Published in Biostatistics on May 11, 2006
Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics (2008) 3.24
Supervised group Lasso with applications to microarray data analysis. BMC Bioinformatics (2007) 1.99
Boosting signal-to-noise in complex biology: prior knowledge is power. Cell (2011) 1.71
INCORPORATING BIOLOGICAL INFORMATION INTO LINEAR MODELS: A BAYESIAN APPROACH TO THE SELECTION OF PATHWAYS AND GENES. Ann Appl Stat (2011) 1.42
Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients. BMC Med Genomics (2011) 1.37
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics (2010) 1.33
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. Genome Biol (2013) 1.26
An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Res (2009) 1.19
Integrating biological knowledge with gene expression profiles for survival prediction of cancer. J Comput Biol (2009) 1.08
Simultaneous supervised clustering and feature selection over a graph. Biometrika (2012) 0.94
Pathway index models for construction of patient-specific risk profiles. Stat Med (2012) 0.93
A model-based analysis to infer the functional content of a gene list. Stat Appl Genet Mol Biol (2012) 0.91
Integrative analysis using module-guided random forests reveals correlated genetic factors related to mouse weight. PLoS Comput Biol (2013) 0.89
Identification of factors contributing to variability in a blood-based gene expression test. PLoS One (2012) 0.87
A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations. BMC Bioinformatics (2008) 0.86
Homogeneity Pursuit. J Am Stat Assoc (2015) 0.84
Finding gene clusters for a replicated time course study. BMC Res Notes (2014) 0.83
Consistent Group Identification and Variable Selection in Regression with Correlated Predictors. J Comput Graph Stat (2013) 0.82
Gene network modular-based classification of microarray samples. BMC Bioinformatics (2012) 0.80
Module-based prediction approach for robust inter-study predictions in microarray data. Bioinformatics (2010) 0.79
Characterization and robust classification of EEG signal from image RSVP events with independent time-frequency features. PLoS One (2012) 0.79
FERAL: network-based classifier with application to breast cancer outcome prediction. Bioinformatics (2015) 0.77
Predictive response-relevant clustering of expression data provides insights into disease processes. Nucleic Acids Res (2010) 0.77
The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping. Technometrics (2014) 0.77
Sparse regression and marginal testing using cluster prototypes. Biostatistics (2015) 0.76
Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach. Genetics (2016) 0.75
Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PLoS Comput Biol (2016) 0.75
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw (2010) 38.65
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A (2002) 30.32
Sparse inverse covariance estimation with the graphical lasso. Biostatistics (2007) 24.38
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics (2009) 12.21
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85
Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol (2002) 10.56
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med (2004) 9.81
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics (2009) 9.40
Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol (2004) 7.68
Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med (2007) 6.80
Classification of gene microarrays by penalized logistic regression. Biostatistics (2004) 6.20
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88
Penalized logistic regression for detecting gene interactions. Biostatistics (2007) 5.53
Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer (2006) 5.39
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol (2003) 4.28
Regularized linear discriminant analysis and its application in microarrays. Biostatistics (2006) 3.66
A framework for feature selection in clustering. J Am Stat Assoc (2010) 3.46
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res (2011) 3.44
Covariance-regularized regression and classification for high-dimensional problems. J R Stat Soc Series B Stat Methodol (2009) 3.31
Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87
A method for calling gains and losses in array CGH data. Biostatistics (2005) 2.86
A network model of a cooperative genetic landscape in brain tumors. JAMA (2009) 2.86
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Presence-only data and the em algorithm. Biometrics (2009) 2.76
Outlier sums for differential gene expression analysis. Biostatistics (2006) 2.75
Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med (2005) 2.56
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
Spectral Regularization Algorithms for Learning Large Incomplete Matrices. J Mach Learn Res (2010) 2.45
Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics (2002) 2.42
Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics (2011) 2.36
Differentiation stage-specific expression of microRNAs in B lymphocytes and diffuse large B-cell lymphomas. Blood (2008) 2.36
Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer. Neoplasia (2005) 2.35
Are clusters found in one dataset present in another dataset? Biostatistics (2006) 2.33
Notch signals positively regulate activity of the mTOR pathway in T-cell acute lymphoblastic leukemia. Blood (2007) 2.29
Sample classification from protein mass spectrometry, by 'peak probability contrasts'. Bioinformatics (2004) 2.28
Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol (2012) 2.12
Global transcriptional response to interferon is a determinant of HCV treatment outcome and is modified by race. Hepatology (2006) 2.03
Early detection of breast cancer based on gene-expression patterns in peripheral blood cells. Breast Cancer Res (2005) 2.00
Disease signatures are robust across tissues and experiments. Mol Syst Biol (2009) 1.93
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol (2008) 1.91
A tail strength measure for assessing the overall univariate significance in a dataset. Biostatistics (2005) 1.90
LMO2 protein expression predicts survival in patients with diffuse large B-cell lymphoma treated with anthracycline-based chemotherapy with and without rituximab. J Clin Oncol (2007) 1.88
Discovery and validation of breast cancer subtypes. BMC Genomics (2006) 1.83
Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol (2010) 1.80
Risk factors for progressive cartilage loss in the knee: a longitudinal magnetic resonance imaging study in forty-three patients. Arthritis Rheum (2002) 1.76
The 'miss rate' for the analysis of gene expression data. Biostatistics (2005) 1.71
An evaluation of tumor oxygenation and gene expression in patients with early stage non-small cell lung cancers. Clin Cancer Res (2006) 1.71
Estimation of Sparse Binary Pairwise Markov Networks using Pseudo-likelihoods. J Mach Learn Res (2009) 1.70
Penalized classification using Fisher's linear discriminant. J R Stat Soc Series B Stat Methodol (2011) 1.69
Patient-derived health state utilities for gastroesophageal reflux disease. Am J Gastroenterol (2005) 1.64
Hybrid hierarchical clustering with applications to microarray data. Biostatistics (2005) 1.56
IRF9 and STAT1 are required for IgG autoantibody production and B cell expression of TLR7 in mice. J Clin Invest (2008) 1.55
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. Genome Biol (2007) 1.54
An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AML. Blood (2008) 1.51
Efficient quadratic regularization for expression arrays. Biostatistics (2004) 1.50
Survival analysis with high-dimensional covariates. Stat Methods Med Res (2009) 1.50
Genomics of childhood leukemias: the virtue of complexity. J Clin Oncol (2008) 1.48
HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma. Blood (2003) 1.47
Gene expression profiles at diagnosis in de novo childhood AML patients identify FLT3 mutations with good clinical outcomes. Blood (2004) 1.41
Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage. Proc Natl Acad Sci U S A (2004) 1.39
Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature. BMC Cancer (2008) 1.37
Expression and prognostic significance of a panel of tissue hypoxia markers in head-and-neck squamous cell carcinomas. Int J Radiat Oncol Biol Phys (2007) 1.36
Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease. Physiol Genomics (2005) 1.22
Immune signatures in follicular lymphoma. N Engl J Med (2005) 1.18
Characterization of variant patterns of nodular lymphocyte predominant hodgkin lymphoma with immunohistologic and clinical correlation. Am J Surg Pathol (2003) 1.16
Flawed analysis, implausible results--move on. CMAJ (2004) 1.14
Disease-specific genomic analysis: identifying the signature of pathologic biology. Bioinformatics (2007) 1.12
Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Blood (2009) 1.11
Microelectrode recording revealing a somatotopic body map in the subthalamic nucleus in humans with Parkinson disease. J Neurosurg (2004) 1.09
Anti-idiotype antibody response after vaccination correlates with better overall survival in follicular lymphoma. Blood (2009) 1.08
Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers. PLoS Genet (2007) 1.07
Adaptive index models for marker-based risk stratification. Biostatistics (2010) 1.07
Radiation-induced gene expression in human subcutaneous fibroblasts is predictive of radiation-induced fibrosis. Radiother Oncol (2007) 1.06
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. Bioinformatics (2009) 1.05
Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate (2009) 1.04
Microarray analysis of the transcriptional response to single or multiple doses of ionizing radiation in human subcutaneous fibroblasts. Radiother Oncol (2005) 1.04
Complementary hierarchical clustering. Biostatistics (2007) 1.04
Mouse strain-specific differences in vascular wall gene expression and their relationship to vascular disease. Arterioscler Thromb Vasc Biol (2004) 0.99
The use of plasma surface-enhanced laser desorption/ionization time-of-flight mass spectrometry proteomic patterns for detection of head and neck squamous cell cancers. Clin Cancer Res (2004) 0.99
hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature. Am J Surg Pathol (2008) 0.98
Mitral annular size predicts Alfieri stitch tension in mitral edge-to-edge repair. J Heart Valve Dis (2004) 0.96
Gene expression profiling differentiates germ cell tumors from other cancers and defines subtype-specific signatures. Proc Natl Acad Sci U S A (2005) 0.95
A fused lasso latent feature model for analyzing multi-sample aCGH data. Biostatistics (2011) 0.94