Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization

jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data

(2014) Hong-Qiang Wang et al.   BIOINFORMATICS

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

(2014)   NATURE BIOTECHNOLOGY

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

(2013) Sara Mostafavi et al.   PLoS One

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

(2013) Franck Rapaport et al.   GENOME BIOLOGY

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng 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

A new discriminant NMF algorithm and its application to the extraction of subtle emotional differences in speech

(2012) Soo-Young Lee et al.   Cognitive Neurodynamics

Nonnegative Matrix Factorization: A Comprehensive Review

(2012) Yu-Xiong Wang et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

R2KS: A Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists

(2012) Shengyu Ni et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simultaneous Non-Negative Matrix Factorization for Multiple Large Scale Gene Expression Datasets in Toxicology

(2012) Clare M. Lee et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Exploring matrix factorization techniques for significant genes identification of Alzheimer’s disease microarray gene expression data

(2011) Wei Kong et al.   BMC BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

(2010) Elina Tjioe et al.   BMC BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology