Published in BMC Bioinformatics on May 09, 2011
Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins. BMC Res Notes (2013) 0.76
Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm. Proteome Sci (2016) 0.75
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Global estimates of the prevalence of diabetes for 2010 and 2030. Diabetes Res Clin Pract (2009) 25.83
Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics (2005) 10.64
Global healthcare expenditure on diabetes for 2010 and 2030. Diabetes Res Clin Pract (2010) 5.16
OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics (2008) 4.41
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics (2003) 3.78
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics (2006) 3.34
Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics (2005) 2.81
Dietary obesity in nine inbred mouse strains. Am J Physiol (1992) 2.77
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
Optimal number of features as a function of sample size for various classification rules. Bioinformatics (2004) 2.37
Tbc1d1 mutation in lean mouse strain confers leanness and protects from diet-induced obesity. Nat Genet (2008) 2.14
Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res (2009) 2.02
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res (2006) 1.95
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinformatics (2009) 1.84
High-accuracy peak picking of proteomics data using wavelet techniques. Pac Symp Biocomput (2006) 1.77
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. BMC Bioinformatics (2007) 1.44
Peak selection from MALDI-TOF mass spectra using ant colony optimization. Bioinformatics (2007) 1.44
Proteomic identification of salivary biomarkers of type-2 diabetes. J Proteome Res (2009) 1.43
Detection of colorectal cancer using MALDI-TOF serum protein profiling. Eur J Cancer (2006) 1.36
Hyperphagia, lower body temperature, and reduced running wheel activity precede development of morbid obesity in New Zealand obese mice. Physiol Genomics (2006) 1.16
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics (2008) 1.08
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation. Bioinformatics (2009) 1.03
Serum peptide profiling using MALDI mass spectrometry: avoiding the pitfalls of coated magnetic beads using well-established ZipTip technology. Proteomics (2007) 1.01
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles. BMC Bioinformatics (2008) 1.01
Comparison of feature selection and classification for MALDI-MS data. BMC Genomics (2009) 0.99
A metabolic syndrome of hypertension, hyperinsulinaemia and hypercholesterolaemia in the New Zealand obese mouse. Eur J Clin Invest (2000) 0.97
Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome. Diabetologia (2009) 0.95
Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer. Clin Chem (2010) 0.95
Development of diabetes in obese, insulin-resistant mice: essential role of dietary carbohydrate in beta cell destruction. Diabetologia (2007) 0.93
MALDI profiling of human lung cancer subtypes. PLoS One (2009) 0.93
A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise. Proteomics (2008) 0.92
Mixed-model of ANOVA for measurement reproducibility in proteomics. J Proteomics (2009) 0.92
A well-characterised peak identification list of MALDI MS profile peaks for human blood serum. Proteomics (2010) 0.87
Biomarker clustering to address correlations in proteomic data. Proteomics (2007) 0.86
Proteomics-based identification of differentially-expressed proteins including galectin-1 in the blood plasma of type 2 diabetic patients. J Proteome Res (2009) 0.86
Mass spectrometry is only one piece of the puzzle in clinical proteomics. Brief Funct Genomic Proteomic (2008) 0.85
Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics (2009) 0.83
High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry. Expert Rev Proteomics (2005) 0.82
Case-control breast cancer study of MALDI-TOF proteomic mass spectrometry data on serum samples. Stat Appl Genet Mol Biol (2008) 0.82
Evaluation of peak-picking algorithms for protein mass spectrometry. Methods Mol Biol (2011) 0.82
Finding diagnostic biomarkers in proteomic spectra. Pac Symp Biocomput (2006) 0.80
Global quantification of mammalian gene expression control. Nature (2011) 22.36
Recent segmental duplications in the human genome. Science (2002) 21.30
SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics (2008) 17.31
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
RazerS--fast read mapping with sensitivity control. Genome Res (2009) 6.53
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics (2008) 4.41
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
Biological profiling of gene groups utilizing Gene Ontology. Genome Inform (2005) 4.10
Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1. Mol Cell (2002) 3.89
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science (2010) 3.35
Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect Immun (2006) 2.27
Tbc1d1 mutation in lean mouse strain confers leanness and protects from diet-induced obesity. Nat Genet (2008) 2.14
Phosphorylation of tyrosine 291 enhances the ability of WASp to stimulate actin polymerization and filopodium formation. Wiskott-Aldrich Syndrome protein. J Biol Chem (2002) 1.88
High-accuracy peak picking of proteomics data using wavelet techniques. Pac Symp Biocomput (2006) 1.77
Gene and protein expression profiling of human ovarian cancer cells treated with the heat shock protein 90 inhibitor 17-allylamino-17-demethoxygeldanamycin. Cancer Res (2007) 1.66
Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics (2002) 1.60
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics (2009) 1.55
Phosphorylation of the WASP-VCA domain increases its affinity for the Arp2/3 complex and enhances actin polymerization by WASP. Mol Cell (2003) 1.53
A meta-analysis of QTL for diabetes-related traits in rodents. Physiol Genomics (2008) 1.52
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics (2007) 1.51
RazerS 3: faster, fully sensitive read mapping. Bioinformatics (2012) 1.47
Segment-based multiple sequence alignment. Bioinformatics (2008) 1.46
Use of multiple metabolic and genetic markers to improve the prediction of type 2 diabetes: the EPIC-Potsdam Study. Diabetes Care (2009) 1.46
A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics (2011) 1.44
A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (2007) 1.44
Oligodb--interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics (2002) 1.36
Difference gel electrophoresis. Proteomics (2008) 1.29
Structure and evolution of barley powdery mildew effector candidates. BMC Genomics (2012) 1.28
Tools for label-free peptide quantification. Mol Cell Proteomics (2012) 1.27
In vivo properties of an anti-GnRH Spiegelmer: an example of an oligonucleotide-based therapeutic substance class. Proc Natl Acad Sci U S A (2002) 1.27
Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med (2009) 1.27
Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res (2013) 1.19
Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. Methods (2011) 1.15
Positional cloning of zinc finger domain transcription factor Zfp69, a candidate gene for obesity-associated diabetes contributed by mouse locus Nidd/SJL. PLoS Genet (2009) 1.15
Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis. Proteomics (2005) 1.14
LC-MSsim--a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics (2008) 1.14
Ablation of the cholesterol transporter adenosine triphosphate-binding cassette transporter G1 reduces adipose cell size and protects against diet-induced obesity. Endocrinology (2006) 1.13
OpenMS and TOPP: open source software for LC-MS data analysis. Methods Mol Biol (2011) 1.12
Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PLoS Pathog (2010) 1.12
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics (2012) 1.10
Conformational changes and orientation of Humicola lanuginosa lipase on a solid hydrophobic surface: an in situ interface Fourier transform infrared-attenuated total reflection study. Biophys J (2002) 1.09
Protein kinase C phosphorylates ribosomal protein S6 kinase betaII and regulates its subcellular localization. Mol Cell Biol (2003) 1.08
Corrigendum: Global quantification of mammalian gene expression control. Nature (2013) 1.08
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. BMC Genomics (2008) 1.08
Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res (2006) 1.07
MSSimulator: Simulation of mass spectrometry data. J Proteome Res (2011) 1.06
Localization of a highly active pool of type II phosphatidylinositol 4-kinase in a p97/valosin-containing-protein-rich fraction of the endoplasmic reticulum. Biochem J (2003) 1.06
High-throughput and single-cell imaging of NF-kappaB oscillations using monoclonal cell lines. BMC Cell Biol (2010) 1.06
Mycobacterium tuberculosis gene expression profiling within the context of protein networks. Microbes Infect (2006) 1.05
Heat shock protein 27 is the major differentially phosphorylated protein involved in renal epithelial cellular stress response and controls focal adhesion organization and apoptosis. J Biol Chem (2005) 1.04
The ARF-like GTPase ARFRP1 is essential for lipid droplet growth and is involved in the regulation of lipolysis. Mol Cell Biol (2009) 1.03
Differential protein synthesis and expression levels in normal and neoplastic human prostate cells and their regulation by type I and II interferons. Oncogene (2004) 1.03
The Rab-GTPase-activating protein TBC1D1 regulates skeletal muscle glucose metabolism. Am J Physiol Endocrinol Metab (2012) 1.02
Extracting information from cDNA arrays. Chaos (2001) 1.02
Mass spectrometry in clinical proteomics - from the present to the future. Proteomics Clin Appl (2008) 1.02
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics (2005) 1.01
Recirculation of germinal center B cells: a multilevel selection strategy for antibody maturation. Immunol Rev (2007) 1.01
Serum peptide profiling using MALDI mass spectrometry: avoiding the pitfalls of coated magnetic beads using well-established ZipTip technology. Proteomics (2007) 1.01
Analytical model of peptide mass cluster centres with applications. Proteome Sci (2006) 1.00
A DNA Spiegelmer to staphylococcal enterotoxin B. Nucleic Acids Res (2003) 1.00
Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study. Phytochemistry (2008) 0.99
Endocytosis of the glucose transporter GLUT8 is mediated by interaction of a dileucine motif with the beta2-adaptin subunit of the AP-2 adaptor complex. J Cell Sci (2006) 0.99
An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons. Proteomics (2008) 0.99
Quantitative amino acid and proteomic analysis: very low excretion of polypeptides >750 Da in normal urine. Kidney Int (2004) 0.99
In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. hordei. Mol Cell Proteomics (2009) 0.99
Proteomic profiling of neuromas reveals alterations in protein composition and local protein synthesis in hyper-excitable nerves. Mol Pain (2008) 0.98
Metabolism of the novel Ca2+-mobilizing messenger nicotinic acid-adenine dinucleotide phosphate via a 2'-specific Ca2+-dependent phosphatase. Biochem J (2002) 0.98
Critical illness myopathy and GLUT4: significance of insulin and muscle contraction. Am J Respir Crit Care Med (2012) 0.98
The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells. Am J Physiol Renal Physiol (2004) 0.97
Proteomics analysis of human obesity reveals the epigenetic factor HDAC4 as a potential target for obesity. PLoS One (2013) 0.97
Glucosinolate-accumulating S-cells in Arabidopsis leaves and flower stalks undergo programmed cell death at early stages of differentiation. Plant J (2010) 0.97
Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics (2004) 0.96
Combined affinity labelling and mass spectrometry analysis of differential cell surface protein expression in normal and prostate cancer cells. Oncogene (2005) 0.96
Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer. Clin Chem (2010) 0.95
Cytokine response of primary human myotubes in an in vitro exercise model. Am J Physiol Cell Physiol (2013) 0.94
TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res (2012) 0.94
Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics (2005) 0.94
Insulin stimulates fusion, but not tethering, of GLUT4 vesicles in skeletal muscle of HA-GLUT4-GFP transgenic mice. Am J Physiol Endocrinol Metab (2012) 0.93
Conventional knockout of Tbc1d1 in mice impairs insulin- and AICAR-stimulated glucose uptake in skeletal muscle. Endocrinology (2013) 0.92
A loss-of-function screen reveals Ras- and Raf-independent MEK-ERK signaling during Chlamydia trachomatis infection. Sci Signal (2010) 0.92
STELLAR: fast and exact local alignments. BMC Bioinformatics (2011) 0.91
MicroRazerS: rapid alignment of small RNA reads. Bioinformatics (2009) 0.91
Differential proteome analysis of replicative senescence in rat embryo fibroblasts. Mol Cell Proteomics (2002) 0.91
Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clin Sci (Lond) (2003) 0.91
Targeted disruption of Slc2a8 (GLUT8) reduces motility and mitochondrial potential of spermatozoa. Mol Membr Biol (2008) 0.90
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min (2009) 0.90
SPOT synthesis: reliability of array-based measurement of peptide binding affinity. Anal Biochem (2005) 0.90
Automatic internal calibration in liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry of protein digests. Rapid Commun Mass Spectrom (2006) 0.90
DNAJB3/HSP-40 cochaperone is downregulated in obese humans and is restored by physical exercise. PLoS One (2013) 0.89
High reproducibility of large-gel two-dimensional electrophoresis. Electrophoresis (2004) 0.89