Published in Proc Natl Acad Sci U S A on February 05, 2009
A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol (2011) 1.78
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct (2010) 1.35
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics (2010) 1.26
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26
Genome sequence of Pseudomonas stutzeri SDM-LAC, a typical strain for studying the molecular mechanism of lactate utilization. J Bacteriol (2012) 1.14
Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microb Biotechnol (2010) 1.13
A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res (2010) 1.11
Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics (2010) 1.11
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem (2011) 1.08
Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing. ISME J (2014) 1.06
Substrate-level phosphorylation is the primary source of energy conservation during anaerobic respiration of Shewanella oneidensis strain MR-1. J Bacteriol (2010) 0.99
Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions. Appl Environ Microbiol (2011) 0.98
Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level. Appl Environ Microbiol (2011) 0.97
Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol (2012) 0.95
Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor. PLoS One (2012) 0.94
Shewanella spp. Use acetate as an electron donor for denitrification but not ferric iron or fumarate reduction. Appl Environ Microbiol (2013) 0.93
Electron donors supporting growth and electroactivity of Geobacter sulfurreducens anode biofilms. Appl Environ Microbiol (2011) 0.92
Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res (2012) 0.91
An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One (2010) 0.87
Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol (2012) 0.86
Preferential utilization of D-lactate by Shewanella oneidensis. Appl Environ Microbiol (2012) 0.86
Lactate oxidation coupled to iron or electrode reduction by Geobacter sulfurreducens PCA. Appl Environ Microbiol (2011) 0.85
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) (2010) 0.85
Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses. Front Microbiol (2014) 0.82
Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools. BMC Genomics (2013) 0.81
Analysis of the BarA/UvrY two-component system in Shewanella oneidensis MR-1. PLoS One (2011) 0.81
Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells. Front Microbiol (2015) 0.79
NAD-dependent lactate dehydrogenase catalyses the first step in respiratory utilization of lactate by Lactococcus lactis. FEBS Open Bio (2013) 0.79
Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor. J Bacteriol (2016) 0.78
An unconventional hexacoordinated flavohemoglobin from Mycobacterium tuberculosis. J Biol Chem (2012) 0.78
Identification of the genes that contribute to lactate utilization in Helicobacter pylori. PLoS One (2014) 0.78
The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol (2015) 0.77
NAD-Independent L-Lactate Dehydrogenase Required for L-Lactate Utilization in Pseudomonas stutzeri A1501. J Bacteriol (2015) 0.76
Utilization of D-Lactate as an Energy Source Supports the Growth of Gluconobacter oxydans. Appl Environ Microbiol (2015) 0.76
Metabolic Characteristics of a Glucose-Utilizing Shewanella oneidensis Strain Grown under Electrode-Respiring Conditions. PLoS One (2015) 0.75
Characterization of the enhancement of zero valent iron on microbial azo reduction. BMC Microbiol (2015) 0.75
Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth. Appl Environ Microbiol (2011) 0.75
An in vivo metabolic approach for deciphering the product specificity of glycerate kinase proves that both E. coli's glycerate kinases generate 2-phosphoglycerate. PLoS One (2015) 0.75
Epithelial Coculture and l-Lactate Promote Growth of Helicobacter cinaedi under H2-Free Aerobic Conditions. Appl Environ Microbiol (2016) 0.75
(13)C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells. Sci Rep (2016) 0.75
CRP Regulates D-Lactate Oxidation in Shewanella oneidensis MR-1. Front Microbiol (2017) 0.75
A bacterial multi-domain NAD-independent d-lactate dehydrogenase utilizes FAD and Fe-S clusters as cofactors and quinone as electron acceptor for d-lactate oxidization. J Bacteriol (2017) 0.75
Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell. Biotechnol Biofuels (2017) 0.75
Investigation of a spontaneous mutant reveals novel features of iron uptake in Shewanella oneidensis. Sci Rep (2017) 0.75
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
Catabolic repression of bacterial sporulation. Proc Natl Acad Sci U S A (1965) 19.70
Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev (2002) 12.84
pBBR1MCS: a broad-host-range cloning vector. Biotechniques (1994) 8.71
A vector for systematic gene inactivation in Bacillus subtilis. Microbiology (1998) 8.00
Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science (1988) 7.27
Growth of desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. Appl Environ Microbiol (1977) 6.14
Intermediary metabolism of organic matter in the sediments of a eutrophic lake. Appl Environ Microbiol (1982) 6.13
Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol (2003) 4.91
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
Bacterial lactate dehydrogenases. Microbiol Rev (1980) 3.89
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Three overlapping lct genes involved in L-lactate utilization by Escherichia coli. J Bacteriol (1993) 2.31
Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol (2004) 2.23
Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. OMICS (2004) 1.92
Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem (2006) 1.57
[Software for analyzing bacterial genomes]. Mol Biol (Mosk) (2000) 1.49
Transport of L-Lactate, D-Lactate, and glycolate by the LldP and GlcA membrane carriers of Escherichia coli. Biochem Biophys Res Commun (2002) 1.42
Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol (2003) 1.41
The ion transporter superfamily. Biochim Biophys Acta (2003) 1.36
Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl Environ Microbiol (2007) 1.27
Characterization of a novel Neisseria meningitidis Fur and iron-regulated operon required for protection from oxidative stress: utility of DNA microarray in the assignment of the biological role of hypothetical genes. Mol Microbiol (2004) 1.24
Isolation of the DLD gene of Saccharomyces cerevisiae encoding the mitochondrial enzyme D-lactate ferricytochrome c oxidoreductase. Mol Gen Genet (1993) 1.19
Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments. J Bacteriol (2006) 1.16
Identification of putative mammalian D-lactate dehydrogenase enzymes. Biochem Biophys Res Commun (2002) 1.15
Membrane-bound D-lactate dehydrogenase from Escherichia coli: purification and properties. Biochemistry (1979) 1.15
Domain organization and a protease-sensitive loop in eukaryotic ornithine decarboxylase. Biochemistry (1995) 1.08
Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli. J Bacteriol (2008) 1.07
Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling. Genome Inform (2007) 1.04
Primary structure, physicochemical properties, and chemical modification of NAD(+)-dependent D-lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site. J Biol Chem (1992) 1.03
Oxidation of D-lactate and L-lactate by Neisseria meningitidis: purification and cloning of meningococcal D-lactate dehydrogenase. J Bacteriol (1993) 1.01
Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard. FEMS Microbiol Ecol (2006) 1.01
Cloning of a Neisseria meningitidis gene for L-lactate dehydrogenase (L-LDH): evidence for a second meningococcal L-LDH with different regulation. J Bacteriol (1996) 0.98
Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. Int J Syst Evol Microbiol (2000) 0.85
Regulation of the Saccharomyces cerevisiae DLD1 gene encoding the mitochondrial protein D-lactate ferricytochrome c oxidoreductase by HAP1 and HAP2/3/4/5. Mol Gen Genet (1999) 0.84
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell (2011) 11.44
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res (2006) 11.15
Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science (2010) 6.04
A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr Purif (2002) 5.72
Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc Natl Acad Sci U S A (2006) 5.26
An agonist of toll-like receptor 5 has radioprotective activity in mouse and primate models. Science (2008) 4.89
From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol (2002) 4.66
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science (2012) 4.41
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 3.15
Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol (2004) 2.86
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res (2002) 2.84
c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis. PLoS Biol (2006) 2.80
Bcl-2 and Bcl-XL regulate proinflammatory caspase-1 activation by interaction with NALP1. Cell (2007) 2.79
Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol (2003) 2.77
Microbial activity at gigapascal pressures. Science (2002) 2.72
Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes Dev (2012) 2.70
An expression vector tailored for large-scale, high-throughput purification of recombinant proteins. Protein Expr Purif (2006) 2.58
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53
Autoregulation and homodimerization are involved in the activation of the plant steroid receptor BRI1. Dev Cell (2005) 2.48
CutDB: a proteolytic event database. Nucleic Acids Res (2006) 2.41
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Isolation of a high-affinity functional protein complex between OmcA and MtrC: Two outer membrane decaheme c-type cytochromes of Shewanella oneidensis MR-1. J Bacteriol (2006) 2.36
Expression profile of microRNAs in serum: a fingerprint for esophageal squamous cell carcinoma. Clin Chem (2010) 2.34
Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl Environ Microbiol (2007) 2.34
New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'? Trends Biochem Sci (2008) 2.30
Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl Environ Microbiol (2004) 2.28
High throughput methods for gene cloning and expression. Protein Expr Purif (2002) 2.26
Comparative metabolic flux profiling of melanoma cell lines: beyond the Warburg effect. J Biol Chem (2011) 2.24
Characterization of an electron conduit between bacteria and the extracellular environment. Proc Natl Acad Sci U S A (2009) 2.20
A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol (2008) 2.16
Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol (2002) 2.14
Structural basis of TLR5-flagellin recognition and signaling. Science (2012) 2.10
Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol Microbiol (2002) 2.06
An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A (2002) 1.95
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
Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA (2003) 1.89
Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc Natl Acad Sci U S A (2007) 1.83
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics (2009) 1.80
Structure and lytic activity of a Bacillus anthracis prophage endolysin. J Biol Chem (2005) 1.79
Structure of a bacterial cell surface decaheme electron conduit. Proc Natl Acad Sci U S A (2011) 1.76
MicroRNA-513 regulates B7-H1 translation and is involved in IFN-gamma-induced B7-H1 expression in cholangiocytes. J Immunol (2009) 1.76
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure (2003) 1.69
Single-crystal metallic nanowires and metal/semiconductor nanowire heterostructures. Nature (2004) 1.67
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics (2013) 1.61
The hemopexin domain of matrix metalloproteinase-9 activates cell signaling and promotes migration of schwann cells by binding to low-density lipoprotein receptor-related protein. J Neurosci (2008) 1.60
Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem (2006) 1.57
Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in cultures of dissimilatory metal-reducing bacteria. Biotechnol Bioeng (2002) 1.56
Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev (2011) 1.55
Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. J Biol Chem (2009) 1.50
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci U S A (2009) 1.47
Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state. Appl Environ Microbiol (2004) 1.47
Reverse TCA cycle flux through isocitrate dehydrogenases 1 and 2 is required for lipogenesis in hypoxic melanoma cells. Pigment Cell Melanoma Res (2012) 1.46
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45
Long non-coding RNA UCA1a(CUDR) promotes proliferation and tumorigenesis of bladder cancer. Int J Oncol (2012) 1.45
ERβ and PEA3 co-activate IL-8 expression and promote the invasion of breast cancer cells. Cancer Biol Ther (2011) 1.45
Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA. J Bacteriol (2008) 1.45
Differentially expressed genes between primary cancer and paired lymph node metastases predict clinical outcome of node-positive breast cancer patients. Breast Cancer Res Treat (2006) 1.40
A Technical Evaluation of Wireless Connectivity from Patient Monitors to an Anesthesia Information Management System During Intensive Care Unit Surgery. Anesth Analg (2016) 1.38
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J Biol Chem (2002) 1.38
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
Short term high fat diet challenge promotes alternative macrophage polarization in adipose tissue via natural killer T cells and interleukin-4. J Biol Chem (2012) 1.35
The low-density lipoprotein receptor-related protein is a pro-survival receptor in Schwann cells: possible implications in peripheral nerve injury. J Neurosci (2006) 1.31
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol (2011) 1.31
Membrane type-1 matrix metalloproteinase (MT1-MMP) exhibits an important intracellular cleavage function and causes chromosome instability. J Biol Chem (2005) 1.30
Inhibition of MCL-1 in breast cancer cells promotes cell death in vitro and in vivo. Cancer Biol Ther (2010) 1.28
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics (2009) 1.28
Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction. Appl Environ Microbiol (2007) 1.27
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics (2010) 1.26
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26