NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data

A practical solution to pseudoreplication bias in single-cell studies

(2021) Kip D. Zimmerman et al.   Nature Communications

Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models

(2020) Liang He et al.   GENETICS

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

(2020) Yingyue Zhou et al.   NATURE MEDICINE

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments

(2020) Brian E. Vestal et al.   BMC BIOINFORMATICS

Transcriptomic and clonal characterization of T cells in the human central nervous system

(2020) Jenna L. Pappalardo et al.   Science Immunology

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

(2020) Helena L. Crowell et al.   Nature Communications

ApoE attenuates unresolvable inflammation by complex formation with activated C1q

(2019) Changjun Yin et al.   NATURE MEDICINE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies

(2019) Yu Yamazaki et al.   Nature Reviews Neurology

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks

(2019) Ege Ulgen et al.   Frontiers in Genetics

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

(2017) Susanne Krasemann et al.   IMMUNITY

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Overview and Findings from the Religious Orders Study

(2013) David A. Bennett et al.   Current Alzheimer Research

Overview and Findings from the Rush Memory and Aging Project

(2013) David A. Bennett et al.   Current Alzheimer Research

Variant of TREM2 Associated with the Risk of Alzheimer's Disease

(2012) Thorlakur Jonsson et al.   NEW ENGLAND JOURNAL OF MEDICINE

TREM2 Variants in Alzheimer's Disease

(2012) Rita Guerreiro et al.   NEW ENGLAND JOURNAL OF MEDICINE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Ignoring overdispersion in hierarchical loglinear models: Possible problems and solutions

(2012) Elasma Milanzi et al.   STATISTICS IN MEDICINE

Estimation of covariate effects in generalized linear mixed models with a misspecified distribution of random intercepts and slopes

(2012) John M. Neuhaus et al.   STATISTICS IN MEDICINE

Estimation of covariate effects in generalized linear mixed models with informative cluster sizes

(2011) J. M. Neuhaus et al.   BIOMETRIKA

Gaussian Variational Approximate Inference for Generalized Linear Mixed Models

(2011) J. T. Ormerod et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

A Family of Generalized Linear Models for Repeated Measures with Normal and Conjugate Random Effects

(2011) Geert Molenberghs et al.   STATISTICAL SCIENCE

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Genetics and molecular pathogenesis of sporadic and hereditary cerebral amyloid angiopathies

(2009) Tamas Revesz et al.   ACTA NEUROPATHOLOGICA

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

(2009) Håvard Rue et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease

(2009) Jean-Charles Lambert et al.   NATURE GENETICS

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease

(2009) Denise Harold et al.   NATURE GENETICS

BRI2 (ITM2b) Inhibits A  Deposition In Vivo

(2008) J. Kim et al.   JOURNAL OF NEUROSCIENCE