Variation-preserving normalization unveils blind spots in gene expression profiling

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

(2016) Yanzhu Lin et al.   BMC GENOMICS

CrossNorm: a novel normalization strategy for microarray data in cancers

(2016) Lixin Cheng et al.   Scientific Reports

Effect of 10 different TiO2and ZrO2(nano)materials on the soil invertebrateEnchytraeus crypticus

(2015) Susana I.L. Gomes et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

The path to routine use of genomic biomarkers in the cancer clinic

(2015) Paul C. Boutros   GENOME RESEARCH

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Cellular Energy Allocation to Assess the Impact of Nanomaterials on Soil Invertebrates (Enchytraeids): The Effect of Cu and Ag

(2015) Susana Gomes et al.   International Journal of Environmental Research and Public Health

quantro: a data-driven approach to guide the choice of an appropriate normalization method

(2015) Stephanie Hicks et al.   GENOME BIOLOGY

Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions

(2014) Marta P Castro-Ferreira et al.   BMC GENOMICS

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis

(2013) Sarah E. Reese et al.   BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

All Things to All People

(2012) Trevor D. Littlewood et al.   CELL

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Using control genes to correct for unwanted variation in microarray data

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

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Using Gene Expression Profiling to Predict Response and Prognosis in Gastrointestinal Cancers—The Promise and the Perils

(2010) Kate H. Brettingham-Moore et al.   ANNALS OF SURGICAL ONCOLOGY

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

(2010) Qianqian Zhu et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Correction for hidden confounders in the genetic analysis of gene expression

(2010) J. Listgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Use of normalization methods for analysis of microarrays containing a high degree of gene effects

(2008) Terri T Ni et al.   BMC BIOINFORMATICS

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods

(2008) Richard D Pearson   BMC BIOINFORMATICS

Normalization of oligonucleotide arrays based on the least-variant set of genes

(2008) Stefano Calza et al.   BMC BIOINFORMATICS

Global mRNA changes in microarray experiments

(2008) Matthew A Hannah et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE