Published in Bioinformatics on May 05, 2011
Translational biomarker discovery in clinical metabolomics: an introductory tutorial. Metabolomics (2012) 2.18
Metabolome in progression to Alzheimer's disease. Transl Psychiatry (2011) 1.33
Review: toxicometabolomics. J Appl Toxicol (2013) 1.03
Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era. Int J Mol Sci (2016) 0.81
Analyzing LC/MS metabolic profiling data in the context of existing metabolic networks. Curr Metabolomics (2013) 0.81
Computational tools for the secondary analysis of metabolomics experiments. Comput Struct Biotechnol J (2013) 0.80
The common ground of genomics and systems biology. BMC Syst Biol (2014) 0.80
MBROLE 2.0-functional enrichment of chemical compounds. Nucleic Acids Res (2016) 0.79
Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci (2016) 0.79
Reconstruction and analysis of correlation networks based on GC-MS metabolomics data for young hypertensive men. Anal Chim Acta (2014) 0.77
Metabolomics in the studies of islet autoimmunity and type 1 diabetes. Rev Diabet Stud (2012) 0.77
Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. Metabolomics (2014) 0.77
MPINet: metabolite pathway identification via coupling of global metabolite network structure and metabolomic profile. Biomed Res Int (2014) 0.77
Animal-Free Chemical Safety Assessment. Front Pharmacol (2016) 0.75
Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight (2016) 0.75
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics. Gigascience (2017) 0.75
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics (2010) 5.77
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics (2006) 5.38
Exhaustive enumeration of protein domain families. J Mol Biol (2003) 4.95
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol (2009) 4.17
Pathways to the analysis of microarray data. Trends Biotechnol (2005) 3.88
Integration of microRNA miR-122 in hepatic circadian gene expression. Genes Dev (2009) 3.64
Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics (2005) 3.21
Data processing for mass spectrometry-based metabolomics. J Chromatogr A (2007) 3.21
PPAR gamma 2 prevents lipotoxicity by controlling adipose tissue expandability and peripheral lipid metabolism. PLoS Genet (2007) 2.91
Ablation of PGC-1beta results in defective mitochondrial activity, thermogenesis, hepatic function, and cardiac performance. PLoS Biol (2006) 2.86
Hypothalamic AMPK and fatty acid metabolism mediate thyroid regulation of energy balance. Nat Med (2010) 2.76
ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res (2005) 2.65
The gut microbiota modulates host energy and lipid metabolism in mice. J Lipid Res (2009) 2.59
The global trace graph, a novel paradigm for searching protein sequence databases. Bioinformatics (2007) 2.52
PairsDB atlas of protein sequence space. Nucleic Acids Res (2007) 2.42
Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects--a monozygotic twin study. PLoS One (2007) 2.38
Overexpression of vascular endothelial growth factor-B in mouse heart alters cardiac lipid metabolism and induces myocardial hypertrophy. Circ Res (2008) 2.15
Adipose tissue inflammation and increased ceramide content characterize subjects with high liver fat content independent of obesity. Diabetes (2007) 2.08
Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression. Cancer Res (2011) 2.07
Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Syst Biol (2007) 2.01
A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS One (2006) 2.01
Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis. Proc Natl Acad Sci U S A (2012) 2.00
Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins. Bioinformatics (2003) 1.99
Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Med (2008) 1.94
Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol (2003) 1.93
Blocking VLDL secretion causes hepatic steatosis but does not affect peripheral lipid stores or insulin sensitivity in mice. J Lipid Res (2008) 1.91
Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans. PLoS Biol (2011) 1.89
Human gut microbes impact host serum metabolome and insulin sensitivity. Nature (2016) 1.85
Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. Am J Hum Genet (2011) 1.80
Mitochondrial myopathy induces a starvation-like response. Hum Mol Genet (2010) 1.78
The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific peroxisome proliferator-activated receptor-gamma2 isoform. Diabetes (2005) 1.76
Farnesoid X receptor deficiency improves glucose homeostasis in mouse models of obesity. Diabetes (2011) 1.73
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics (2007) 1.54
Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proc Natl Acad Sci U S A (2006) 1.53
Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinformatics (2006) 1.51
Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics (2007) 1.50
Early familial dilated cardiomyopathy: identification with determination of disease state parameter from cine MR image data. Radiology (2008) 1.48
Cord serum lipidome in prediction of islet autoimmunity and type 1 diabetes. Diabetes (2013) 1.47
Deletion of the metabolic transcriptional coactivator PGC1β induces cardiac arrhythmia. Cardiovasc Res (2011) 1.46
PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics (2005) 1.42
Comparison of lipid and fatty acid composition of the liver, subcutaneous and intra-abdominal adipose tissue, and serum. Obesity (Silver Spring) (2009) 1.39
Informatics and computational strategies for the study of lipids. Mol Biosyst (2007) 1.37
Triacylglycerol fatty acid composition in diet-induced weight loss in subjects with abnormal glucose metabolism--the GENOBIN study. PLoS One (2008) 1.31
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
POBO, transcription factor binding site verification with bootstrapping. Nucleic Acids Res (2004) 1.25
Hepatic stearoyl-CoA desaturase (SCD)-1 activity and diacylglycerol but not ceramide concentrations are increased in the nonalcoholic human fatty liver. Diabetes (2008) 1.24
Ketogenic diet slows down mitochondrial myopathy progression in mice. Hum Mol Genet (2010) 1.17
Integrative biological analysis of the APOE*3-leiden transgenic mouse. OMICS (2004) 1.13
Bioinformatics and computational methods for lipidomics. J Chromatogr B Analyt Technol Biomed Life Sci (2009) 1.13
Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Res (2012) 1.13
ApoCIII-enriched LDL in type 2 diabetes displays altered lipid composition, increased susceptibility for sphingomyelinase, and increased binding to biglycan. Diabetes (2009) 1.12
Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol. J Lipid Res (2010) 1.10
Evolution of the GDNF family ligands and receptors. Brain Behav Evol (2006) 1.09
Gender-dependent progression of systemic metabolic states in early childhood. Mol Syst Biol (2008) 1.08
Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model. OMICS (2004) 1.08
Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis. New Phytol (2013) 1.07
How to study lipidomes. J Mol Endocrinol (2008) 1.06
Peroxisomal and microsomal lipid pathways associated with resistance to hepatic steatosis and reduced pro-inflammatory state. J Biol Chem (2010) 1.03
Automated detection of remote homology. Curr Opin Struct Biol (2002) 1.02
Differences in muscle and adipose tissue gene expression and cardio-metabolic risk factors in the members of physical activity discordant twin pairs. PLoS One (2010) 1.02
Insulin signaling regulates fatty acid catabolism at the level of CoA activation. PLoS Genet (2012) 1.02
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics (2005) 1.00
Gut microbiota affects lens and retinal lipid composition. Exp Eye Res (2009) 1.00
Oligomerization of hantavirus nucleocapsid protein: analysis of the N-terminal coiled-coil domain. J Virol (2006) 0.99
Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. PLoS Pathog (2012) 0.98
Human tear fluid lipidome: from composition to function. PLoS One (2011) 0.98
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinformatics (2009) 0.98
Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Mol Biosyst (2009) 0.96
Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS One (2009) 0.96
Generation of Gene Ontology benchmark datasets with various types of positive signal. BMC Bioinformatics (2009) 0.96
Towards structured output prediction of enzyme function. BMC Proc (2008) 0.95
Adaptation and failure of pancreatic beta cells in murine models with different degrees of metabolic syndrome. Dis Model Mech (2009) 0.95
Fatty fish intake decreases lipids related to inflammation and insulin signaling--a lipidomics approach. PLoS One (2009) 0.95
Prediction of non-alcoholic fatty-liver disease and liver fat content by serum molecular lipids. Diabetologia (2013) 0.95
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. BMC Bioinformatics (2012) 0.94
Genomic, transcriptomic, and lipidomic profiling highlights the role of inflammation in individuals with low high-density lipoprotein cholesterol. Arterioscler Thromb Vasc Biol (2013) 0.93
Multivariate multi-way analysis of multi-source data. Bioinformatics (2010) 0.92
Circulating triacylglycerol signatures in nonalcoholic fatty liver disease associated with the I148M variant in PNPLA3 and with obesity. Diabetes (2013) 0.92
POXO: a web-enabled tool series to discover transcription factor binding sites. Nucleic Acids Res (2006) 0.92
Accurate detection of very sparse sequence motifs. J Comput Biol (2004) 0.91
Genome sequence of Lactobacillus crispatus ST1. J Bacteriol (2010) 0.91
Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana. Nucleic Acids Res (2006) 0.91
Bioinformatics strategies for the analysis of lipids. Methods Mol Biol (2009) 0.90
Connecting genes to metabolites by a systems biology approach. Proc Natl Acad Sci U S A (2004) 0.90
Adaptive changes of the Insig1/SREBP1/SCD1 set point help adipose tissue to cope with increased storage demands of obesity. Diabetes (2013) 0.89
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. Bioinformatics (2012) 0.89
Loss of neurturin in frog--comparative genomics study of GDNF family ligand-receptor pairs. Mol Cell Neurosci (2006) 0.88
Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction. World J Gastroenterol (2008) 0.88
Data integration and visualization system for enabling conceptual biology. Bioinformatics (2005) 0.88
Evaluation of different domain-based methods in protein interaction prediction. Biochem Biophys Res Commun (2009) 0.88
Effect of probiotic Lactobacillus rhamnosus GG intervention on global serum lipidomic profiles in healthy adults. World J Gastroenterol (2008) 0.88
Decreased cord-blood phospholipids in young age-at-onset type 1 diabetes. Diabetes (2013) 0.87
The effect of fatty or lean fish intake on inflammatory gene expression in peripheral blood mononuclear cells of patients with coronary heart disease. Eur J Nutr (2009) 0.87