Published in J Proteome Res on February 01, 2007
Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res (2007) 4.53
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci Transl Med (2012) 2.06
Building consensus spectral libraries for peptide identification in proteomics. Nat Methods (2008) 1.96
Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal Chem (2009) 1.96
Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res (2010) 1.52
Proteomic contributions to personalized cancer care. Mol Cell Proteomics (2008) 1.46
Comparative human salivary and plasma proteomes. J Dent Res (2010) 1.41
Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes. J Proteome Res (2010) 1.25
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res (2008) 1.23
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res (2008) 1.17
The development of an integrated platform to identify breast cancer glycoproteome changes in human serum. J Chromatogr A (2009) 1.06
Biomarkers of HIV-1 associated dementia: proteomic investigation of sera. Proteome Sci (2009) 1.06
Challenges for biomarker discovery in body fluids using SELDI-TOF-MS. J Biomed Biotechnol (2009) 1.05
A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics (2011) 1.02
Use of high density antibody arrays to validate and discover cancer serum biomarkers. Mol Oncol (2007) 1.02
Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl (2009) 1.00
Identification and quantification of preterm birth biomarkers in human cervicovaginal fluid by liquid chromatography/tandem mass spectrometry. J Proteome Res (2009) 0.98
Proteomic serum biomarkers and their potential application in cancer screening programs. Int J Mol Sci (2010) 0.94
A mouse model repository for cancer biomarker discovery. J Proteome Res (2008) 0.94
Nanoparticle technology: Addressing the fundamental roadblocks to protein biomarker discovery. J Mater Chem (2009) 0.94
Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res (2013) 0.93
Protein expression profiles of human lymph and plasma mapped by 2D-DIGE and 1D SDS-PAGE coupled with nanoLC-ESI-MS/MS bottom-up proteomics. J Proteomics (2012) 0.93
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinformatics (2012) 0.93
Proteomics studies of pancreatic cancer. Proteomics Clin Appl (2007) 0.92
The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science. Korean J Lab Med (2011) 0.91
A systematic model of the LC-MS proteomics pipeline. BMC Genomics (2012) 0.88
Discovery of prognostic biomarker candidates of lacunar infarction by quantitative proteomics of microvesicles enriched plasma. PLoS One (2014) 0.87
MALDI-MS-Based Profiling of Serum Proteome: Detection of Changes Related to Progression of Cancer and Response to Anticancer Treatment. Int J Proteomics (2012) 0.85
Biomarker validation by targeted mass spectrometry. Nat Biotechnol (2009) 0.85
Proteomics of microparticles with SILAC Quantification (PROMIS-Quan): a novel proteomic method for plasma biomarker quantification. Mol Cell Proteomics (2015) 0.84
Clinical proteomics and OMICS clues useful in translational medicine research. Proteome Sci (2012) 0.83
Relevant phosphoproteomic and mass spectrometry: approaches useful in clinical research. Clin Transl Med (2012) 0.83
Utilizing spectral counting to quantitatively characterize tandem removal of abundant proteins (TRAP) in human plasma. Anal Chem (2010) 0.83
Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis (2014) 0.81
Analytical validation considerations of multiplex mass-spectrometry-based proteomic platforms for measuring protein biomarkers. J Proteome Res (2014) 0.81
Detection of metals and metalloproteins in the plasma of stroke patients by mass spectrometry methods. Metallomics (2012) 0.81
Discovery of the serum biomarker proteins in severe preeclampsia by proteomic analysis. Exp Mol Med (2011) 0.80
The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments. BMC Bioinformatics (2007) 0.80
Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res (2013) 0.80
Maternal serum serpin B7 is associated with early spontaneous preterm birth. Am J Obstet Gynecol (2014) 0.77
Multiple liquid chromatography separations and nanoESI-ion trap detection of plasma proteins in search of stroke biomarkers: A pilot study. J Sep Sci (2012) 0.77
Score regularization for peptide identification. BMC Bioinformatics (2011) 0.76
Analysis of peptides by denaturing ultrafiltration and LC-MALDI-TOF-MS. Methods Mol Biol (2013) 0.75
Enhancement in MALDI-TOF MS analysis of the low molecular weight human serum proteome. J Mass Spectrom (2011) 0.75
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Selective killing of oncogenically transformed cells through a ROS-mediated mechanism by beta-phenylethyl isothiocyanate. Cancer Cell (2006) 10.10
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol (2009) 9.67
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis. Nature (2011) 8.62
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol (2004) 7.69
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
Genetic structure of the purebred domestic dog. Science (2004) 6.39
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
Gemcitabine plus nab-paclitaxel is an active regimen in patients with advanced pancreatic cancer: a phase I/II trial. J Clin Oncol (2011) 6.16
Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med (2007) 6.01
A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science (2011) 5.91
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Targeting autophagy augments the anticancer activity of the histone deacetylase inhibitor SAHA to overcome Bcr-Abl-mediated drug resistance. Blood (2007) 4.91
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
High-level coexpression of JAG1 and NOTCH1 is observed in human breast cancer and is associated with poor overall survival. Cancer Res (2005) 4.61
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
Immuno gold nanocages with tailored optical properties for targeted photothermal destruction of cancer cells. Nano Lett (2007) 4.37
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res (2006) 4.32
Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome. J Virol (2004) 4.30
CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res (2005) 4.13
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
Gold nanocages: bioconjugation and their potential use as optical imaging contrast agents. Nano Lett (2005) 3.96
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
Management of coronary artery fistulae. Patient selection and results of transcatheter closure. J Am Coll Cardiol (2002) 3.84
Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev (2006) 3.80
EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (2012) 3.74
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics (2002) 3.57
Long-term entecavir therapy results in the reversal of fibrosis/cirrhosis and continued histological improvement in patients with chronic hepatitis B. Hepatology (2010) 3.57
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (2008) 3.51
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol (2006) 3.49
Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 3.48
UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. Cell (2008) 3.41
Trial of celecoxib in amyotrophic lateral sclerosis. Ann Neurol (2006) 3.39
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics (2006) 3.35
Increased regulatory T cells correlate with CD8 T-cell impairment and poor survival in hepatocellular carcinoma patients. Gastroenterology (2007) 3.34
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
Ovarian cancer biomarker performance in prostate, lung, colorectal, and ovarian cancer screening trial specimens. Cancer Prev Res (Phila) (2011) 3.33
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics (2006) 3.32
Weekly nab-paclitaxel in combination with carboplatin versus solvent-based paclitaxel plus carboplatin as first-line therapy in patients with advanced non-small-cell lung cancer: final results of a phase III trial. J Clin Oncol (2012) 3.28
Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet (2011) 3.23
How much will Herceptin really cost? BMJ (2006) 3.23
Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal Chem (2006) 3.22
Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat Genet (2012) 3.19
Heterosynaptic dopamine neurotransmission selects sets of corticostriatal terminals. Neuron (2004) 3.16
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 3.15
Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci U S A (2007) 3.12
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res (2006) 3.10
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res (2010) 3.08
Radiation-mediated proteolysis of CDT1 by CUL4-ROC1 and CSN complexes constitutes a new checkpoint. Nat Cell Biol (2003) 3.04
A framework for evaluating biomarkers for early detection: validation of biomarker panels for ovarian cancer. Cancer Prev Res (Phila) (2011) 3.03
High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces. Anal Chem (2005) 2.99
PD-1 up-regulation is correlated with HIV-specific memory CD8+ T-cell exhaustion in typical progressors but not in long-term nonprogressors. Blood (2007) 2.93
CAND1 binds to unneddylated CUL1 and regulates the formation of SCF ubiquitin E3 ligase complex. Mol Cell (2002) 2.92
Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal (2009) 2.92
Moesin controls cortical rigidity, cell rounding, and spindle morphogenesis during mitosis. Curr Biol (2008) 2.92
A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol (2011) 2.91
Gait analysis using wearable sensors. Sensors (Basel) (2012) 2.90
MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics (2008) 2.89
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87
Beta1 integrin inhibitory antibody induces apoptosis of breast cancer cells, inhibits growth, and distinguishes malignant from normal phenotype in three dimensional cultures and in vivo. Cancer Res (2006) 2.86
A human proteome detection and quantitation project. Mol Cell Proteomics (2009) 2.80
Toxoplasma gondii sequesters lysosomes from mammalian hosts in the vacuolar space. Cell (2006) 2.79
Cytosolic FoxO1 is essential for the induction of autophagy and tumour suppressor activity. Nat Cell Biol (2010) 2.78
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res (2007) 2.77
The identification of vesicular glutamate transporter 3 suggests novel modes of signaling by glutamate. Proc Natl Acad Sci U S A (2002) 2.77
Lynch syndrome (hereditary nonpolyposis colorectal cancer) diagnostics. J Natl Cancer Inst (2007) 2.77