Published in J Natl Cancer Inst on January 01, 2003
Gene selection and classification of microarray data using random forest. BMC Bioinformatics (2006) 12.45
The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics (2006) 12.45
Analysis of gene expression data using BRB-ArrayTools. Cancer Inform (2007) 6.09
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
Genetic prognostic and predictive markers in colorectal cancer. Nat Rev Cancer (2009) 3.99
Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One (2010) 3.96
Classifying gene expression profiles from pairwise mRNA comparisons. Stat Appl Genet Mol Biol (2004) 3.45
Criteria for the use of omics-based predictors in clinical trials. Nature (2013) 3.15
Sources of bias in specimens for research about molecular markers for cancer. J Clin Oncol (2009) 2.86
Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci U S A (2009) 2.84
Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. Proc Natl Acad Sci U S A (2004) 2.74
MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Breast Cancer Res (2009) 2.59
An 86-probe-set gene-expression signature predicts survival in cytogenetically normal acute myeloid leukemia. Blood (2008) 2.46
Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma. Blood (2009) 2.43
Kidney transplant rejection and tissue injury by gene profiling of biopsies and peripheral blood lymphocytes. Am J Transplant (2004) 2.35
T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Res (2009) 2.26
Molecular classification of rhabdomyosarcoma--genotypic and phenotypic determinants of diagnosis: a report from the Children's Oncology Group. Am J Pathol (2009) 2.14
Gene expression signatures of morphologically normal breast tissue identify basal-like tumors. Breast Cancer Res (2006) 2.12
Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data. Br J Cancer (2003) 2.08
The new molecular markers DDIT3, STT3A, ARG2 and FAM129A are not useful in diagnosing thyroid follicular tumors. Mod Pathol (2011) 2.08
Effectiveness of gene expression profiling for response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy. J Clin Oncol (2005) 2.07
GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. BMC Bioinformatics (2007) 2.06
Next station in microarray data analysis: GEPAS. Nucleic Acids Res (2006) 2.05
A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft. Kidney Int (2015) 2.02
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res (2005) 1.97
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Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics (2006) 1.93
New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res (2004) 1.89
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Challenges translating breast cancer gene signatures into the clinic. Nat Rev Clin Oncol (2011) 1.86
A comparative study of discriminating human heart failure etiology using gene expression profiles. BMC Bioinformatics (2005) 1.85
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Gene expression signature-based prognostic risk score in gastric cancer. Clin Cancer Res (2011) 1.83
Identification of a 4-microRNA signature for clear cell renal cell carcinoma metastasis and prognosis. PLoS One (2012) 1.80
Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia with a normal karyotype: a Cancer and Leukemia Group B study. Blood (2006) 1.74
Entropy-based gene ranking without selection bias for the predictive classification of microarray data. BMC Bioinformatics (2003) 1.71
Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures. Cancer Res (2012) 1.69
Using cross-validation to evaluate predictive accuracy of survival risk classifiers based on high-dimensional data. Brief Bioinform (2011) 1.69
A gene expression signature that can predict the recurrence of tamoxifen-treated primary breast cancer. Clin Cancer Res (2008) 1.66
Translating microarray data for diagnostic testing in childhood leukaemia. BMC Cancer (2006) 1.61
Classification of ductal carcinoma in situ by gene expression profiling. Breast Cancer Res (2006) 1.59
Evaluating microarray-based classifiers: an overview. Cancer Inform (2008) 1.56
Altered immune phenotype in peripheral blood cells of patients with scleroderma-associated pulmonary hypertension. Clin Transl Sci (2010) 1.56
Optimal classifier selection and negative bias in error rate estimation: an empirical study on high-dimensional prediction. BMC Med Res Methodol (2009) 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
Developing symptom-based predictive models of endometriosis as a clinical screening tool: results from a multicenter study. Fertil Steril (2012) 1.50
Ovarian clear cell adenocarcinoma: a continuing enigma. J Clin Pathol (2006) 1.48
A preoperative diagnostic test that distinguishes benign from malignant thyroid carcinoma based on gene expression. J Clin Invest (2004) 1.48
MicroRNA expression aberration as potential peripheral blood biomarkers for schizophrenia. PLoS One (2011) 1.47
Clinical trial designs for evaluating the medical utility of prognostic and predictive biomarkers in oncology. Per Med (2010) 1.47
The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures. PLoS One (2011) 1.46
Should we abandon the t-test in the analysis of gene expression microarray data: a comparison of variance modeling strategies. PLoS One (2010) 1.44
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. Nucleic Acids Res (2007) 1.43
MicroRNA signature analysis in colorectal cancer: identification of expression profiles in stage II tumors associated with aggressive disease. Int J Colorectal Dis (2011) 1.43
Metastasis predictive signature profiles pre-exist in normal tissues. Clin Exp Metastasis (2006) 1.43
Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics (2009) 1.40
Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study. PLoS Genet (2010) 1.39
Microrna profiling analysis of differences between the melanoma of young adults and older adults. J Transl Med (2010) 1.39
Molecular signature of a right heart failure program in chronic severe pulmonary hypertension. Am J Respir Cell Mol Biol (2011) 1.36
A Review of Challenges in the Use of fMRI for Disease Classification / Characterization and A Projection Pursuit Application from Multi-site fMRI Schizophrenia Study. Brain Imaging Behav (2008) 1.33
Gene expression profiling for survival prediction in pediatric rhabdomyosarcomas: a report from the children's oncology group. J Clin Oncol (2010) 1.33
Implementing prognostic and predictive biomarkers in CRC clinical trials. Nat Rev Clin Oncol (2011) 1.31
What should physicians look for in evaluating prognostic gene-expression signatures? Nat Rev Clin Oncol (2010) 1.29
Recent advances in systemic therapy: new diagnostics and biological predictors of outcome in early breast cancer. Breast Cancer Res (2009) 1.28
Improved risk prediction for Crohn's disease with a multi-locus approach. Hum Mol Genet (2011) 1.28
A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. Crit Care (2012) 1.27
A gene expression model of intrinsic tumor radiosensitivity: prediction of response and prognosis after chemoradiation. Int J Radiat Oncol Biol Phys (2009) 1.24
Identification and validation of genes involved in cervical tumourigenesis. BMC Cancer (2011) 1.24
Challenges in the analysis of mass-throughput data: a technical commentary from the statistical machine learning perspective. Cancer Inform (2007) 1.23
The impact of expression profiling on prognostic and predictive testing in breast cancer. J Clin Pathol (2006) 1.21
Gene selection algorithms for microarray data based on least squares support vector machine. BMC Bioinformatics (2006) 1.21
Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease. Proc Natl Acad Sci U S A (2007) 1.20
Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data. Nucleic Acids Res (2005) 1.19
On the statistical assessment of classifiers using DNA microarray data. BMC Bioinformatics (2006) 1.18
Predictive and prognostic molecular markers for cancer medicine. Ther Adv Med Oncol (2010) 1.18
DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage. BMC Med Genomics (2008) 1.17
Development of a clinically feasible molecular assay to predict recurrence of stage II colon cancer. J Mol Diagn (2008) 1.17
Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery. PLoS One (2014) 1.17
Microarray-based cancer prediction using single genes. BMC Bioinformatics (2011) 1.16
Stratification bias in low signal microarray studies. BMC Bioinformatics (2007) 1.16
Genome-wide gene expression profiling suggests distinct radiation susceptibilities in sporadic and post-Chernobyl papillary thyroid cancers. Br J Cancer (2007) 1.14
Optimally splitting cases for training and testing high dimensional classifiers. BMC Med Genomics (2011) 1.13
An empirical assessment of validation practices for molecular classifiers. Brief Bioinform (2011) 1.13
In vivo NCL targeting affects breast cancer aggressiveness through miRNA regulation. J Exp Med (2013) 1.13
Detection of gene pathways with predictive power for breast cancer prognosis. BMC Bioinformatics (2010) 1.12
A new method for class prediction based on signed-rank algorithms applied to Affymetrix microarray experiments. BMC Bioinformatics (2008) 1.11
Outcome prediction based on microarray analysis: a critical perspective on methods. BMC Bioinformatics (2009) 1.11
Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. Nucleic Acids Res (2013) 1.11
Ovarian cancer: pathology, biology, and disease models. Front Biosci (Landmark Ed) (2009) 1.11
Development and Validation of Biomarker Classifiers for Treatment Selection. J Stat Plan Inference (2008) 1.10
Discovery of the gene signature for acute lung injury in patients with sepsis. Physiol Genomics (2009) 1.10
Invasive Breast Cancer: Recognition of Molecular Subtypes. Breast Care (Basel) (2011) 1.09
Clinical relevance of multidrug resistance gene expression in ovarian serous carcinoma effusions. Mol Pharm (2011) 1.06
Immune Signature to Predict Trastuzumab Benefit: Potential and Pitfalls. J Clin Oncol (2015) 1.06
Personalized medicine and development of targeted therapies: The upcoming challenge for diagnostic molecular pathology. A review. Virchows Arch (2006) 1.05
The liver pharmacological and xenobiotic gene response repertoire. Mol Syst Biol (2008) 1.04
Smoking-related genomic signatures in non-small cell lung cancer. Am J Respir Crit Care Med (2008) 1.03
Analysis of DNA microarray expression data. Best Pract Res Clin Haematol (2009) 1.03
American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol (2006) 25.12
Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A (2003) 13.00
Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. J Clin Oncol (2013) 12.57
American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. Arch Pathol Lab Med (2007) 8.02
IDH1 and IDH2 gene mutations identify novel molecular subsets within de novo cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol (2010) 5.62
MicroRNA expression in cytogenetically normal acute myeloid leukemia. N Engl J Med (2008) 4.91
Prognostic significance of, and gene and microRNA expression signatures associated with, CEBPA mutations in cytogenetically normal acute myeloid leukemia with high-risk molecular features: a Cancer and Leukemia Group B Study. J Clin Oncol (2008) 4.09
A paradigm for class prediction using gene expression profiles. J Comput Biol (2002) 3.64
Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): explanation and elaboration. PLoS Med (2012) 3.62
Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics (2002) 3.31
Randomized clinical trials with biomarkers: design issues. J Natl Cancer Inst (2010) 3.30
TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol (2011) 3.01
Favorable prognostic impact of NPM1 mutations in older patients with cytogenetically normal de novo acute myeloid leukemia and associated gene- and microRNA-expression signatures: a Cancer and Leukemia Group B study. J Clin Oncol (2009) 2.78
Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. Arch Pathol Lab Med (2013) 2.54
ASXL1 mutations identify a high-risk subgroup of older patients with primary cytogenetically normal AML within the ELN Favorable genetic category. Blood (2011) 2.50
MicroRNA expression differentiates histology and predicts survival of lung cancer. Clin Cancer Res (2010) 2.48
An international Ki67 reproducibility study. J Natl Cancer Inst (2013) 2.46
Overexpression of the ETS-related gene, ERG, predicts a worse outcome in acute myeloid leukemia with normal karyotype: a Cancer and Leukemia Group B study. J Clin Oncol (2005) 2.41
Sp1/NFkappaB/HDAC/miR-29b regulatory network in KIT-driven myeloid leukemia. Cancer Cell (2010) 2.37
The prognostic and functional role of microRNAs in acute myeloid leukemia. Blood (2010) 2.33
Age-related prognostic impact of different types of DNMT3A mutations in adults with primary cytogenetically normal acute myeloid leukemia. J Clin Oncol (2012) 1.98
Assessing surrogates as trial endpoints using mixed models. Stat Med (2005) 1.94
Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration. BMC Med (2012) 1.85
Biospecimen reporting for improved study quality (BRISQ). Cancer Cytopathol (2011) 1.85
RUNX1 mutations are associated with poor outcome in younger and older patients with cytogenetically normal acute myeloid leukemia and with distinct gene and MicroRNA expression signatures. J Clin Oncol (2012) 1.79
miR-3151 interplays with its host gene BAALC and independently affects outcome of patients with cytogenetically normal acute myeloid leukemia. Blood (2012) 1.77
Chromosome transfer induced aneuploidy results in complex dysregulation of the cellular transcriptome in immortalized and cancer cells. Cancer Res (2004) 1.74
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics (2004) 1.74
Prognostic importance of MN1 transcript levels, and biologic insights from MN1-associated gene and microRNA expression signatures in cytogenetically normal acute myeloid leukemia: a cancer and leukemia group B study. J Clin Oncol (2009) 1.63
Prognostic significance of expression of a single microRNA, miR-181a, in cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol (2010) 1.59
Albumin turnover: FcRn-mediated recycling saves as much albumin from degradation as the liver produces. Am J Physiol Gastrointest Liver Physiol (2005) 1.59
Challenges in projecting clustering results across gene expression-profiling datasets. J Natl Cancer Inst (2007) 1.52
Biospecimen reporting for improved study quality (BRISQ). J Proteome Res (2011) 1.48
Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol (2006) 1.46
Design of studies using DNA microarrays. Genet Epidemiol (2002) 1.45
Profiling human serum antibodies with a carbohydrate antigen microarray. J Proteome Res (2009) 1.39
Optimal gene expression analysis by microarrays. Cancer Cell (2002) 1.34
A perspective on challenges and issues in biomarker development and drug and biomarker codevelopment. J Natl Cancer Inst (2009) 1.31
Mutations of the Wilms tumor 1 gene (WT1) in older patients with primary cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. Blood (2010) 1.30
Identification of clinically useful cancer prognostic factors: what are we missing? J Natl Cancer Inst (2005) 1.27
Randomized phase II trial designs with biomarkers. J Clin Oncol (2012) 1.26
Biomarker studies: a call for a comprehensive biomarker study registry. Nat Rev Clin Oncol (2011) 1.26
Stage-specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis. Genes Chromosomes Cancer (2007) 1.26
On the question of sporadic or atypical bovine spongiform encephalopathy and Creutzfeldt-Jakob disease. Emerg Infect Dis (2006) 1.25
Identification of a 24-gene prognostic signature that improves the European LeukemiaNet risk classification of acute myeloid leukemia: an international collaborative study. J Clin Oncol (2013) 1.15
Evidence of clinical utility: an unmet need in molecular diagnostics for patients with cancer. Clin Cancer Res (2014) 1.13
Molecular signatures in acute myeloid leukemia. Curr Opin Hematol (2009) 1.13
Biospecimen Reporting for Improved Study Quality. Biopreserv Biobank (2011) 1.12
Low expression of MN1 associates with better treatment response in older patients with de novo cytogenetically normal acute myeloid leukemia. Blood (2011) 1.12
Statistical and practical considerations for clinical evaluation of predictive biomarkers. J Natl Cancer Inst (2013) 1.10
Effects of pooling mRNA in microarray class comparisons. Bioinformatics (2004) 1.10
Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics (2004) 1.05
STAT1-dependent and STAT1-independent gene expression in murine immune cells following stimulation with interferon-alpha. Cancer Immunol Immunother (2007) 1.03
An investigation of two multivariate permutation methods for controlling the false discovery proportion. Stat Med (2007) 1.03
Gene expression profiling reveals similarities between the in vitro and in vivo responses of immune effector cells to IFN-alpha. Clin Cancer Res (2008) 1.02
Experimental design of DNA microarray experiments. Biotechniques (2003) 1.01
A class comparison method with filtering-enhanced variable selection for high-dimensional data sets. Stat Med (2008) 1.00
Statistical challenges in the evaluation of treatments for small patient populations. Sci Transl Med (2013) 0.98
Comparison of confidence interval methods for an intra-class correlation coefficient (ICC). BMC Med Res Methodol (2014) 0.96
Objective method of comparing DNA microarray image analysis systems. Biotechniques (2004) 0.95
Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data. Stat Med (2007) 0.95
MicroRNA expression in acute myeloid leukemia. Curr Hematol Malig Rep (2009) 0.95
Heritable polymorphism predisposes to high BAALC expression in acute myeloid leukemia. Proc Natl Acad Sci U S A (2012) 0.91
MicroRNA expression profiling in acute myeloid and chronic lymphocytic leukaemias. Best Pract Res Clin Haematol (2009) 0.91
Evaluation of normalization methods for two-channel microRNA microarrays. J Transl Med (2010) 0.90
Biospecimen reporting for improved study quality (BRISQ). Clin Chim Acta (2012) 0.89
Biospecimen Reporting for improved study quality (BRISQ). Transfusion (2013) 0.88
Designing biomarker studies for head and neck cancer. Head Neck (2014) 0.78
Refining Prognosis in Lung Cancer: A Report on the Quality and Relevance of Clinical Prognostic Tools. J Thorac Oncol (2015) 0.76
Prostate cancer in patients with screening serum prostate specific antigen values less than 4.0 ng/dl: results from the cooperative prostate cancer tissue resource. J Urol (2005) 0.75
Imaging biomarkers exist and they underpin clinical decision-making. Nat Rev Clin Oncol (2017) 0.75