Published in BMC Bioinformatics on July 21, 2008
The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab (2011) 3.54
eulerAPE: drawing area-proportional 3-Venn diagrams using ellipses. PLoS One (2014) 2.26
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics (2010) 1.31
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics (2011) 1.24
YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics (2009) 1.20
Search engine processor: Filtering and organizing peptide spectrum matches. Proteomics (2012) 1.15
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res (2011) 1.14
Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics (2011) 1.11
Analyzing shotgun proteomic data with PatternLab for proteomics. Curr Protoc Bioinformatics (2010) 1.10
XDIA: improving on the label-free data-independent analysis. Bioinformatics (2010) 1.08
Restricting fermentative potential by proteome remodeling: an adaptive strategy evidenced in Bacillus cereus. Mol Cell Proteomics (2012) 1.08
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Sci (2009) 1.05
Proteome analysis of the surface of Trichomonas vaginalis reveals novel proteins and strain-dependent differential expression. Mol Cell Proteomics (2010) 1.04
Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME J (2011) 1.03
Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal Chem (2009) 0.94
Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol. J Proteomics (2010) 0.93
Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry. J Proteomics (2010) 0.92
Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods. Mol Cell Proteomics (2014) 0.88
Chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol. J Proteome Res (2010) 0.88
Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J Chromatogr A (2011) 0.87
The proteome of mouse brain microvessel membranes and basal lamina. J Cereb Blood Flow Metab (2011) 0.87
Modified MuDPIT separation identified 4488 proteins in a system-wide analysis of quiescence in yeast. J Proteome Res (2013) 0.87
Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): a novel glycan-relative quantification strategy. J Am Soc Mass Spectrom (2013) 0.85
A Deeper Look into Comet-Implementation and Features. J Am Soc Mass Spectrom (2015) 0.84
Plasma membrane proteomics of human breast cancer cell lines identifies potential targets for breast cancer diagnosis and treatment. PLoS One (2014) 0.84
A bayesian mixture model for comparative spectral count data in shotgun proteomics. Mol Cell Proteomics (2011) 0.84
Proteomic profiling of the influence of iron availability on Cryptococcus gattii. J Proteome Res (2011) 0.84
Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose. Proteome Sci (2011) 0.84
Analyzing marginal cases in differential shotgun proteomics. Bioinformatics (2010) 0.84
A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement. BMC Plant Biol (2014) 0.83
Candidate hippocampal biomarkers of susceptibility and resilience to stress in a rat model of depression. Mol Cell Proteomics (2012) 0.83
Proteomics identifies Bacillus cereus EntD as a pivotal protein for the production of numerous virulence factors. Front Microbiol (2015) 0.82
Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale. Front Plant Sci (2012) 0.81
Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry. J Proteome Res (2013) 0.81
Proteomic profile of Cryptococcus neoformans biofilm reveals changes in metabolic processes. J Proteome Res (2014) 0.81
Salt Stress Induced Changes in the Exoproteome of the Halotolerant Bacterium Tistlia consotensis Deciphered by Proteogenomics. PLoS One (2015) 0.80
Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579. PLoS One (2014) 0.80
Secretome of the biocontrol agent metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection. J Proteome Res (2014) 0.79
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses. BMC Bioinformatics (2012) 0.79
From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics. J Am Soc Mass Spectrom (2015) 0.78
Mechanisms of acute kidney injury induced by experimental Lonomia obliqua envenomation. Arch Toxicol (2014) 0.78
OMICS in ecology: systems level analyses of Halobacterium salinarum reveal large-scale temperature-mediated changes and a requirement of CctA for thermotolerance. OMICS (2013) 0.77
The influence of iron on the proteomic profile of Chromobacterium violaceum. BMC Microbiol (2014) 0.77
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook (2014) 0.77
Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics. J Ind Microbiol Biotechnol (2012) 0.76
Ecto-Fc MS identifies ligand-receptor interactions through extracellular domain Fc fusion protein baits and shotgun proteomic analysis. Nat Protoc (2014) 0.76
Understanding butanol tolerance and assimilation in Pseudomonas putida BIRD-1: an integrated omics approach. Microb Biotechnol (2016) 0.76
Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase. J Ind Microbiol Biotechnol (2012) 0.76
Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense. Mol Cell Proteomics (2013) 0.76
Reproducible cancer biomarker discovery in SELDI-TOF MS using different pre-processing algorithms. PLoS One (2011) 0.75
Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin. Sci Rep (2016) 0.75
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol (2001) 28.01
The significance of digital gene expression profiles. Genome Res (1997) 23.90
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem (1995) 9.39
Analysis of microarray data using Z score transformation. J Mol Diagn (2003) 6.82
Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem (2003) 4.72
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics (2003) 3.75
Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res (2006) 3.51
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics (2005) 3.21
Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics (2005) 3.21
A streamlined platform for high-content functional proteomics of primary human specimens. Nat Methods (2005) 3.00
An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors. BMC Med Inform Decis Mak (2006) 2.29
Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Anal Chem (2006) 2.03
Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res (2007) 1.84
Determination of the differentially expressed genes in microarray experiments using local FDR. BMC Bioinformatics (2004) 1.78
Biomarker discovery in urine by proteomics. J Proteome Res (2003) 1.57
Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics (2004) 1.39
Application of the GA/KNN method to SELDI proteomics data. Bioinformatics (2004) 1.06
Differential protein expression patterns obtained by mass spectrometry can aid in the diagnosis of Hodgkin's disease. J Exp Ther Oncol (2007) 0.86
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
Wnt proteins are lipid-modified and can act as stem cell growth factors. Nature (2003) 12.54
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res (2003) 12.31
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
A role for the P-body component GW182 in microRNA function. Nat Cell Biol (2005) 7.54
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol (2006) 6.85
A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol (2003) 6.32
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p. Cell (2002) 5.91
A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev (2004) 5.23
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature (2005) 5.15
Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell (2009) 5.05
Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell (2006) 5.01
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science (2004) 4.97
The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell (2004) 4.91
The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol (2006) 4.89
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom (2004) 4.76
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods (2004) 4.62
Analysis of the myosin-II-responsive focal adhesion proteome reveals a role for β-Pix in negative regulation of focal adhesion maturation. Nat Cell Biol (2011) 4.59
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell (2009) 4.57
Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature (2008) 4.52
Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell (2006) 4.50
Global analysis of protein palmitoylation in yeast. Cell (2006) 4.43
PRAK is essential for ras-induced senescence and tumor suppression. Cell (2007) 4.30
The biological impact of mass-spectrometry-based proteomics. Nature (2007) 4.24
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell (2007) 4.22
Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell (2009) 4.22
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network. Dev Cell (2007) 4.17
The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem (2003) 4.13
Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 3.86
Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science (2008) 3.77
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci U S A (2002) 3.70
Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science (2003) 3.64
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods (2004) 3.62
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
Molecular architecture of the human pre-mRNA 3' processing complex. Mol Cell (2009) 3.52
Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science (2007) 3.46
Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface. Mol Cell (2010) 3.44
Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell (2009) 3.43
The perivascular niche regulates breast tumour dormancy. Nat Cell Biol (2013) 3.36
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. J Cell Biol (2005) 3.18
Chemical and biological approaches synergize to ameliorate protein-folding diseases. Cell (2008) 3.11
Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc Natl Acad Sci U S A (2007) 3.08
Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science (2006) 3.05
A streamlined platform for high-content functional proteomics of primary human specimens. Nat Methods (2005) 3.00
Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol (2004) 2.98
Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem (2002) 2.94
Architecture of the budding yeast kinetochore reveals a conserved molecular core. J Cell Biol (2003) 2.92
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem (2003) 2.91
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem (2003) 2.89
Proteomic analysis of isolated chlamydomonas centrioles reveals orthologs of ciliary-disease genes. Curr Biol (2005) 2.86
TOR complex 2 integrates cell movement during chemotaxis and signal relay in Dictyostelium. Mol Biol Cell (2005) 2.76
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem (2003) 2.74
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 2.73
Automatic quality assessment of peptide tandem mass spectra. Bioinformatics (2004) 2.70
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis. Nat Chem Biol (2009) 2.70
Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity. Dev Cell (2005) 2.65
Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature (2012) 2.64
The application of mass spectrometry to membrane proteomics. Nat Biotechnol (2003) 2.61
Global analysis of protein sumoylation in Saccharomyces cerevisiae. J Biol Chem (2004) 2.60
LRRTM2 interacts with Neurexin1 and regulates excitatory synapse formation. Neuron (2009) 2.60
Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Mol Cell Biol (2004) 2.55
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 2.53
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods (2012) 2.48
Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem (2003) 2.48
Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol (2005) 2.40
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem (2004) 2.40
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics (2007) 2.37
Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science (2009) 2.37
ZW10 links mitotic checkpoint signaling to the structural kinetochore. J Cell Biol (2005) 2.36
Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell (2012) 2.35
Attenuation of a phosphorylation-dependent activator by an HDAC-PP1 complex. Nat Struct Biol (2003) 2.32
Mass spectrometry for proteomics. Curr Opin Chem Biol (2008) 2.31
Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain. Nat Cell Biol (2004) 2.30
A hormone-dependent module regulating energy balance. Cell (2011) 2.30
PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis. Plant J (2009) 2.29
Molecular analysis of kinetochore architecture in fission yeast. EMBO J (2005) 2.29
Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci U S A (2002) 2.27
Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Cell (2002) 2.23
Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem (2003) 2.20
One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs. RNA (2002) 2.19
Sirt1 mediates neuroprotection from mutant huntingtin by activation of the TORC1 and CREB transcriptional pathway. Nat Med (2011) 2.17
Adaptation of energy metabolism in breast cancer brain metastases. Cancer Res (2007) 2.17
The human kinetochore Ska1 complex facilitates microtubule depolymerization-coupled motility. Dev Cell (2009) 2.14
TFG-1 function in protein secretion and oncogenesis. Nat Cell Biol (2011) 2.13
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression. EMBO J (2007) 2.07
Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site. Mol Cell (2010) 2.02