TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository

Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

(2020) Shanrong Zhao et al.   RNA

Comprehensive analysis of the SLC16A gene family in pancreatic cancer via integrated bioinformatics

(2020) Shan Yu et al.   Scientific Reports

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines

(2019) Xing Yi Woo et al.   BMC Medical Genomics

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

(2019) Yuanhang Liu et al.   Scientific Reports

A protocol to evaluate RNA sequencing normalization methods

(2019) Zachary B. Abrams et al.   BMC BIOINFORMATICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

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

(2016) Yanzhu Lin et al.   BMC GENOMICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research

(2014) M. Hidalgo et al.   Cancer Discovery

A Correction to the Research Article Titled: "Inositol Polyphosphate Multikinase Is a Coactivator of p53-Mediated Transcription and Cell Death" by R. Xu, N. Sen, B. D. Paul, A. M. Snowman, F. Rao, M. S. Vandiver, J. Xu, S. H. Snyder

(2013)   Science Signaling

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

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

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

A Comparison of Hierarchical Methods for Clustering Functional Data

(2009) Laura Ferreira et al.   COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION

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