Alternative empirical Bayes models for adjusting for batch effects in genomic studies

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

(2017) Mumtahena Rahman et al.   Genome Medicine

BatchQC: interactive software for evaluating sample and batch effects in genomic data

(2016) Solaiappan Manimaran et al.   BIOINFORMATICS

Test set bias affects reproducibility of gene signatures

(2015) Prasad Patil et al.   BIOINFORMATICS

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways

(2015) Ying Shen et al.   BIOINFORMATICS

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

A Bronchial Genomic Classifier for the Diagnostic Evaluation of Lung Cancer

(2015) Gerard A. Silvestri et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

A Dynamic Bronchial Airway Gene Expression Signature of Chronic Obstructive Pulmonary Disease and Lung Function Impairment

(2013) Katrina Steiling et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

High-throughput sequencing for biology and medicine

(2013) W. W. Soon et al.   Molecular Systems Biology

Modeling precision treatment of breast cancer

(2013) Anneleen Daemen et al.   GENOME BIOLOGY

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

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Batch correction of microarray data substantially improves the identification of genes differentially expressed in Rheumatoid Arthritis and Osteoarthritis

(2012) Peter Kupfer et al.   BMC Medical Genomics

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Using control genes to correct for unwanted variation in microarray data

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

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles

(2010) Robert R Kitchen et al.   BMC GENOMICS

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

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

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

Cross-Platform Microarray Data Normalisation for Regulatory Network Inference

(2010) Alina Sîrbu et al.   PLoS One

Airway PI3K Pathway Activation Is an Early and Reversible Event in Lung Cancer Development

(2010) A. M. Gustafson et al.   Science Translational Medicine

Merging two gene-expression studies via cross-platform normalization

(2008) Andrey A. Shabalin et al.   BIOINFORMATICS