Published in Proteomics on November 01, 2005
Human body fluid proteome analysis. Proteomics (2006) 2.39
Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models. Biometrics (2007) 2.01
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinformatics (2009) 1.84
Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform (2005) 1.52
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. BMC Bioinformatics (2007) 1.44
Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics (2008) 1.30
Microproteomics: analysis of protein diversity in small samples. Mass Spectrom Rev (2008) 1.26
Challenges in the analysis of mass-throughput data: a technical commentary from the statistical machine learning perspective. Cancer Inform (2007) 1.23
A novel comprehensive wave-form MS data processing method. Bioinformatics (2009) 1.20
Normalization in MALDI-TOF imaging datasets of proteins: practical considerations. Anal Bioanal Chem (2011) 1.17
PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics (2006) 1.13
A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One (2011) 1.12
Bioinformatics tools for cancer metabolomics. Metabolomics (2011) 1.10
Computational methods for protein identification from mass spectrometry data. PLoS Comput Biol (2008) 1.10
Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data. J Proteome Res (2010) 1.10
Sensitive and specific peak detection for SELDI-TOF mass spectrometry using a wavelet/neural-network based approach. PLoS One (2012) 1.06
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search. J Proteome Res (2012) 1.04
Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry. PLoS One (2015) 1.00
Comparison of feature selection and classification for MALDI-MS data. BMC Genomics (2009) 0.99
A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise. Proteomics (2008) 0.92
A method for improving SELDI-TOF mass spectrometry data quality. Proteome Sci (2007) 0.92
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
Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model. Bioinformatics (2008) 0.90
N-glycans in liver-secreted and immunoglogulin-derived protein fractions. J Proteomics (2012) 0.88
Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Cancer Inform (2007) 0.88
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
A general-purpose baseline estimation algorithm for spectroscopic data. Anal Chim Acta (2010) 0.87
Image analysis tools and emerging algorithms for expression proteomics. Proteomics (2010) 0.86
Design and preliminary analysis of a study to assess intra-device and inter-device variability of fluorescence spectroscopy instruments for detecting cervical neoplasia. Gynecol Oncol (2005) 0.85
Comparison of computational algorithms for the classification of liver cancer using SELDI mass spectrometry: a case study. Cancer Inform (2007) 0.84
Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset. BMC Bioinformatics (2011) 0.83
A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data. Proteomics (2009) 0.83
A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics. Mol Brain (2013) 0.82
Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data. BMC Bioinformatics (2010) 0.81
Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Sci (2009) 0.80
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies. BMC Bioinformatics (2010) 0.79
Differential intrahepatic phospholipid zonation in simple steatosis and nonalcoholic steatohepatitis. PLoS One (2013) 0.79
A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model. BMC Genomics (2015) 0.78
Feature detection techniques for preprocessing proteomic data. Int J Biomed Imaging (2010) 0.78
iTRAQ-based shotgun neuroproteomics. Methods Mol Biol (2009) 0.78
Statistical contributions to proteomic research. Methods Mol Biol (2010) 0.77
Using collective expert judgements to evaluate quality measures of mass spectrometry images. Bioinformatics (2015) 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
Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. BMC Bioinformatics (2015) 0.75
Preprocessing and Analysis of LC-MS-Based Proteomic Data. Methods Mol Biol (2016) 0.75
Bayesian mass spectra peak alignment from mass charge ratios. Cancer Inform (2008) 0.75
The C-terminal fragment of prostate-specific antigen, a 2331 Da peptide, as a new urinary pathognomonic biomarker candidate for diagnosing prostate cancer. PLoS One (2014) 0.75
Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library. PLoS One (2015) 0.75
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure. BMC Bioinformatics (2014) 0.75
Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. BMC Bioinformatics (2017) 0.75
Detection of bladder cancer using proteomic profiling of urine sediments. PLoS One (2012) 0.75
High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform. Methods Mol Biol (2012) 0.75
Locally Adaptive Bayes Nonparametric Regression via Nested Gaussian Processes. J Am Stat Assoc (2013) 0.75
Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer. Chem Sci (2017) 0.75
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data. BMC Bioinformatics (2014) 0.75
Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles. AMIA Annu Symp Proc (2010) 0.75
Workflow and methods of high-content time-lapse analysis for quantifying intracellular calcium signals. Neuroinformatics (2008) 0.75
Statistical Methods for Proteomic Biomarker Discovery based on Feature Extraction or Functional Modeling Approaches. Stat Interface (2012) 0.75
The FAST-AIMS Clinical Mass Spectrometry Analysis System. Adv Bioinformatics (2009) 0.75
PTEN activation contributes to tumor inhibition by trastuzumab, and loss of PTEN predicts trastuzumab resistance in patients. Cancer Cell (2004) 10.89
Metformin and pathologic complete responses to neoadjuvant chemotherapy in diabetic patients with breast cancer. J Clin Oncol (2009) 10.18
Dual regulation of Snail by GSK-3beta-mediated phosphorylation in control of epithelial-mesenchymal transition. Nat Cell Biol (2004) 9.80
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Cancer Res (2008) 8.12
IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a. Cell (2004) 6.13
ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation. Nat Cell Biol (2008) 5.19
Mechanisms of disease: understanding resistance to HER2-targeted therapy in human breast cancer. Nat Clin Pract Oncol (2006) 4.91
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics (2004) 4.58
IKK beta suppression of TSC1 links inflammation and tumor angiogenesis via the mTOR pathway. Cell (2007) 4.48
Circulating tumour cells in non-metastatic breast cancer: a prospective study. Lancet Oncol (2012) 4.44
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics (2005) 4.26
Upregulation of CXCR4 is essential for HER2-mediated tumor metastasis. Cancer Cell (2004) 4.17
Survival of cancer cells is maintained by EGFR independent of its kinase activity. Cancer Cell (2008) 3.95
Erk associates with and primes GSK-3beta for its inactivation resulting in upregulation of beta-catenin. Mol Cell (2005) 3.89
Body mass index and risk, age of onset, and survival in patients with pancreatic cancer. JAMA (2009) 3.86
p53 regulates epithelial-mesenchymal transition and stem cell properties through modulating miRNAs. Nat Cell Biol (2011) 3.85
Steps toward mapping the human vasculature by phage display. Nat Med (2002) 3.82
Akt-mediated phosphorylation of EZH2 suppresses methylation of lysine 27 in histone H3. Science (2005) 3.80
Nuclear interaction of EGFR and STAT3 in the activation of the iNOS/NO pathway. Cancer Cell (2005) 3.67
Epidermal growth factor receptor cooperates with signal transducer and activator of transcription 3 to induce epithelial-mesenchymal transition in cancer cells via up-regulation of TWIST gene expression. Cancer Res (2007) 3.53
Mammography before diagnosis among women age 80 years and older with breast cancer. J Clin Oncol (2008) 3.49
Phosphorylation of CBP by IKKalpha promotes cell growth by switching the binding preference of CBP from p53 to NF-kappaB. Mol Cell (2007) 3.42
Sentinel lymph node surgery after neoadjuvant chemotherapy in patients with node-positive breast cancer: the ACOSOG Z1071 (Alliance) clinical trial. JAMA (2013) 3.38
Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases. Cancer Cell (2009) 3.36
Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer. Cancer Cell (2013) 3.32
Interplay among BRCA1, SIRT1, and Survivin during BRCA1-associated tumorigenesis. Mol Cell (2008) 3.32
Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst (2005) 3.31
Degradation of Mcl-1 by beta-TrCP mediates glycogen synthase kinase 3-induced tumor suppression and chemosensitization. Mol Cell Biol (2007) 3.23
Non-parametric quantification of protein lysate arrays. Bioinformatics (2007) 3.18
Regulation of tumor angiogenesis by EZH2. Cancer Cell (2010) 3.10
Generation and characterization of androgen receptor knockout (ARKO) mice: an in vivo model for the study of androgen functions in selective tissues. Proc Natl Acad Sci U S A (2002) 3.08
Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics (2003) 3.06
TRIM24 links a non-canonical histone signature to breast cancer. Nature (2010) 2.99
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
Effect of primary tumor extirpation in breast cancer patients who present with stage IV disease and an intact primary tumor. Ann Surg Oncol (2006) 2.84
Pharmacological inactivation of Skp2 SCF ubiquitin ligase restricts cancer stem cell traits and cancer progression. Cell (2013) 2.81
Phase II trial of the combination of bevacizumab and erlotinib in patients who have advanced hepatocellular carcinoma. J Clin Oncol (2009) 2.69
EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2. Nature (2013) 2.67
The HER-2-targeting antibodies trastuzumab and pertuzumab synergistically inhibit the survival of breast cancer cells. Cancer Res (2004) 2.64
A new mutational AKTivation in the PI3K pathway. Cancer Cell (2007) 2.62
Novel prognostic value of nuclear epidermal growth factor receptor in breast cancer. Cancer Res (2005) 2.58
The Expression Patterns of ER, PR, HER2, CK5/6, EGFR, Ki-67 and AR by Immunohistochemical Analysis in Breast Cancer Cell Lines. Breast Cancer (Auckl) (2010) 2.57
KrasG12D-induced IKK2/β/NF-κB activation by IL-1α and p62 feedforward loops is required for development of pancreatic ductal adenocarcinoma. Cancer Cell (2012) 2.55
EZH2 promotes expansion of breast tumor initiating cells through activation of RAF1-β-catenin signaling. Cancer Cell (2011) 2.54
Breast cancer on the world wide web: cross sectional survey of quality of information and popularity of websites. BMJ (2002) 2.53
Binding at and transactivation of the COX-2 promoter by nuclear tyrosine kinase receptor ErbB-2. Cancer Cell (2004) 2.53
Phase II trial of infusional fluorouracil, irinotecan, and bevacizumab for metastatic colorectal cancer: efficacy and circulating angiogenic biomarkers associated with therapeutic resistance. J Clin Oncol (2009) 2.52
Long-term complications associated with breast-conservation surgery and radiotherapy. Ann Surg Oncol (2002) 2.51
Targeting mammalian target of rapamycin synergistically enhances chemotherapy-induced cytotoxicity in breast cancer cells. Clin Cancer Res (2004) 2.50
Posttherapy pathologic stage predicts survival in patients with esophageal carcinoma receiving preoperative chemoradiation. Cancer (2005) 2.49
P27(kip1) down-regulation is associated with trastuzumab resistance in breast cancer cells. Cancer Res (2004) 2.48
Tyrosine phosphorylation controls PCNA function through protein stability. Nat Cell Biol (2006) 2.45
Determinants of rapamycin sensitivity in breast cancer cells. Clin Cancer Res (2004) 2.44
Evaluation of a breast cancer nomogram for predicting risk of ipsilateral breast tumor recurrences in patients with ductal carcinoma in situ after local excision. J Clin Oncol (2012) 2.40
Microarrays: retracing steps. Nat Med (2007) 2.39
CDK1-dependent phosphorylation of EZH2 suppresses methylation of H3K27 and promotes osteogenic differentiation of human mesenchymal stem cells. Nat Cell Biol (2010) 2.36
beta-catenin interacts with and inhibits NF-kappa B in human colon and breast cancer. Cancer Cell (2002) 2.33
The Skp2-SCF E3 ligase regulates Akt ubiquitination, glycolysis, herceptin sensitivity, and tumorigenesis. Cell (2012) 2.30
Characterization of a novel tripartite nuclear localization sequence in the EGFR family. J Biol Chem (2007) 2.30
Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes. Clin Cancer Res (2013) 2.30
Positive surgical margins and ipsilateral breast tumor recurrence predict disease-specific survival after breast-conserving therapy. Cancer (2003) 2.29
A new fork for clinical application: targeting forkhead transcription factors in cancer. Clin Cancer Res (2009) 2.27
LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker. Nat Med (2012) 2.24
Validation of a breast cancer nomogram for predicting nonsentinel lymph node metastases after a positive sentinel node biopsy. Ann Surg Oncol (2006) 2.23
Role of ultrasound-guided fine-needle aspiration of indeterminate and suspicious axillary lymph nodes in the initial staging of breast carcinoma. Cancer (2002) 2.21
Endosomal transport of ErbB-2: mechanism for nuclear entry of the cell surface receptor. Mol Cell Biol (2005) 2.20
Lymphovascular invasion and lobular histology are associated with increased incidence of isolated tumor cells in sentinel lymph nodes from early-stage breast cancer patients. Ann Surg Oncol (2008) 2.17
Delays in primary surgical treatment are not associated with significant tumor size progression in breast cancer patients. Ann Surg (2011) 2.16
The VEGF-C/Flt-4 axis promotes invasion and metastasis of cancer cells. Cancer Cell (2006) 2.13
Trends in and outcomes from sentinel lymph node biopsy (SLNB) alone vs. SLNB with axillary lymph node dissection for node-positive breast cancer patients: experience from the SEER database. Ann Surg Oncol (2010) 2.12
Nuclear-cytoplasmic transport of EGFR involves receptor endocytosis, importin beta1 and CRM1. J Cell Biochem (2006) 2.11
Myeloid cell leukemia-1 inversely correlates with glycogen synthase kinase-3beta activity and associates with poor prognosis in human breast cancer. Cancer Res (2007) 2.10
14-3-3zeta Cooperates with ErbB2 to promote ductal carcinoma in situ progression to invasive breast cancer by inducing epithelial-mesenchymal transition. Cancer Cell (2009) 2.09
The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic (2005) 2.08
Lipofilling of the Breast Does Not Increase the Risk of Recurrence of Breast Cancer: A Matched Controlled Study. Plast Reconstr Surg (2016) 2.05
Krüppel-like factor 8 induces epithelial to mesenchymal transition and epithelial cell invasion. Cancer Res (2007) 2.02
The crosstalk of mTOR/S6K1 and Hedgehog pathways. Cancer Cell (2012) 2.02
Overdispersed logistic regression for SAGE: modelling multiple groups and covariates. BMC Bioinformatics (2004) 2.01
Loss of trimethylation at lysine 27 of histone H3 is a predictor of poor outcome in breast, ovarian, and pancreatic cancers. Mol Carcinog (2008) 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
Breast conservation after neoadjuvant chemotherapy: the MD Anderson cancer center experience. J Clin Oncol (2004) 2.00
Serum proteomics profiling--a young technology begins to mature. Nat Biotechnol (2005) 1.98
Epithelial-mesenchymal transition induced by TNF-α requires NF-κB-mediated transcriptional upregulation of Twist1. Cancer Res (2012) 1.97
Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncol (2008) 1.96
Physiological regulation of Akt activity and stability. Am J Transl Res (2010) 1.95
Preferential DNA damage and poor repair determine ras gene mutational hotspot in human cancer. J Natl Cancer Inst (2002) 1.95
Multidisciplinary considerations in the implementation of the findings from the American College of Surgeons Oncology Group (ACOSOG) Z0011 study: a practice-changing trial. Ann Surg Oncol (2011) 1.93
Role for intraoperative margin assessment in patients undergoing breast-conserving surgery. Ann Surg Oncol (2007) 1.92
EGFR signaling pathway in breast cancers: from traditional signal transduction to direct nuclear translocalization. Breast Cancer Res Treat (2006) 1.92
GSK-3 beta targets Cdc25A for ubiquitin-mediated proteolysis, and GSK-3 beta inactivation correlates with Cdc25A overproduction in human cancers. Cancer Cell (2008) 1.91
Sentinel lymph node surgery after neoadjuvant chemotherapy is accurate and reduces the need for axillary dissection in breast cancer patients. Ann Surg (2009) 1.89
Phase II study of capecitabine and oxaliplatin for advanced adenocarcinoma of the small bowel and ampulla of Vater. J Clin Oncol (2009) 1.88
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