f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

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

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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

PASTA: splice junction identification from RNA-Sequencing data

(2013) Shaojun Tang et al.   BMC BIOINFORMATICS

Nonparametric Bayesian Evaluation of Differential Protein Quantification

(2013) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

A Non-parametric Cutout Index for Robust Evaluation of Identified Proteins

(2013) Oliver Serang et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

A hybrid approach to protein differential expression in mass spectrometry-based proteomics

(2012) Xuan Wang et al.   BIOINFORMATICS

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

(2012) Kang Ning et al.   JOURNAL OF PROTEOME RESEARCH

Protein homeostasis: live long, won't prosper

(2012) Brandon H. Toyama et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

k-Nearest Neighbor Based Consistent Entropy Estimation for Hyperspherical Distributions

(2011) Shengqiao Li et al.   Entropy

PepC: proteomics software for identifying differentially expressed proteins based on spectral counting

(2010) N. L. Heinecke et al.   BIOINFORMATICS

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

(2010) Qianqian Zhu et al.   BMC BIOINFORMATICS

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

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