Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity

(2013) Katie S Viljoen et al.   BMC GENOMICS

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes

(2013) Vonn Walter et al.   PLoS One

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

Batch effect correction for genome-wide methylation data with Illumina Infinium platform

(2011) Zhifu Sun et al.   BMC Medical Genomics

Phase 2 trial of oxaliplatin and pemetrexed as an induction regimen in locally advanced head and neck cancer

(2011) Jill Gilbert et al.   CANCER

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

(2011) Carlo Colantuoni et al.   NATURE

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

(2010) Elana J. Fertig et al.   BIOINFORMATICS

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Insulin-like growth factor-1 receptor inhibitor, AMG-479, in cetuximab-refractory head and neck squamous cell carcinoma

(2010) Christine H. Chung et al.   HEAD AND NECK-JOURNAL FOR THE SCIENCES AND SPECIALTIES OF THE HEAD AND NECK

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Refining the diagnosis of oropharyngeal squamous cell carcinoma using human papillomavirus testing

(2010) Max Robinson et al.   ORAL ONCOLOGY

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastatic head and neck squamous cell carcinoma

(2009) C. H. Chung et al.   ANNALS OF ONCOLOGY

A Feed-Forward Loop Involving Protein Kinase C  and MicroRNAs Regulates Tumor Cell Cycle

(2008) E. E.W. Cohen et al.   CANCER RESEARCH