Published in Bioinformatics on January 26, 2005
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Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis. Int J Mass Spectrom (2007) 1.73
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Evaluating the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies. J Proteome Res (2010) 1.03
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A step towards the discrimination of beta-lactamase-producing clinical isolates of Enterobacteriaceae and Pseudomonas aeruginosa by MALDI-TOF mass spectrometry. Med Sci Monit (2012) 0.91
Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet. Bioinformatics (2010) 0.91
Laser capture sampling and analytical issues in proteomics. Expert Rev Proteomics (2007) 0.91
Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics (2009) 0.91
Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model. Bioinformatics (2008) 0.90
Reproducibility of SELDI Spectra Across Time and Laboratories. Cancer Inform (2011) 0.87
BPDA - a Bayesian peptide detection algorithm for mass spectrometry. BMC Bioinformatics (2010) 0.87
Image analysis tools and emerging algorithms for expression proteomics. Proteomics (2010) 0.86
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
BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. Bioinformatics (2011) 0.83
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Matrix-assisted laser desorption/ionization tissue profiling of secretoneurin in the nucleus accumbens shell from cocaine-sensitized rats. J Mass Spectrom (2010) 0.82
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Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data. BMC Bioinformatics (2010) 0.81
A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass. Proteome Sci (2012) 0.81
Computational Systems Bioinformatics and Bioimaging for Pathway Analysis and Drug Screening. Proc IEEE Inst Electr Electron Eng (2008) 0.80
Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Sci (2009) 0.80
A novel preprocessing method using Hilbert Huang Transform for MALDI-TOF and SELDI-TOF mass spectrometry data. PLoS One (2010) 0.79
Differential intrahepatic phospholipid zonation in simple steatosis and nonalcoholic steatohepatitis. PLoS One (2013) 0.79
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. BMC Bioinformatics (2010) 0.79
Outcome prediction in pneumonia induced ALI/ARDS by clinical features and peptide patterns of BALF determined by mass spectrometry. PLoS One (2011) 0.78
Recursive feature elimination for brain tumor classification using desorption electrospray ionization mass spectrometry imaging. Conf Proc IEEE Eng Med Biol Soc (2012) 0.78
A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model. BMC Genomics (2015) 0.78
A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles. BMC Bioinformatics (2008) 0.78
Feature detection techniques for preprocessing proteomic data. Int J Biomed Imaging (2010) 0.78
Statistical contributions to proteomic research. Methods Mol Biol (2010) 0.77
Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS. J Oral Microbiol (2015) 0.77
Automated assignment of ionization states in broad-mass matrix-assisted laser desorption/ionization spectra of protein mixtures. Rapid Commun Mass Spectrom (2010) 0.77
A data-mining approach to biomarker identification from protein profiles using discrete stationary wavelet transform. J Zhejiang Univ Sci B (2008) 0.76
Statistical Methods for Proteomic Biomarker Discovery based on Feature Extraction or Functional Modeling Approaches. Stat Interface (2012) 0.75
A Bayesian approach to the alignment of mass spectra. Bioinformatics (2009) 0.75
High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform. Methods Mol Biol (2012) 0.75
Streaming visualisation of quantitative mass spectrometry data based on a novel raw signal decomposition method. Proteomics (2015) 0.75
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data. BMC Bioinformatics (2014) 0.75
A hybrid feature subset selection algorithm for analysis of high correlation proteomic data. J Med Signals Sens (2012) 0.75
Locally Adaptive Bayes Nonparametric Regression via Nested Gaussian Processes. J Am Stat Assoc (2013) 0.75
A unified modeling framework for metabonomic profile development and covariate selection for acute trauma subjects. Stat Med (2008) 0.75
Bayesian mass spectra peak alignment from mass charge ratios. Cancer Inform (2008) 0.75
Detection of bladder cancer using proteomic profiling of urine sediments. PLoS One (2012) 0.75
Discrimination of normal and esophageal cancer plasma proteomes by MALDI-TOF mass spectrometry. Dig Dis Sci (2015) 0.75
Detection and Quantification of Protein Spots by Pinnacle. Methods Mol Biol (2016) 0.75
IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a. Cell (2004) 6.13
A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature (2005) 5.13
Phosphorylation of beta-catenin by AKT promotes beta-catenin transcriptional activity. J Biol Chem (2007) 4.60
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics (2004) 4.58
HDAC6 modulates cell motility by altering the acetylation level of cortactin. Mol Cell (2007) 3.99
Steps toward mapping the human vasculature by phage display. Nat Med (2002) 3.82
Insulin-like growth factor-I receptor/human epidermal growth factor receptor 2 heterodimerization contributes to trastuzumab resistance of breast cancer cells. Cancer Res (2005) 3.78
CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol (2006) 3.49
An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48
Tumor suppressor ARF degrades B23, a nucleolar protein involved in ribosome biogenesis and cell proliferation. Mol Cell (2003) 3.42
Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst (2005) 3.31
Non-parametric quantification of protein lysate arrays. Bioinformatics (2007) 3.18
Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. Clin Cancer Res (2005) 2.98
Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis. Clin Cancer Res (2004) 2.96
CAND1 binds to unneddylated CUL1 and regulates the formation of SCF ubiquitin E3 ligase complex. Mol Cell (2002) 2.92
SHREC, an effector complex for heterochromatic transcriptional silencing. Cell (2007) 2.90
Functional proteomic profiling of AML predicts response and survival. Blood (2008) 2.90
Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat Struct Mol Biol (2007) 2.87
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
Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. J Natl Cancer Inst (2012) 2.79
Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res (2005) 2.76
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68
A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Nat Chem Biol (2010) 2.53
Tyrosine phosphorylation controls PCNA function through protein stability. Nat Cell Biol (2006) 2.45
Microarrays: retracing steps. Nat Med (2007) 2.39
L2DTL/CDT2 interacts with the CUL4/DDB1 complex and PCNA and regulates CDT1 proteolysis in response to DNA damage. Cell Cycle (2006) 2.37
Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes. Clin Cancer Res (2013) 2.30
microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood (2010) 2.25
Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol (2005) 2.21
The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic (2005) 2.08
Applications of beta-mixture models in bioinformatics. Bioinformatics (2005) 2.04
Identification of cell cycle regulatory genes as principal targets of p53-mediated transcriptional repression. J Biol Chem (2006) 2.01
Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models. Biometrics (2007) 2.01
A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics (2003) 2.01
The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data. Cancer Inform (2009) 1.98
Serum proteomics profiling--a young technology begins to mature. Nat Biotechnol (2005) 1.98
Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncol (2008) 1.96
The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation. Cell (2005) 1.94
Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. Mol Cancer Ther (2008) 1.92
Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem (2003) 1.88
Obtaining reliable information from minute amounts of RNA using cDNA microarrays. BMC Genomics (2002) 1.75
Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA (2002) 1.71
Variable slope normalization of reverse phase protein arrays. Bioinformatics (2009) 1.66
Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. J Biol Chem (2004) 1.63
Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J (2006) 1.63
Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients. Clin Cancer Res (2011) 1.59
Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits. Mol Cell Biol (2002) 1.55
ISWI remodeling complexes in Xenopus egg extracts: identification as major chromosomal components that are regulated by INCENP-aurora B. Mol Biol Cell (2002) 1.53
L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1 complexes. Cell Cycle (2006) 1.53
Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform (2005) 1.52
Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL. Brief Bioinform (2006) 1.52
Prognostic impact and targeting of CRM1 in acute myeloid leukemia. Blood (2013) 1.52
Protein components of mitochondrial DNA nucleoids in higher eukaryotes. Mol Cell Proteomics (2003) 1.48
Analysis of mass spectrometry profiles of the serum proteome. Clin Chem (2005) 1.46
Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res (2005) 1.45
Stimulation of lung innate immunity protects against lethal pneumococcal pneumonia in mice. Am J Respir Crit Care Med (2008) 1.44
Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities. Oncogene (2005) 1.43
Recurrent expression signatures of cytokines and chemokines are present and are independently prognostic in acute myelogenous leukemia and myelodysplasia. Blood (2010) 1.43
Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS One (2010) 1.41
Peritoneal and subperitoneal stroma may facilitate regional spread of ovarian cancer. Clin Cancer Res (2005) 1.39
Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data. Biotechniques (2005) 1.39
miRNA expression profiles in head and neck squamous cell carcinoma and adjacent normal tissue. Head Neck (2009) 1.38
Functional proteomic analysis of advanced serous ovarian cancer using reverse phase protein array: TGF-beta pathway signaling indicates response to primary chemotherapy. Clin Cancer Res (2010) 1.38
Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS. Anal Chem (2004) 1.38
SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities. Mol Cell Biol (2011) 1.35
Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity. EMBO J (2003) 1.35
Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia. Blood (2011) 1.34
Population frequency of myotonic dystrophy: higher than expected frequency of myotonic dystrophy type 2 (DM2) mutation in Finland. Eur J Hum Genet (2011) 1.33
Prognostic biomarkers for esophageal adenocarcinoma identified by analysis of tumor transcriptome. PLoS One (2010) 1.33
Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer. Clin Proteomics (2011) 1.32
Dual targeting of EphA2 and FAK in ovarian carcinoma. Cancer Biol Ther (2009) 1.30
Highly phosphorylated FOXO3A is an adverse prognostic factor in acute myeloid leukemia. Clin Cancer Res (2010) 1.30
Involvement of the conserved adaptor protein Alix in actin cytoskeleton assembly. J Biol Chem (2006) 1.30
Gene expression profile of metastatic human pancreatic cancer cells depends on the organ microenvironment. Cancer Res (2007) 1.29
Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. Biometrics (2003) 1.28
High expression of activation-induced cytidine deaminase (AID) and splice variants is a distinctive feature of poor-prognosis chronic lymphocytic leukemia. Blood (2003) 1.28
Flow experience and health-related quality of life in community dwelling elderly Japanese. Nurs Health Sci (2012) 1.27
Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability. PLoS One (2009) 1.27
Monitoring autophagy in glioblastoma with antibody against isoform B of human microtubule-associated protein 1 light chain 3. Autophagy (2008) 1.27
Clinical evaluation of chemotherapy response predictors developed from breast cancer cell lines. Breast Cancer Res Treat (2009) 1.25
Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays. BMC Genomics (2008) 1.25
Cardiomyocyte PDGFR-beta signaling is an essential component of the mouse cardiac response to load-induced stress. J Clin Invest (2010) 1.25
Survivin is highly expressed in CD34(+)38(-) leukemic stem/progenitor cells and predicts poor clinical outcomes in AML. Blood (2012) 1.25
Functional characterization of CLPTM1L as a lung cancer risk candidate gene in the 5p15.33 locus. PLoS One (2012) 1.24
Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines. Brain (2009) 1.22
Pivotal role of the cyclin-dependent kinase inhibitor p21WAF1/CIP1 in apoptosis and autophagy. J Biol Chem (2007) 1.20