Published in Genome Biol Evol on May 16, 2012
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature (2012) 2.15
Next-generation phylogenomics. Biol Direct (2013) 1.57
The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb Perspect Biol (2014) 1.20
Reevaluating the green contribution to diatom genomes. Genome Biol Evol (2012) 1.12
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol Biol Evol (2014) 1.02
Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors. Proc Natl Acad Sci U S A (2012) 0.97
Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryot Cell (2013) 0.89
Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc Biol Sci (2016) 0.88
Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae. BMC Evol Biol (2015) 0.86
Genomic perspectives on the birth and spread of plastids. Proc Natl Acad Sci U S A (2015) 0.86
Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution. BMC Genomics (2014) 0.82
Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms. Genome Biol Evol (2014) 0.81
What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes. Cold Spring Harb Perspect Biol (2014) 0.80
Cryptic organelle homology in apicomplexan parasites: insights from evolutionary cell biology. Curr Opin Microbiol (2013) 0.79
Probabilistic models of eukaryotic evolution: time for integration. Philos Trans R Soc Lond B Biol Sci (2015) 0.79
Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome. Genome Biol Evol (2015) 0.78
Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes. Genome Biol Evol (2014) 0.78
The rise and fall of Picobiliphytes: how assumed autotrophs turned out to be heterotrophs. Bioessays (2014) 0.76
Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mob Genet Elements (2013) 0.76
Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes. J Mol Evol (2014) 0.75
Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mob Genet Elements (2014) 0.75
Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement. PLoS One (2016) 0.75
Algal genes in aplastidic eukaryotes are not necessarily derived from historical plastids. Mob Genet Elements (2012) 0.75
Re-analyses of "Algal" Genes Suggest a Complex Evolutionary History of Oomycetes. Front Plant Sci (2017) 0.75
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res (2008) 13.51
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (2009) 9.81
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74
The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature (2008) 6.70
Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Gene transfer to the nucleus and the evolution of chloroplasts. Nature (1998) 3.79
Phylogenomics: the beginning of incongruence? Trends Genet (2006) 3.68
Plastid evolution. Annu Rev Plant Biol (2008) 3.39
Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science (2009) 3.31
The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol (2008) 2.94
A photosynthetic alveolate closely related to apicomplexan parasites. Nature (2008) 2.91
Phylogenomics reshuffles the eukaryotic supergroups. PLoS One (2007) 2.67
The puzzle of plastid evolution. Curr Biol (2009) 2.49
A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci U S A (2010) 2.41
The origin and establishment of the plastid in algae and plants. Annu Rev Genet (2007) 2.32
How good are deep phylogenetic trees? Curr Opin Genet Dev (1998) 2.24
The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci (2010) 2.22
The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci (2012) 2.12
Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr Biol (2006) 2.03
The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol Biol Evol (2006) 1.99
Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol (2008) 1.95
Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A (2003) 1.87
Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol (2005) 1.86
Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol (2007) 1.82
Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol (2004) 1.61
The plant tree of life: an overview and some points of view. Am J Bot (2004) 1.54
Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS One (2008) 1.38
Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol (2005) 1.32
Transit peptide diversity and divergence: A global analysis of plastid targeting signals. Bioessays (2007) 1.32
Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? BMC Genomics (2009) 1.32
Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol Biol (2008) 1.31
Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol (2011) 1.29
PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol Biol (2008) 1.23
Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol Biol Evol (2008) 1.16
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
Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef. Protist (2011) 1.14
Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. Eukaryot Cell (2011) 1.09
Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution. PLoS One (2011) 1.05
Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evol Biol (2011) 1.05
Algal genes in the closest relatives of animals. Mol Biol Evol (2010) 1.02
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74
A promoter-level mammalian expression atlas. Nature (2014) 6.25
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet (2006) 3.68
Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. J Infect Dis (2010) 3.21
A photosynthetic alveolate closely related to apicomplexan parasites. Nature (2008) 2.91
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol (2010) 2.76
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71
Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov (2008) 2.58
Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proc Natl Acad Sci U S A (2007) 2.41
A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci U S A (2010) 2.41
Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res (2009) 2.24
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature (2012) 2.15
The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. Cell Host Microbe (2010) 2.13
The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci (2012) 2.12
Microsporidia evolved from ancestral sexual fungi. Curr Biol (2008) 2.11
Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature (2011) 2.06
The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol Biol Evol (2006) 1.99
Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol (2009) 1.89
Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A (2003) 1.87
Plasmodium falciparum var gene expression is modified by host immunity. Proc Natl Acad Sci U S A (2009) 1.86
Cell biology. Irremediable complexity? Science (2010) 1.85
CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol (2012) 1.84
The evolution and diversity of kinetoplastid flagellates. Trends Parasitol (2006) 1.79
The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat Commun (2010) 1.75
Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi. PLoS Pathog (2009) 1.73
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res (2002) 1.72
Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. Proc Natl Acad Sci U S A (2006) 1.70
Towards multilocus sequence typing of the Leishmania donovani complex: resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GPI, NH1, NH2, PGD). Int J Parasitol (2006) 1.67
Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell (2006) 1.67
Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol (2012) 1.64
RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J Biol Chem (2004) 1.58
On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol (2005) 1.56
Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics (2010) 1.55
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol (2014) 1.51
Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proc Natl Acad Sci U S A (2008) 1.51
Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet (2002) 1.49
Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol (2007) 1.49
TbRGG1, an essential protein involved in kinetoplastid RNA metabolism that is associated with a novel multiprotein complex. RNA (2008) 1.47
Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga. Mol Microbiol (2011) 1.45
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog (2012) 1.44
A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc Natl Acad Sci U S A (2005) 1.43
Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot Cell (2004) 1.43
Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in rhizaria. Curr Biol (2013) 1.42
Complex protein targeting to dinoflagellate plastids. J Mol Biol (2005) 1.41
Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol (2003) 1.39
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol Biol (2010) 1.39
The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia. Protist (2002) 1.38
Kinetoplastid guide RNA biogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase. RNA (2009) 1.37
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Res (2007) 1.36
A scalable pipeline for highly effective genetic modification of a malaria parasite. Nat Methods (2011) 1.31
Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina. Mol Biol Evol (2008) 1.31
The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biol (2006) 1.31
A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol (2014) 1.31
Genome compaction and stability in microsporidian intracellular parasites. Curr Biol (2004) 1.28
How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life (2011) 1.28
Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS One (2009) 1.24
Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes. Proc Natl Acad Sci U S A (2012) 1.24
Evolution of the sex-related locus and genomic features shared in microsporidia and fungi. PLoS One (2010) 1.23
Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A (2009) 1.23
Functional characterization of the Plasmodium falciparum and P. berghei homologues of macrophage migration inhibitory factor. Infect Immun (2006) 1.23
A tertiary plastid uses genes from two endosymbionts. J Mol Biol (2006) 1.22
Differential var gene expression in the organs of patients dying of falciparum malaria. Mol Microbiol (2007) 1.22
The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J Mol Biol (2007) 1.21
Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms. PLoS One (2008) 1.21
First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution. Genome Biol Evol (2011) 1.20
Microsporidian mitosomes retain elements of the general mitochondrial targeting system. Proc Natl Acad Sci U S A (2006) 1.19
Re-examining alveolate evolution using multiple protein molecular phylogenies. J Eukaryot Microbiol (2002) 1.17
A bacterial proteorhodopsin proton pump in marine eukaryotes. Nat Commun (2011) 1.17
Widespread recycling of processed cDNAs in dinoflagellates. Curr Biol (2008) 1.17
Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int J Syst Evol Microbiol (2003) 1.17
Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi. PLoS One (2007) 1.16
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Genome Biol (2009) 1.16
Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities. BMC Genomics (2008) 1.16
The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS One (2010) 1.16
Plasmodium falciparum antigenic variation: relationships between in vivo selection, acquired antibody response, and disease severity. J Infect Dis (2005) 1.14
Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein. Mol Biol Evol (2006) 1.14
Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids. Eukaryot Cell (2005) 1.14
The evolutionary history of kinetoplastids and their kinetoplasts. Mol Biol Evol (2002) 1.13
Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei. Int J Parasitol (2008) 1.13
Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi. Genomics (2008) 1.13
Molecular and morphological analysis of the family Calonymphidae with a description of Calonympha chia sp. nov., Snyderella kirbyi sp. nov., Snyderella swezyae sp. nov. and Snyderella yamini sp. nov. Int J Syst Evol Microbiol (2010) 1.13
A model for taxonomic work on homoxenous coccidia: redescription, host specificity, and molecular phylogeny of Eimeria ranae Dobell, 1909, with a review of anuran-host Eimeria (Apicomplexa: Eimeriorina). J Eukaryot Microbiol (2009) 1.12
Evolution of the haem synthetic pathway in kinetoplastid flagellates: an essential pathway that is not essential after all? Int J Parasitol (2009) 1.11
Genetic polymorphism within the leishmania donovani complex: correlation with geographic origin. Am J Trop Med Hyg (2004) 1.11
Architecture of the trypanosome RNA editing accessory complex, MRB1. Nucleic Acids Res (2012) 1.10
Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution. Eukaryot Cell (2003) 1.10
A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol Biol Evol (2003) 1.10
Alteration of host cell phenotype by Theileria annulata and Theileria parva: mining for manipulators in the parasite genomes. Int J Parasitol (2005) 1.09
Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and beta-tubulin. Int J Syst Evol Microbiol (2003) 1.08