Whole-genome analysis of photosynthetic prokaryotes.

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78

Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A (2005) 4.37

'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50

Horizontal gene transfer: a critical view. Proc Natl Acad Sci U S A (2003) 3.27

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A (2008) 2.97

Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet (2005) 2.71

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol (2004) 2.51

The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11

Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J Bacteriol (2007) 1.80

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol (2005) 1.79

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol (2006) 1.66

Rooting the tree of life by transition analyses. Biol Direct (2006) 1.66

Genome evolution in cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci U S A (2008) 1.58

Remarkable diversity of phototrophic purple bacteria in a permanently frozen Antarctic lake. Appl Environ Microbiol (2003) 1.50

Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth Res (2003) 1.42

Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol Genet Genomics (2007) 1.39

Thinking about the evolution of photosynthesis. Photosynth Res (2004) 1.34

The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics (2012) 1.32

Early evolution of photosynthesis. Plant Physiol (2010) 1.29

Representative freshwater bacterioplankton isolated from Crater Lake, Oregon. Appl Environ Microbiol (2004) 1.28

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol (2008) 1.24

Homologs of plant PsbP and PsbQ proteins are necessary for regulation of photosystem ii activity in the cyanobacterium Synechocystis 6803. Plant Cell (2004) 1.23

A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics (2004) 1.22

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol (2013) 1.22

Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol (2009) 1.17

The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem (2011) 1.14

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A (2014) 1.13

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics (2011) 1.13

Decoding the genomic tree of life. Proc Natl Acad Sci U S A (2005) 1.11

An improved probability mapping approach to assess genome mosaicism. BMC Genomics (2003) 1.10

Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Front Microbiol (2011) 1.10

Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol (2004) 1.09

Signature proteins for the major clades of Cyanobacteria. BMC Evol Biol (2010) 1.07

Discovering functional novelty in metagenomes: examples from light-mediated processes. J Bacteriol (2008) 1.06

Early evolution without a tree of life. Biol Direct (2011) 1.05

Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study. Proc Natl Acad Sci U S A (2006) 1.04

Evidence for an early prokaryotic endosymbiosis. Nature (2009) 1.02

Insights and inferences about integron evolution from genomic data. BMC Genomics (2008) 1.02

Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: implications for the phylogenetic origin of cyanobacterial and algal hydrogenases. J Mol Evol (2006) 1.00

Comparative genomics of NAD biosynthesis in cyanobacteria. J Bacteriol (2006) 1.00

Speciation in Chlamydia: genomewide phylogenetic analyses identified a reliable set of acquired genes. J Mol Evol (2003) 0.98

Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics (2005) 0.97

BranchClust: a phylogenetic algorithm for selecting gene families. BMC Bioinformatics (2007) 0.92

Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol Evol (2013) 0.91

Evolutionary relationships among photosynthetic bacteria. Photosynth Res (2003) 0.91

Automatic selection of representative proteins for bacterial phylogeny. BMC Evol Biol (2005) 0.89

Data mining for proteins characteristic of clades. Nucleic Acids Res (2006) 0.89

Visualization of the phylogenetic content of five genomes using dekapentagonal maps. Genome Biol (2004) 0.88

Proteomic responses of Roseobacter litoralis OCh149 to starvation and light regimen. Microbes Environ (2012) 0.88

Energy, ecology and the distribution of microbial life. Philos Trans R Soc Lond B Biol Sci (2013) 0.86

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120. BMC Microbiol (2009) 0.86

Phylogeny of galactolipid synthase homologs together with their enzymatic analyses revealed a possible origin and divergence time for photosynthetic membrane biogenesis. DNA Res (2011) 0.86

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinformatics (2004) 0.86

Phylogenetic analyses of the core antenna domain: investigating the origin of photosystem I. J Mol Evol (2005) 0.85

Photosynthesis: what color was its origin? Genome Biol (2006) 0.84

POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes. Nucleic Acids Res (2013) 0.84

Evolutionary constraints or opportunities? Biosystems (2014) 0.83

Structural analysis of alternative complex III in the photosynthetic electron transfer chain of Chloroflexus aurantiacus. Biochemistry (2010) 0.81

The role of reticulate evolution in creating innovation and complexity. Int J Evol Biol (2012) 0.80

Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution. Front Cell Infect Microbiol (2012) 0.80

Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PLoS One (2011) 0.79

The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans. Environ Microbiol (2015) 0.78

Time line of discoveries: anoxygenic bacterial photosynthesis. Photosynth Res (2004) 0.78

PentaPlot: a software tool for the illustration of genome mosaicism. BMC Bioinformatics (2005) 0.77

Evolutionary biology. Bacteria shared photosynthesis genes. Science (2002) 0.75

Current awareness on comparative and functional genomics. Comp Funct Genomics (2003) 0.75

On the free energy that drove primordial anabolism. Int J Mol Sci (2009) 0.75

Gene essentiality, conservation index and co-evolution of genes in cyanobacteria. PLoS One (2017) 0.75

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi. Proc Natl Acad Sci U S A (2017) 0.75

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature (2007) 7.08

Two-dimensional spectroscopy of electronic couplings in photosynthesis. Nature (2005) 4.72

The natural history of nitrogen fixation. Mol Biol Evol (2003) 3.07

Estimating the size of the bacterial pan-genome. Trends Genet (2009) 2.61

Long-lived quantum coherence in photosynthetic complexes at physiological temperature. Proc Natl Acad Sci U S A (2010) 2.47

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res (2006) 2.46

Prokaryotic evolution and the tree of life are two different things. Biol Direct (2009) 2.17

On the origin of prokaryotic species. Genome Res (2009) 1.92

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci U S A (2009) 1.78

Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology (2010) 1.77

Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci U S A (2008) 1.70

Inteins: structure, function, and evolution. Annu Rev Microbiol (2002) 1.67

Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol (2012) 1.63

The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol (2006) 1.61

The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria. Photosynth Res (2009) 1.60

Cross-peak-specific two-dimensional electronic spectroscopy. Proc Natl Acad Sci U S A (2007) 1.60

An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proc Natl Acad Sci U S A (2005) 1.58

Evolution of photosynthesis. Annu Rev Plant Biol (2011) 1.56

Were arachnids the first to use combinatorial peptide libraries? Peptides (2005) 1.55

Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J (2007) 1.54

Membrane orientation of the FMO antenna protein from Chlorobaculum tepidum as determined by mass spectrometry-based footprinting. Proc Natl Acad Sci U S A (2009) 1.53

Biased gene transfer in microbial evolution. Nat Rev Microbiol (2011) 1.50

The structure of the FMO protein from Chlorobium tepidum at 2.2 A resolution. Photosynth Res (2003) 1.48

Searching for species in haloarchaea. Proc Natl Acad Sci U S A (2007) 1.46

Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene. Proc Natl Acad Sci U S A (2005) 1.43

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. BMC Genomics (2002) 1.42

Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments. Environ Microbiol (2008) 1.39

Phycobilisomes supply excitations to both photosystems in a megacomplex in cyanobacteria. Science (2013) 1.37

Visualization of excitonic structure in the Fenna-Matthews-Olson photosynthetic complex by polarization-dependent two-dimensional electronic spectroscopy. Biophys J (2008) 1.36

Genome mosaicism and organismal lineages. Trends Genet (2004) 1.34

Thinking about the evolution of photosynthesis. Photosynth Res (2004) 1.34

Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet (2004) 1.33

Characterization of Chlorobium tepidum chlorosomes: a calculation of bacteriochlorophyll c per chlorosome and oligomer modeling. Biophys J (2003) 1.32

Carbohydrate metabolism and carbon fixation in Roseobacter denitrificans OCh114. PLoS One (2009) 1.32

Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments. Appl Environ Microbiol (2006) 1.30

Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol (2008) 1.29

Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies. Anal Chem (2011) 1.25

A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics (2004) 1.22

Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. J Bacteriol (2005) 1.19

New class of bacterial membrane oxidoreductases. Biochemistry (2005) 1.17

Isolation and characterization of the B798 light-harvesting baseplate from the chlorosomes of Chloroflexus aurantiacus. Biochemistry (2003) 1.16

Conservation of distantly related membrane proteins: photosynthetic reaction centers share a common structural core. Mol Biol Evol (2006) 1.16

Molecular mechanism of photoactivation and structural location of the cyanobacterial orange carotenoid protein. Biochemistry (2013) 1.13

A viewpoint: why chlorophyll a? Photosynth Res (2009) 1.13

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics (2011) 1.13

Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii. J Bacteriol (2007) 1.11

Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ Microbiol (2008) 1.11

An improved probability mapping approach to assess genome mosaicism. BMC Genomics (2003) 1.10

Expanding the solar spectrum used by photosynthesis. Trends Plant Sci (2011) 1.09

The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol Biol (2007) 1.09

Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol (2007) 1.09

Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos Trans R Soc Lond B Biol Sci (2003) 1.08

Spectral signatures of photosynthesis. I. Review of Earth organisms. Astrobiology (2007) 1.08

Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci (2009) 1.08

Ancient gene duplications and the root(s) of the tree of life. Protoplasma (2005) 1.07

Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol Evol (2009) 1.06

Native electrospray and electron-capture dissociation in FTICR mass spectrometry provide top-down sequencing of a protein component in an intact protein assembly. J Am Soc Mass Spectrom (2010) 1.06

Native mass spectrometry characterization of intact nanodisc lipoprotein complexes. Anal Chem (2012) 1.06

Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements. BMC Evol Biol (2009) 1.04

Biased gene transfer mimics patterns created through shared ancestry. Proc Natl Acad Sci U S A (2010) 1.03

Role of the AcsF protein in Chloroflexus aurantiacus. J Bacteriol (2009) 1.03

Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics (2010) 1.02

Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer. Ann N Y Acad Sci (2009) 1.02

Concerted gene recruitment in early plant evolution. Genome Biol (2008) 1.02

The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol (2008) 1.01

Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol (2012) 1.00

Trees in the web of life. J Biol (2009) 1.00

Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS One (2011) 0.99

Rooting the ribosomal tree of life. Mol Biol Evol (2010) 0.99

Purification and characterization of the B808-866 light-harvesting complex from green filamentous bacterium Chloroflexus aurantiacus. Photosynth Res (2005) 0.98

Native electrospray mass spectrometry reveals the nature and stoichiometry of pigments in the FMO photosynthetic antenna protein. Biochemistry (2011) 0.98

Effect of iron on growth and ultrastructure of Acaryochloris marina. Appl Environ Microbiol (2005) 0.97

Time-resolved absorption and emission show that the CP43' antenna ring of iron-stressed synechocystis sp. PCC6803 is efficiently coupled to the photosystem I reaction center core. Biochemistry (2003) 0.97

Light harvesting in photosystem I supercomplexes. Biochemistry (2006) 0.97

Spectroscopic studies of two spectral variants of light-harvesting complex 2 (LH2) from the photosynthetic purple sulfur bacterium Allochromatium vinosum. Biochim Biophys Acta (2012) 0.96

A rooted net of life. Biol Direct (2011) 0.96

Ecology. How bacterial lineages emerge. Science (2012) 0.96

Bacteriochlorophyll f: properties of chlorosomes containing the "forbidden chlorophyll". Front Microbiol (2012) 0.94

Spectroscopic properties of the main-form and high-salt peridinin-chlorophyll a proteins from Amphidinium carterae. Biochemistry (2004) 0.93

Robustness of electronic coherence in the Fenna-Matthews-Olson complex to vibronic and structural modifications. Faraday Discuss (2011) 0.93

The evolution of eukaryotes. Science (2007) 0.93

Extinction coefficient for red-shifted chlorophylls: chlorophyll d and chlorophyll f. Biochim Biophys Acta (2012) 0.92

Both forward and reverse TCA cycles operate in green sulfur bacteria. J Biol Chem (2010) 0.92

Mass spectrometry footprinting reveals the structural rearrangements of cyanobacterial orange carotenoid protein upon light activation. Biochim Biophys Acta (2014) 0.92

Chlorosome antenna complexes from green photosynthetic bacteria. Photosynth Res (2013) 0.92

BranchClust: a phylogenetic algorithm for selecting gene families. BMC Bioinformatics (2007) 0.92

Mass spectrometry-based carboxyl footprinting of proteins: method evaluation. Int J Mass Spectrom (2012) 0.91

Structural model and spectroscopic characteristics of the FMO antenna protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum. Biochim Biophys Acta (2010) 0.91

Characterization of the FMO protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum. Photosynth Res (2010) 0.91

Spectral signatures of photosynthesis. II. Coevolution with other stars and the atmosphere on extrasolar worlds. Astrobiology (2007) 0.91

Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth. BMC Microbiol (2010) 0.91

Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics (2013) 0.90

Structure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus. J Bacteriol (2009) 0.90

Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores. J Bacteriol (2011) 0.90

Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea. J Bacteriol (2011) 0.89

Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints. J R Soc Interface (2012) 0.89