Published in J Proteome Res on March 30, 2011
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. J Proteome Res (2012) 1.07
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinformatics (2012) 0.92
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics (2012) 0.85
ChlR protein of Synechococcus sp. PCC 7002 is a transcription activator that uses an oxygen-sensitive [4Fe-4S] cluster to control genes involved in pigment biosynthesis. J Biol Chem (2014) 0.84
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification. Bioinformatics (2011) 0.81
Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res (2013) 0.80
Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide. BMC Bioinformatics (2012) 0.77
Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra. Proteomics (2013) 0.75
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. Database (Oxford) (2015) 0.75
Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol (2006) 4.74
An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics (2002) 4.10
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science (2012) 3.39
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A (2002) 3.19
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res (2006) 3.10
Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem (2005) 2.29
The tricarboxylic acid cycle in cyanobacteria. Science (2011) 2.14
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J (2008) 2.11
Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal Chem (2003) 2.00
Protein composition of the vaccinia virus mature virion. Virology (2006) 1.93
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One (2009) 1.83
Chlorophyll biosynthesis in bacteria: the origins of structural and functional diversity. Annu Rev Microbiol (2007) 1.77
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res (2008) 1.68
Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic (2008) 1.63
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal Chem (2006) 1.59
Establishing the proteome of normal human cerebrospinal fluid. PLoS One (2010) 1.53
Comparative bacterial proteomics: analysis of the core genome concept. PLoS One (2008) 1.49
Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes. Plant Cell (2003) 1.47
Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci U S A (2009) 1.47
Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol (2009) 1.45
Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation. Methods Mol Biol (2004) 1.44
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
Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes. Proc Natl Acad Sci U S A (2009) 1.41
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics (2009) 1.40
Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front Microbiol (2011) 1.38
'Candidatus Thermochlorobacter aerophilum:' an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics. ISME J (2012) 1.36
Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc Natl Acad Sci U S A (2002) 1.36
Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Mol Cell Proteomics (2006) 1.36
Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA. Front Microbiol (2011) 1.34
Proteomic analysis of stationary phase in the marine bacterium "Candidatus Pelagibacter ubique". Appl Environ Microbiol (2008) 1.33
Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. J Proteome Res (2006) 1.33
Expression of genes in cyanobacteria: adaptation of endogenous plasmids as platforms for high-level gene expression in Synechococcus sp. PCC 7002. Methods Mol Biol (2011) 1.32
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J (2011) 1.31
Regulatory roles for IscA and SufA in iron homeostasis and redox stress responses in the cyanobacterium Synechococcus sp. strain PCC 7002. J Bacteriol (2006) 1.30
Chlorobium tepidum mutant lacking bacteriochlorophyll c made by inactivation of the bchK gene, encoding bacteriochlorophyll c synthase. J Bacteriol (2002) 1.29
Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J (2011) 1.28
Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry. Anal Chem (2005) 1.28
Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria. Environ Microbiol (2011) 1.25
Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria. Arch Microbiol (2004) 1.24
Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. J Bacteriol (2004) 1.23
Assembly of photosystem I. I. Inactivation of the rubA gene encoding a membrane-associated rubredoxin in the cyanobacterium Synechococcus sp. PCC 7002 causes a loss of photosystem I activity. J Biol Chem (2002) 1.23
Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics. Environ Microbiol (2011) 1.22
Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1. Front Microbiol (2012) 1.21
The bchU gene of Chlorobium tepidum encodes the c-20 methyltransferase in bacteriochlorophyll c biosynthesis. J Bacteriol (2004) 1.21
Long-range organization of bacteriochlorophyll in chlorosomes of Chlorobium tepidum investigated by cryo-electron microscopy. FEBS Lett (2007) 1.20
Molecular contacts for chlorosome envelope proteins revealed by cross-linking studies with chlorosomes from Chlorobium tepidum. Biochemistry (2006) 1.20
Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome. Appl Environ Microbiol (2008) 1.19
Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ Microbiol (2007) 1.19
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis. OMICS (2004) 1.19
Redirecting reductant flux into hydrogen production via metabolic engineering of fermentative carbon metabolism in a cyanobacterium. Appl Environ Microbiol (2010) 1.18
Membrane stresses induced by overproduction of free fatty acids in Escherichia coli. Appl Environ Microbiol (2011) 1.18
Bacteriochlorophyllide c C-8(2) and C-12(1) methyltransferases are essential for adaptation to low light in Chlorobaculum tepidum. J Bacteriol (2007) 1.17
The biochemical basis for structural diversity in the carotenoids of chlorophototrophic bacteria. Photosynth Res (2008) 1.17
Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions. Front Microbiol (2012) 1.17
Acclimation of the Global Transcriptome of the Cyanobacterium Synechococcus sp. Strain PCC 7002 to Nutrient Limitations and Different Nitrogen Sources. Front Microbiol (2012) 1.17
Tocopherols protect Synechocystis sp. strain PCC 6803 from lipid peroxidation. Plant Physiol (2005) 1.17
The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. Biochim Biophys Acta (2006) 1.17
Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res (2006) 1.16
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J (2012) 1.15
Enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. J Proteome Res (2003) 1.14
UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. J Biol Chem (2004) 1.14
Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. J Bacteriol (2004) 1.14
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics (2008) 1.12
Altered carbohydrate metabolism in glycogen synthase mutants of Synechococcus sp. strain PCC 7002: Cell factories for soluble sugars. Metab Eng (2012) 1.11
alpha-Tocopherol plays a role in photosynthesis and macronutrient homeostasis of the cyanobacterium Synechocystis sp. PCC 6803 that is independent of its antioxidant function. Plant Physiol (2006) 1.11
Subcellular localization of chlorosome proteins in Chlorobium tepidum and characterization of three new chlorosome proteins: CsmF, CsmH, and CsmX. Biochemistry (2002) 1.11
Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots. J Am Chem Soc (2004) 1.11
Assembly of photosystem I. II. Rubredoxin is required for the in vivo assembly of F(X) in Synechococcus sp. PCC 7002 as shown by optical and EPR spectroscopy. J Biol Chem (2002) 1.11
Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A (2007) 1.10
The use of accurate mass tags for high-throughput microbial proteomics. OMICS (2002) 1.10
A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns. J Proteome Res (2007) 1.10
Roles of xanthophyll carotenoids in protection against photoinhibition and oxidative stress in the cyanobacterium Synechococcus sp. strain PCC 7002. Arch Biochem Biophys (2010) 1.10
Characterization of a plant-like protochlorophyllide a divinyl reductase in green sulfur bacteria. J Biol Chem (2006) 1.09
The sufR gene (sll0088 in Synechocystis sp. strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria. J Bacteriol (2004) 1.09
Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis. J Bacteriol (2008) 1.09
A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res (2008) 1.09
Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. J Proteome Res (2006) 1.07
The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery. Biomark Med (2007) 1.06
Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor. Biochim Biophys Acta (2008) 1.05
Transcriptional regulation of the CO2-concentrating mechanism in a euryhaline, coastal marine cyanobacterium, Synechococcus sp. Strain PCC 7002: role of NdhR/CcmR. J Bacteriol (2007) 1.05
Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol (2012) 1.05
Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. Environ Sci Technol (2010) 1.04
SufR coordinates two [4Fe-4S]2+, 1+ clusters and functions as a transcriptional repressor of the sufBCDS operon and an autoregulator of sufR in cyanobacteria. J Biol Chem (2007) 1.03
A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res (2008) 1.02
Cultivation and genomic, nutritional, and lipid biomarker characterization of Roseiflexus strains closely related to predominant in situ populations inhabiting Yellowstone hot spring microbial mats. J Bacteriol (2010) 1.02
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol (2013) 1.01
Roles for heme-copper oxidases in extreme high-light and oxidative stress response in the cyanobacterium Synechococcus sp. PCC 7002. Arch Microbiol (2006) 1.00
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics (2010) 1.00
Biogenesis of phycobiliproteins: I. cpcS-I and cpcU mutants of the cyanobacterium Synechococcus sp. PCC 7002 define a heterodimeric phyococyanobilin lyase specific for beta-phycocyanin and allophycocyanin subunits. J Biol Chem (2008) 1.00
Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME J (2010) 1.00
Two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium Chlorobium tepidum. J Bacteriol (2006) 1.00