Published in BMC Bioinformatics on February 15, 2011
The utility of metabolomics in natural product and biomarker characterization. Biochim Biophys Acta (2014) 0.84
A tree of cellular life inferred from a genomic census of molecular functions. J Mol Evol (2014) 0.79
Reconstruction of phyletic trees by global alignment of multiple metabolic networks. BMC Bioinformatics (2013) 0.79
Metabolic classification of microbial genomes using functional probes. BMC Genomics (2012) 0.77
Novel Approach to Classify Plants Based on Metabolite-Content Similarity. Biomed Res Int (2017) 0.75
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A (1990) 50.63
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
Open source clustering software. Bioinformatics (2004) 23.17
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics (2007) 11.03
Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature (2004) 7.18
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol (1994) 6.26
The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U S A (2004) 2.79
Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res (2000) 1.89
In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res (2003) 1.48
The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci U S A (2007) 1.31
Metabolic pathfinding using RPAIR annotation. J Mol Biol (2009) 1.13
Phylogenetic comparison of metabolic capacities of organisms at genome level. Mol Phylogenet Evol (2004) 1.09
Phylogenetic reconstruction from non-genomic data. Bioinformatics (2007) 1.04
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics (2006) 1.00
Analysis of phenetic trees based on metabolic capabilites across the three domains of life. J Mol Biol (2004) 0.99
Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. BMC Bioinformatics (2006) 0.93
Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol (2009) 0.93
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinformatics (2010) 0.86
MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom (2010) 6.16
Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 3.41
Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics (2003) 2.57
Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene (2005) 1.46
DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res (2010) 1.41
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics (2010) 1.30
Trypsin-induced proteome alteration during cell subculture in mammalian cells. J Biomed Sci (2010) 1.29
Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Syst Biol (2007) 1.25
Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Anal Chem (2009) 1.25
Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of XC847, a 3'-5' oligoribonuclease from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 1.19
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics (2006) 1.18
Integrated omics approaches in plant systems biology. Curr Opin Chem Biol (2009) 1.17
Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Syst Biol (2011) 1.17
GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA). BMC Bioinformatics (2011) 1.15
Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa). J Biol Chem (2002) 1.12
Predicting helix-helix interactions from residue contacts in membrane proteins. Bioinformatics (2009) 1.11
Relationship between protein structures and disulfide-bonding patterns. Proteins (2003) 1.07
Identification of MYO18A as a novel interacting partner of the PAK2/betaPIX/GIT1 complex and its potential function in modulating epithelial cell migration. Mol Biol Cell (2009) 1.07
CPDB: a database of circular permutation in proteins. Nucleic Acids Res (2008) 1.05
Relationship between local structural entropy and protein thermostability. Proteins (2004) 1.04
Protein structural similarity search by Ramachandran codes. BMC Bioinformatics (2007) 1.04
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol (2008) 1.03
Databases on food phytochemicals and their health-promoting effects. J Agric Food Chem (2011) 1.02
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB). BMC Genomics (2012) 1.00
Proteomics study of oxidative stress and Src kinase inhibition in H9C2 cardiomyocytes: a cell model of heart ischemia-reperfusion injury and treatment. Free Radic Biol Med (2010) 0.99
Binding mechanism of nonspecific lipid transfer proteins and their role in plant defense. Biochemistry (2004) 0.99
Time-resolved metabolomics reveals metabolic modulation in rice foliage. BMC Syst Biol (2008) 0.97
GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene (2013) 0.96
Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells. Proteomics (2010) 0.96
Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets. Proteins (2003) 0.95
Mitochondrial proteomics analysis of tumorigenic and metastatic breast cancer markers. Funct Integr Genomics (2011) 0.94
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin. Proteins (2007) 0.92
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J Proteome Res (2008) 0.92
Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation. J Biol Chem (2006) 0.91
Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids. Proteins (2006) 0.90
Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. PLoS One (2011) 0.90
Identification of putative miRNAs from the deep-branching unicellular flagellates. Genomics (2011) 0.90
Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa. Protein Sci (2004) 0.90
Biosynthesis of camptothecin. In silico and in vivo tracer study from [1-13C]glucose. Plant Physiol (2003) 0.90
Proteomic analysis of gemcitabine-induced drug resistance in pancreatic cancer cells. Mol Biosyst (2011) 0.89
iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res (2009) 0.89
Crystal structure of the dopamine N-acetyltransferase-acetyl-CoA complex provides insights into the catalytic mechanism. Biochem J (2012) 0.87
NMR structure note--solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris. J Biomol NMR (2005) 0.86
Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites. J Mol Biol (2010) 0.86
Prazosin displays anticancer activity against human prostate cancers: targeting DNA and cell cycle. Neoplasia (2007) 0.86
Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry (2005) 0.85
SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana. DNA Res (2008) 0.85
Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalytic bilin attachment. Biochemistry (2006) 0.85
Deciphering the preference and predicting the viability of circular permutations in proteins. PLoS One (2012) 0.85
Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks. Anal Chem (2005) 0.85
Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding. Proteins (2008) 0.84
Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells. J Proteomics (2012) 0.84
Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase. Biochem J (2007) 0.84
Anti-atherogenic effect of berberine on LXRalpha-ABCA1-dependent cholesterol efflux in macrophages. J Cell Biochem (2010) 0.84
MRMPROBS: a data assessment and metabolite identification tool for large-scale multiple reaction monitoring based widely targeted metabolomics. Anal Chem (2013) 0.84
Design and synthesis of alpha-ketoamides as cathepsin S inhibitors with potential applications against tumor invasion and angiogenesis. J Med Chem (2010) 0.83
Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists. ChemMedChem (2010) 0.83
Preparation, crystallization and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.83
Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: the role of the DFG motif in the design of epidermal growth factor receptor inhibitors. J Med Chem (2013) 0.83
Exploration of polar lipid accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico. Biosci Biotechnol Biochem (2014) 0.82
Purification and characterization of a novel 7-kDa non-specific lipid transfer protein-2 from rice (Oryza sativa). Biochem Biophys Res Commun (2002) 0.82
Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. J Phys Condens Matter (2015) 0.81
WRC-213, an l-methionine-conjugated mitoxantrone derivative, displays anticancer activity with reduced cardiotoxicity and drug resistance: identification of topoisomerase II inhibition and apoptotic machinery in prostate cancers. Biochem Pharmacol (2007) 0.81
Fluctuating noise drives Brownian transport. J R Soc Interface (2012) 0.81
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One (2010) 0.81
Cytoskeleton network and cellular migration modulated by nuclear-localized receptor tyrosine kinase ROR1. Anticancer Res (2011) 0.81
Enhanced entrainability of genetic oscillators by period mismatch. J R Soc Interface (2013) 0.81
Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis. Mol Biosyst (2011) 0.81
Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold. Proteins (2006) 0.81
Nuclear localization of orphan receptor protein kinase (Ror1) is mediated through the juxtamembrane domain. BMC Cell Biol (2010) 0.81
Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms. Mol Biosyst (2012) 0.80
Metabolomic characterization of a low phytic acid and high anti-oxidative cultivar of turmeric. Nat Prod Commun (2015) 0.80
Anti-phosphopeptide antibody, P-STM as a novel tool for detecting mitotic phosphoproteins: identification of lamins A and C as two major targets. J Cell Biochem (2005) 0.80
Proteomic analysis of proteins responsible for the development of doxorubicin resistance in human uterine cancer cells. J Proteomics (2012) 0.80
Evaluation of corneal endothelial pump function with a cold stress test. Cornea (2005) 0.80
Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One (2012) 0.80
Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity. J Med Chem (2009) 0.80
Indol-1-yl acetic acids as peroxisome proliferator-activated receptor agonists: design, synthesis, structural biology, and molecular docking studies. J Med Chem (2006) 0.80
Nested structure acquired through simple evolutionary process. J Theor Biol (2010) 0.80
Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor. Proteins (2009) 0.80
A molten globule-to-ordered structure transition of Drosophila melanogaster crammer is required for its ability to inhibit cathepsin. Biochem J (2012) 0.79
CPred: a web server for predicting viable circular permutations in proteins. Nucleic Acids Res (2012) 0.79
Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity. Chem Commun (Camb) (2012) 0.79
Mutagenesis study on the zebra fish SOX9 high-mobility group: comparison of sequence and non-sequence specific HMG domains. Biochemistry (2003) 0.79
Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics. BMC Syst Biol (2011) 0.79
Structural basis for the structure-activity relationships of peroxisome proliferator-activated receptor agonists. J Med Chem (2006) 0.79
Phylogenomic and domain analysis of iterative polyketide synthases in Aspergillus species. Evol Bioinform Online (2012) 0.79
Structural and functional comparison of cytokine interleukin-1 beta from chicken and human. Mol Immunol (2011) 0.78
Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase. Biochem Biophys Res Commun (2011) 0.78
Distinct unfolding and refolding pathways of lipid transfer proteins LTP1 and LTP2. Protein J (2004) 0.78
Comparative analysis of receptor binding by chicken and human interleukin-1β. J Mol Model (2010) 0.77
3D-QSAR studies on PU3 analogues by comparative molecular field analysis. Bioorg Med Chem Lett (2004) 0.77
NMR assignments of a hypothetical pseudo-knotted protein HP0242 from Helicobacter pylori. Biomol NMR Assign (2013) 0.77
Japanese encephalitis virus NS2B-NS3 protease binding to phage-displayed human brain proteins with the domain of trypsin inhibitor and basic region leucine zipper. Virus Res (2005) 0.77
Characterization of photodynamic therapy responses elicited in A431 cells containing intracellular organelle-localized photofrin. J Cell Biochem (2010) 0.77
A putative polyketide-synthesis protein XC5357 from Xanthomonas campestris: heterologous expression, crystallization and preliminary X-ray analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.77
Cloning, purification crystallization and preliminary X-ray characterization of a conserved hypothetical protein XC6422 from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.77
Metabolic classification of microbial genomes using functional probes. BMC Genomics (2012) 0.77
Retraction: MMP-13 is involved in oral cancer cell metastasis. Oncotarget (2016) 0.76