) 2.10
Stable nuclear transformation of the diatom Phaeodactylum tricornutum. Mol Gen Genet (1996) 1.98
Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Mol Biol Evol (2010) 1.95
Prediction of organellar targeting signals. Biochim Biophys Acta (2001) 1.93
Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biol Lett (2009) 1.78
Toxoplasma gondii Tic20 is essential for apicoplast protein import. Proc Natl Acad Sci U S A (2008) 1.78
Evolution: red algal genome affirms a common origin of all plastids. Curr Biol (2004) 1.63
An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol (2006) 1.58
On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol (2005) 1.56
Genetic evidence that an endosymbiont-derived endoplasmic reticulum-associated protein degradation (ERAD) system functions in import of apicoplast proteins. J Biol Chem (2009) 1.55
Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastids. Plant J (2005) 1.42
Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol (2003) 1.39
Der1-mediated preprotein import into the periplastid compartment of chromalveolates? Mol Biol Evol (2007) 1.39
Transit peptide diversity and divergence: A global analysis of plastid targeting signals. Bioessays (2007) 1.32
Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol Biol (2008) 1.31
An unusual ERAD-like complex is targeted to the apicoplast of Plasmodium falciparum. Eukaryot Cell (2009) 1.31
Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Philos Trans R Soc Lond B Biol Sci (2003) 1.25
Plastid ultrastructure defines the protein import pathway in dinoflagellates. J Cell Sci (2003) 1.22
Protein targeting into the complex plastid of cryptophytes. J Mol Evol (2006) 1.20
Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol Biol Evol (2008) 1.16
Protein targeting to the malaria parasite plastid. Traffic (2007) 1.15
Characterization of two putative protein translocation components in the apicoplast of Plasmodium falciparum. Eukaryot Cell (2009) 1.14
ERAD-derived preprotein transport across the second outermost plastid membrane of diatoms. Mol Biol Evol (2009) 1.13
The route of entry of cytoplasmically synthesized proteins into chloroplasts of algae possessing chloroplast ER. J Cell Sci (1979) 1.09
Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol (2009) 1.08
Protein targeting into secondary plastids. J Eukaryot Microbiol (2009) 1.07
Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms. Mol Biol Evol (2006) 1.06
Have you HRD? Understanding ERAD is DOAble! Cell (2006) 1.06
Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates. J Biol Chem (2009) 1.06
Transport of nuclear-encoded proteins into secondarily evolved plastids. Biol Chem (2007) 1.03
Evidence for Golgi-independent transport from the early secretory pathway to the plastid in malaria parasites. Mol Microbiol (2006) 1.02
Sizing up the genomic footprint of endosymbiosis. Bioessays (2009) 0.97
New mechanistic insights into pre-protein transport across the second outermost plastid membrane of diatoms. Mol Microbiol (2010) 0.88
Evolutionary origin of a preprotein translocase in the periplastid membrane of complex plastids: a hypothesis. Plant Biol (Stuttg) (2004) 0.78
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet (2004) 17.22
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol (2004) 7.95
Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet (2004) 5.51
Eukaryotic evolution, changes and challenges. Nature (2006) 5.10
The energetics of genome complexity. Nature (2010) 4.58
Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science (2009) 3.31
Genetics and geography of wild cereal domestication in the near east. Nat Rev Genet (2002) 3.30
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A (2008) 2.97
Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet (2010) 2.70
Activation of natural regulatory T cells by IgG Fc-derived peptide "Tregitopes". Blood (2008) 2.50
General protein diffusion barriers create compartments within bacterial cells. Cell (2012) 2.48
The evolutionary root of flowering plants. Syst Biol (2012) 2.46
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol (2004) 2.32
The tree of one percent. Genome Biol (2006) 2.23
Prokaryotic evolution and the tree of life are two different things. Biol Direct (2009) 2.17
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature (2012) 2.15
DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol (2009) 2.12
On the origin of genomes and cells within inorganic compartments. Trends Genet (2005) 2.04
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A (2007) 1.96
The rocky roots of the acetyl-CoA pathway. Trends Biochem Sci (2004) 1.92
Optimizing esthetics for implant restorations in the anterior maxilla: anatomic and surgical considerations. Int J Oral Maxillofac Implants (2004) 1.84
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc Natl Acad Sci U S A (2002) 1.79
The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum. Appl Environ Microbiol (2009) 1.76
Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics. Clin Immunol (2009) 1.73
Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol (2008) 1.62
Protein targeting into complex diatom plastids: functional characterisation of a specific targeting motif. Plant Mol Biol (2007) 1.61
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res (2011) 1.58
HIV vaccine development by computer assisted design: the GAIA vaccine. Vaccine (2005) 1.56
Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol (2007) 1.55
Mitochondria as we don't know them. Trends Biochem Sci (2002) 1.49
Substrate binding disrupts dimerization and induces nucleotide exchange of the chloroplast GTPase Toc33. Biochem J (2011) 1.49
Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics (2006) 1.49
Testing hypotheses without considering predictions. Bioessays (2007) 1.48
A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell (2003) 1.46
Immuno-informatics: Mining genomes for vaccine components. Immunol Cell Biol (2002) 1.46
Utility of the neutrophil to lymphocyte ratio in predicting long-term outcomes in acute decompensated heart failure. Am J Cardiol (2011) 1.44
Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol (2010) 1.42
A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor. Mol Biol Evol (2009) 1.41
Prognosis of endodontically treated teeth? Point. Quintessence Int (2003) 1.39
Low immunogenicity predicted for emerging avian-origin H7N9: implication for influenza vaccine design. Hum Vaccin Immunother (2013) 1.38
Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times. Mol Biol Evol (2003) 1.37
How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays (2010) 1.33
An unusual ERAD-like complex is targeted to the apicoplast of Plasmodium falciparum. Eukaryot Cell (2009) 1.31
A positive definition of prokaryotes. Nature (2006) 1.29
Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides. Proc Natl Acad Sci U S A (2004) 1.28
Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol (2005) 1.27
Rhodopsin-mediated photoreception in cryptophyte flagellates. Biophys J (2005) 1.26
Evolutionary biology: essence of mitochondria. Nature (2003) 1.25
The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol Lett (2007) 1.25
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. Mol Biol Evol (2010) 1.24
The evolution of chloroplast RNA editing. Mol Biol Evol (2006) 1.24
Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria. J Biol Chem (2006) 1.22
Complex chloroplast RNA metabolism: just debugging the genetic programme? BMC Biol (2008) 1.21
Protein targeting into the complex plastid of cryptophytes. J Mol Evol (2006) 1.20
Networks uncover hidden lexical borrowing in Indo-European language evolution. Proc Biol Sci (2010) 1.18
Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol Biol Evol (2008) 1.16
Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci (2009) 1.15
Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4(+) T cells against the swine-origin H1N1 influenza virus. Vaccine (2011) 1.14
166Ho-DOTMP radiation-absorbed dose estimation for skeletal targeted radiotherapy. J Nucl Med (2006) 1.14
ERAD-derived preprotein transport across the second outermost plastid membrane of diatoms. Mol Biol Evol (2009) 1.13
Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer. Eur J Biochem (2002) 1.12
Acetate formation in the energy metabolism of parasitic helminths and protists. Int J Parasitol (2010) 1.11
Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry. Philos Trans R Soc Lond B Biol Sci (2008) 1.11
HelicoVax: epitope-based therapeutic Helicobacter pylori vaccination in a mouse model. Vaccine (2011) 1.09
RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genomics (2009) 1.09
Evolutionary biology: out of thin air. Nature (2007) 1.09
Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach. Vaccine (2003) 1.07
Utility of FDG-PET/CT in follow-up of children treated for Hodgkin and non-Hodgkin lymphoma. J Pediatr Hematol Oncol (2006) 1.07
Protein targeting into secondary plastids. J Eukaryot Microbiol (2009) 1.07
Diatoms in biotechnology: modern tools and applications. Appl Microbiol Biotechnol (2008) 1.07
Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms. Mol Biol Evol (2006) 1.06
Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates. J Biol Chem (2009) 1.06
The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution. BMC Evol Biol (2008) 1.05
Epitope-based vaccination against pneumonic tularemia. Vaccine (2009) 1.05
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites. Mol Biol Evol (2008) 1.04
The difference between organelles and endosymbionts. Curr Biol (2006) 1.03
Transport of nuclear-encoded proteins into secondarily evolved plastids. Biol Chem (2007) 1.03
Epitope-driven TB vaccine development: a streamlined approach using immuno-informatics, ELISpot assays, and HLA transgenic mice. Curr Mol Med (2007) 1.02
Carvedilol alone or in combination with digoxin for the management of atrial fibrillation in patients with heart failure? J Am Coll Cardiol (2003) 1.02
Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol (2010) 1.02
Sulfide : quinone oxidoreductase (SQR) from the lugworm Arenicola marina shows cyanide- and thioredoxin-dependent activity. FEBS J (2008) 1.00
Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods (2004) 1.00
Making vaccines "on demand": a potential solution for emerging pathogens and biodefense? Hum Vaccin Immunother (2013) 1.00
Novel function of complement C3d as an autologous helper T-cell target. Immunol Cell Biol (2008) 0.99
Microalgae as bioreactors for bioplastic production. Microb Cell Fact (2011) 0.99
Mitochondrial trans-2-enoyl-CoA reductase of wax ester fermentation from Euglena gracilis defines a new family of enzymes involved in lipid synthesis. J Biol Chem (2004) 0.98
Acetate:succinate CoA-transferase in the hydrogenosomes of Trichomonas vaginalis: identification and characterization. J Biol Chem (2007) 0.98
In silico and in vivo investigations of proteins of a minimized eukaryotic cytoplasm. Genome Biol Evol (2011) 0.98
Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer. Environ Microbiol (2003) 0.97