Andrew E Jaffe

Human splicing diversity across the Sequence Read Archive

The paper analyzes human RNA-seq data from the SRA to identify unannotated splicing junctions and their tissue-specific expression, creating a resource called intropolis.

Flexible expressed region analysis for RNA-seq with derfinder

The paper introduces derfinder, a tool for RNA-seq analysis that identifies differentially expressed regions at single base resolution without relying on gene annotations, showing it works well with incomplete annotations and large datasets.

A framework for RNA quality correction in differential expression analysis

This paper introduces a framework to correct RNA quality effects in differential expression analysis, showing improved replication rates in schizophrenia studies.

recount: A large-scale resource of analysis-ready RNA-seq expression data

recount provides a large-scale, processed RNA-seq resource with tools for analysis, including differential expression and meta-analysis, using data from the Sequence Read Archive.

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age

The paper identifies epigenetic memory in cultured human fibroblasts related to their origin and donor age, showing widespread DNA methylation and transcriptome differences.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Rail-RNA efficiently and accurately aligns RNA-seq samples and generates coverage files, enabling population-level analysis of splicing and expression variation.

regionReport: Interactive reports for region-based analyses

regionReport generates interactive genomic reports with quality checks and templates for analyzing RNA-seq differential expression results.

Flexible analysis of transcriptome assemblies with Ballgown

The paper introduces Ballgown, a tool for analyzing transcriptome assemblies from RNA-seq data, focusing on gene structure reconstruction and expression analysis.

Polyester: simulating RNA-seq datasets with differential transcript expression

Polyester simulates RNA-seq data with differential transcript expression to evaluate statistical methods for differential expression analysis.

The methylome of the human frontal cortex across development

The paper characterizes DNA methylation changes in the human frontal cortex across development, identifying differentially methylated regions and their associations with gene expression and disease risk.