User profiles for A. E. Jaffe
 | Andrew E. JaffeVP, Head of Data Sciences, Neumora Therapeutics Verified email at neumoratx.com Cited by 23429 |
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
Heterogeneity and latent variables are now widely recognized as major sources of bias and
variability in high-throughput experiments. The most well-known source of latent variation in …
variability in high-throughput experiments. The most well-known source of latent variation in …
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Motivation: The recently released Infinium HumanMethylation450 array (the ‘450k’ array)
provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci …
provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci …
[HTML][HTML] DNA methylation age of blood predicts all-cause mortality in later life
Background DNA methylation levels change with age. Recent studies have identified
biomarkers of chronological age based on DNA methylation levels. It is not yet known whether …
biomarkers of chronological age based on DNA methylation levels. It is not yet known whether …
[HTML][HTML] Accounting for cellular heterogeneity is critical in epigenome-wide association studies
AE Jaffe, RA Irizarry - Genome biology, 2014 - Springer
Background Epigenome-wide association studies of human disease and other quantitative
traits are becoming increasingly common. A series of papers reporting age-related changes …
traits are becoming increasingly common. A series of papers reporting age-related changes …
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
INTRODUCTION Our understanding of the pathophysiology of psychiatric disorders, including
autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD), lags …
autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD), lags …
Comprehensive functional genomic resource and integrative model for the human brain
INTRODUCTION Strong genetic associations have been found for a number of psychiatric
disorders. However, understanding the underlying molecular mechanisms remains …
disorders. However, understanding the underlying molecular mechanisms remains …
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
Background During the past 5 years, high-throughput technologies have been successfully
used by epidemiology studies, but almost all have focused on sequence variation through …
used by epidemiology studies, but almost all have focused on sequence variation through …
Ballgown bridges the gap between transcriptome assembly and expression analysis
To the Editor: Analysis of raw reads from RNA sequencing (RNA-seq) makes it possible to
reconstruct complete gene structures, including multiple splice variants, without relying on …
reconstruct complete gene structures, including multiple splice variants, without relying on …
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex
DNA methylation (DNAm) is important in brain development and is potentially important in
schizophrenia. We characterized DNAm in prefrontal cortex from 335 non-psychiatric controls …
schizophrenia. We characterized DNAm in prefrontal cortex from 335 non-psychiatric controls …
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
We used the 10x Genomics Visium platform to define the spatial topography of gene expression
in the six-layered human dorsolateral prefrontal cortex. We identified extensive layer-…
in the six-layered human dorsolateral prefrontal cortex. We identified extensive layer-…