Contrastive latent variable modeling with application to case-control sequencing experiments

Exploring high-dimensional biological data with sparse contrastive principal component analysis

(2020) Philippe Boileau et al.   BIOINFORMATICS

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Equality tests of high-dimensional covariance matrices under the strongly spiked eigenvalue model

(2019) Aki Ishii et al.   JOURNAL OF STATISTICAL PLANNING AND INFERENCE

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

Two-sample tests for high-dimension, strongly spiked eigenvalue models

(2018) Makoto Aoshima et al.   STATISTICA SINICA

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding et al.   Nature Communications

Exploring patterns enriched in a dataset with contrastive principal component analysis

(2018) Abubakar Abid et al.   Nature Communications

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes

(2015) Sheida Nabavi et al.   BIOINFORMATICS

Testing differential networks with applications to the detection of gene-gene interactions

(2015) Yin Xia et al.   BIOMETRIKA

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Two-Sample Covariance Matrix Testing and Support Recovery in High-Dimensional and Sparse Settings

(2013) Tony Cai et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Passing Messages between Biological Networks to Refine Predicted Interactions

(2013) Kimberly Glass et al.   PLoS One

Two sample tests for high-dimensional covariance matrices

(2012) Jun Li et al.   ANNALS OF STATISTICS

Testing the equality of several covariance matrices with fewer observations than the dimension

(2010) Muni S. Srivastava et al.   JOURNAL OF MULTIVARIATE ANALYSIS

Multivariate analysis and Jacobi ensembles: Largest eigenvalue, Tracy–Widom limits and rates of convergence

(2009) Iain M. Johnstone   ANNALS OF STATISTICS

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

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

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA