Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq

Solar Simulated Ultraviolet Radiation Induces Global Histone Hypoacetylation in Human Keratinocytes

(2016) Xiaoru Zhang et al.   PLoS One

Systematic characterization of lncRNAs’ cell-to-cell expression heterogeneity in glioblastoma cells

(2016) Dekang Lv et al.   Oncotarget

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

The landscape of genomic imprinting across diverse adult human tissues

(2015) Yael Baran et al.   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

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

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

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data

(2015) Nysia I. George et al.   PLoS One

Behavioral idiosyncrasy reveals genetic control of phenotypic variability

(2015) Julien F. Ayroles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development

(2015) Yu Hasegawa et al.   PLoS Genetics

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

(2014) Mark A van de Wiel et al.   BMC BIOINFORMATICS

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Charity W Law et al.   GENOME BIOLOGY

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

(2013) Mikel Esnaola et al.   BMC BIOINFORMATICS

Meta-analysis of SNPs involved in variance heterogeneity using Levene’s test for equal variances

(2013) Wei Q Deng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A Versatile Omnibus Test for Detecting Mean and Variance Heterogeneity

(2013) Ying Cao et al.   GENETIC EPIDEMIOLOGY

The roles of protein kinases in learning and memory

(2013) K. P. Giese et al.   LEARNING & MEMORY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Brain Regulation of Thrombosis and Hemostasis

(2013) Mark J. Fisher   STROKE

Tau protein kinases: Involvement in Alzheimer's disease

(2012) Ludovic Martin et al.   AGEING RESEARCH REVIEWS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Genetic Variants Contribute to Gene Expression Variability in Humans

(2012) A. M. Hulse et al.   GENETICS

FTO genotype is associated with phenotypic variability of body mass index

(2012) Jian Yang et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Roles of AMP-activated Protein Kinase in Alzheimer’s Disease

(2012) Zhiyou Cai et al.   NEUROMOLECULAR MEDICINE

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

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

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana

(2012) Xia Shen et al.   PLoS Genetics

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq

(2011) Ming Hu et al.   BIOINFORMATICS

High-Dimensional Heteroscedastic Regression with an Application to eQTL Data Analysis

(2011) Z. John Daye et al.   BIOMETRICS

Periventricular and deep white matter leukoaraiosis have a closer association with cerebral microbleeds than age

(2011) S. Yamada et al.   EUROPEAN JOURNAL OF NEUROLOGY

Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses

(2011) Lars Rönnegård et al.   GENETICS

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Genomic Analysis of QTLs and Genes Altering Natural Variation in Stochastic Noise

(2011) Jose M. Jimenez-Gomez et al.   PLoS Genetics

Variance heterogeneity analysis for detection of potentially interacting genetic loci: method and its limitations

(2010) Maksim V Struchalin et al.   BMC GENETICS

Modelling species abundance using the Poisson-Tweedie family

(2010) Abdel H. El-Shaarawi et al.   ENVIRONMETRICS

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

The Current State of Chromatin Immunoprecipitation

(2010) Philippe Collas   MOLECULAR BIOTECHNOLOGY

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

(2010) Seema B. Plaisier et al.   NUCLEIC ACIDS RESEARCH

Do not log-transform count data

(2010) Robert B. O’Hara et al.   Methods in Ecology and Evolution

Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility

(2010) Jingjing Li et al.   PLoS Computational Biology

On the Use of Variance per Genotype as a Tool to Identify Quantitative Trait Interaction Effects: A Report from the Women's Genome Health Study

(2010) Guillaume Paré et al.   PLoS Genetics

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

A resampling-based meta-analysis for detection of differential gene expression in breast cancer

(2009) Bala Gur-Dedeoglu et al.   BMC CANCER

Transient cell–cell interactions in neural circuit formation

(2009) Daniel L. Chao et al.   NATURE REVIEWS NEUROSCIENCE

Technical Analysis of cDNA Microarrays

(2009) Cinda P. Scott et al.   PLoS One

Differential variability analysis of gene expression and its application to human diseases

(2008) J. W.K. Ho et al.   BIOINFORMATICS

Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene Expression

(2008) Wessel N. van Wieringen et al.   BIOMETRICS

Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process

(2008) Afshin Raouf et al.   Cell Stem Cell

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Target Identification for CNS Diseases by Transcriptional Profiling

(2008) C Anthony Altar et al.   NEUROPSYCHOPHARMACOLOGY

Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set

(2008) Winnie S. Liang et al.   PHYSIOLOGICAL GENOMICS