Published in J Natl Cancer Inst on September 06, 2006
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In multiple myeloma, 14q32 translocations are nonrandom chromosomal fusions driving high expression levels of the respective partner genes. Genes Chromosomes Cancer (2014) 0.86
From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells. BMC Bioinformatics (2008) 0.84
Molecular sub-classification of renal epithelial tumors using meta-analysis of gene expression microarrays. PLoS One (2011) 0.83
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Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst (2006) 8.38
Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification. J Natl Cancer Inst (2006) 2.79
The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med (2002) 24.07
Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells. N Engl J Med (2004) 12.20
Prediction error estimation: a comparison of resampling methods. Bioinformatics (2005) 6.41
The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. Cancer Cell (2003) 6.11
Molecular diagnosis of Burkitt's lymphoma. N Engl J Med (2006) 6.10
Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J Exp Med (2003) 6.06
Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med (2003) 5.45
Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J Natl Cancer Inst (2010) 4.80
Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics (2006) 4.52
A paradigm for class prediction using gene expression profiles. J Comput Biol (2002) 3.64
Standards of reporting for MRI-targeted biopsy studies (START) of the prostate: recommendations from an International Working Group. Eur Urol (2013) 3.34
Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics (2002) 3.31
Diffuse large B-cell lymphoma subgroups have distinct genetic profiles that influence tumor biology and improve gene-expression-based survival prediction. Blood (2005) 3.12
Adaptive signature design: an adaptive clinical trial design for generating and prospectively testing a gene expression signature for sensitive patients. Clin Cancer Res (2005) 3.02
Biomarker-adaptive threshold design: a procedure for evaluating treatment with possible biomarker-defined subset effect. J Natl Cancer Inst (2007) 2.68
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Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics (2010) 2.52
Distinguishing right from left colon by the pattern of gene expression. Cancer Epidemiol Biomarkers Prev (2003) 2.22
Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness. Cancer Res (2002) 2.21
Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer. J Natl Cancer Inst (2010) 2.16
Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc Natl Acad Sci U S A (2002) 2.15
The cross-validated adaptive signature design. Clin Cancer Res (2010) 2.12
Effectiveness of gene expression profiling for response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy. J Clin Oncol (2005) 2.07
Cediranib for metastatic alveolar soft part sarcoma. J Clin Oncol (2013) 1.99
Evaluation of normalization methods for microarray data. BMC Bioinformatics (2003) 1.97
Evaluation of randomized discontinuation design. J Clin Oncol (2005) 1.89
Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics (2005) 1.72
Calculating confidence intervals for prediction error in microarray classification using resampling. Stat Appl Genet Mol Biol (2008) 1.70
Expansion and functional relevance of high-avidity myelin-specific CD4+ T cells in multiple sclerosis. J Immunol (2004) 1.56
BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource. Cancer Inform (2008) 1.53
Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking- and prognosis-related molecular profiles. Cancer Res (2002) 1.53
Predicting survival in patients with metastatic kidney cancer by gene-expression profiling in the primary tumor. Proc Natl Acad Sci U S A (2003) 1.53
Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas. Cancer Res (2007) 1.53
Combined breast ductal lavage and ductal endoscopy for the evaluation of the high-risk breast: a feasibility study. J Surg Oncol (2006) 1.51
Evidence of increased centrally enhanced bladder compliance with ageing in a mouse model. BJU Int (2014) 1.47
Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. J Natl Cancer Inst (2003) 1.45
A comparison of bootstrap methods and an adjusted bootstrap approach for estimating the prediction error in microarray classification. Stat Med (2007) 1.40
Development and validation of therapeutically relevant multi-gene biomarker classifiers. J Natl Cancer Inst (2005) 1.37
The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analyses. Clin Cancer Res (2002) 1.35
An evaluation of resampling methods for assessment of survival risk prediction in high-dimensional settings. Stat Med (2010) 1.34
Adaptive clinical trial designs for simultaneous testing of matched diagnostics and therapeutics. Clin Cancer Res (2011) 1.32
Aneuploidy-dependent massive deregulation of the cellular transcriptome and apparent divergence of the Wnt/beta-catenin signaling pathway in human rectal carcinomas. Cancer Res (2006) 1.31
What should physicians look for in evaluating prognostic gene-expression signatures? Nat Rev Clin Oncol (2010) 1.29
Gene Set Expression Comparison kit for BRB-ArrayTools. Bioinformatics (2007) 1.28
B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus-associated acute liver failure. Proc Natl Acad Sci U S A (2010) 1.26
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. Bioinformatics (2009) 1.26
In silico simulation of inhibitor drug effects on nuclear factor-kappaB pathway dynamics. Mol Pharmacol (2004) 1.21
Microarray-based cancer prediction using single genes. BMC Bioinformatics (2011) 1.16
A powerful combination: the use of positional scanning libraries and biometrical analysis to identify cross-reactive T cell epitopes. Mol Immunol (2004) 1.15
Overfitting in prediction models - is it a problem only in high dimensions? Contemp Clin Trials (2013) 1.09
Adaptive enrichment designs for clinical trials. Biostatistics (2013) 1.08
Application of support vector machines for T-cell epitopes prediction. Bioinformatics (2003) 1.05
An adaptive method for cDNA microarray normalization. BMC Bioinformatics (2005) 1.03
An investigation of two multivariate permutation methods for controlling the false discovery proportion. Stat Med (2007) 1.03
Molecular differentiation of high- and moderate-grade human prostate cancer by cDNA microarray analysis. Diagn Mol Pathol (2003) 1.00
Treatment of recurrent malignant gliomas with stereotactic intensity modulated radiation therapy. Am J Clin Oncol (2002) 0.99
A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings. J Transl Med (2003) 0.99
A two-stage Bayesian design for co-development of new drugs and companion diagnostics. Stat Med (2012) 0.96
Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data. Stat Med (2007) 0.95
Gene expression deconvolution in clinical samples. Genome Med (2010) 0.93
A comparison of phase II study strategies. Clin Cancer Res (2009) 0.93
Estimating the order of mutations during tumorigenesis from tumor genome sequencing data. Bioinformatics (2012) 0.92
Iterative class discovery and feature selection using Minimal Spanning Trees. BMC Bioinformatics (2004) 0.90
Combinatorial peptide library-based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity. Eur J Immunol (2002) 0.88
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview. BMC Bioinformatics (2011) 0.87
Identification of potential synthetic lethal genes to p53 using a computational biology approach. BMC Med Genomics (2013) 0.87
IRF5 gene polymorphisms in melanoma. J Transl Med (2012) 0.86
High level of cross-reactivity in influenza virus hemagglutinin-specific CD4+ T-cell response: implications for the initiation of autoimmune response in multiple sclerosis. J Neuroimmunol (2005) 0.86
Positional scanning-synthetic peptide library-based analysis of self- and pathogen-derived peptide cross-reactivity with tumor-reactive Melan-A-specific CTL. J Immunol (2002) 0.85
Redundancy in antigen-presenting function of the HLA-DR and -DQ molecules in the multiple sclerosis-associated HLA-DR2 haplotype. J Immunol (2006) 0.85
Developing and validating continuous genomic signatures in randomized clinical trials for predictive medicine. Clin Cancer Res (2012) 0.82
Trap-vaccinate-release program to control raccoon rabies, New York, USA. Emerg Infect Dis (2012) 0.81
Identification of peptides from human pathogens able to cross-activate an HIV-1-gag-specific CD4+ T cell clone. Eur J Immunol (2006) 0.81
Findings on T cell specificity revealed by synthetic combinatorial libraries. J Immunol Methods (2002) 0.80
Development and validation of predictive indices for a continuous outcome using gene expression profiles. Cancer Inform (2010) 0.80
Combining positional scanning peptide libraries, HLA-DR transfectants and bioinformatics to dissect the epitope spectrum of HLA class II cross-restricted CD4+ T cell clones. J Immunol Methods (2009) 0.79
Probabilistic classifiers with high-dimensional data. Biostatistics (2010) 0.79
T-cell epitope prediction with combinatorial peptide libraries. J Comput Biol (2002) 0.79
Targets for treatment success. Nat Clin Pract Oncol (2006) 0.78
Estimating the number of rate limiting genomic changes for human breast cancer. Breast Cancer Res Treat (2005) 0.78
Bioinformatics in cancer therapeutics--hype or hope? Nat Clin Pract Oncol (2005) 0.78
Genomewide conserved epitope profiles of HIV-1 predicted by biophysical properties of MHC binding peptides. J Comput Biol (2004) 0.78
A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis. Bioinformatics (2002) 0.77
Candidate epitope identification using peptide property models: application to cancer immunotherapy. Methods (2004) 0.76
Stable disease is not preferentially observed with targeted therapies and as currently defined has limited value in drug development. Cancer J (2009) 0.76
Two-stage adaptive cutoff design for building and validating a prognostic biomarker signature. Stat Med (2014) 0.76
Genomic Alteration-Driven Clinical Trial Designs in Oncology. Ann Intern Med (2016) 0.76
Does topoisomerase II-alpha gene amplification provide useful information for treatment selection in patients with breast carcinoma? J Clin Oncol (2011) 0.75
Run-in phase III trial design with pharmacodynamics predictive biomarkers. J Natl Cancer Inst (2013) 0.75
PSA velocity and prostate cancer. N Engl J Med (2004) 0.75
Novel trial designs for novel agents. Interview by Helen Saul. Eur J Cancer (2008) 0.75
Overfitting, generalization, and MSE in class probability estimation with high-dimensional data. Biom J (2013) 0.75
Artificial intelligence methods for predicting T-cell epitopes. Methods Mol Biol (2007) 0.75