Lior Pachter

Transcriptomic responses to endurance exercise training in rats

The paper analyzes RNA-seq data from rats to show gene expression predicts exercise training levels, reveals isoform-level changes, and identifies a potential novel virus affecting physiological measurements.

Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays

PROBer is a statistical model that addresses computational challenges in sequencing-based toeprinting assays by learning isoform-specific chemical modification profiles.

Differential analysis of RNA-Seq incorporating quantification uncertainty

The paper introduces a method for differential RNA-Seq analysis that separates biological and inferential variance using bootstrapping and response error modeling, implemented in the sleuth app.

The Lair: A resource for exploratory analysis of published RNA-Seq data

The Lair provides tools to analyze published RNA-Seq data from the Short Read Archive, enabling accessible and extendable exploration without technical expertise.

Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts

This paper introduces a fast and accurate method for single-cell RNA-Seq analysis by clustering transcript-compatibility counts, showing it is faster and more broadly applicable than existing approaches.

Shannon: An Information-Optimal de Novo RNA-Seq Assembler

Shannon is an RNA-Seq assembler that uses information theory to optimally reconstruct transcripts, achieving higher sensitivity and specificity than existing methods.