Fairlie Reese

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

The paper introduces perplexity as a metric to quantify isoform diversity in the human transcriptome using long-read RNA-sequencing data, showing it provides interpretable and reproducible measurements.

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains captures global and local expression variation

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

The paper uses long-read RNA-seq from diverse human populations to reveal ancestry bias in gene annotations and shows improved transcript discovery with personal genome assemblies.

Long-read sequencing transcriptome quantification with lr-kallisto

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

rDNAcaller: a fast and robust pipeline to call ribosomal DNA variants

The paper introduces rDNAcaller, a pipeline for accurate rDNA variant detection using short-read whole-genome sequencing, achieving 94% precision and identifying 5,607 novel variant positions across human populations.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease

This study uses spatial transcriptomics and single-nucleus RNA-seq to compare genetic and sporadic Alzheimer's Disease, finding similar spatial and cell-type specific changes between sporadic AD and AD in Down Syndrome.

The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states

The paper identifies regulatory programs in postnatal mouse development using single-nucleus data, revealing cell-type-specific and common regulatory topics across multiple tissues.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD

The paper introduces Topyfic, a reproducible LDA method, to identify cellular programs in single-cell data and shows sex-specific differences in microglial activation in Alzheimer's disease mouse models.

L-GIREMI uncovers RNA editing sites in long-read RNA-seq

L-GIREMI detects RNA editing sites in long-read RNA-seq with high accuracy by addressing sequencing errors and biases.

PyWGCNA: A Python package for weighted gene co-expression network analysis

PyWGCNA is a Python package for weighted gene co-expression network analysis, enabling module identification and comparison in RNA-seq data.

High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

This paper introduces hdWGCNA, a framework for analyzing co-expression networks in high-dimensional transcriptomics data, demonstrating its application in identifying disease-relevant modules in single-cell datasets.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

Long-read sequencing and profiling of RNA-binding proteins reveals the pathogenic mechanism of aberrant splicing of an SCN1A poison exon in epilepsy

The paper investigates how SCN1A variants in a poison exon cause aberrant splicing, reduced Nav1.1 protein, and epilepsy through RBP interactions.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

A catalog of transcription start sites across 115 human tissue and cell types

The paper generates a catalog of experimentally validated transcription start sites (TSSs) across 115 human tissues and cell types, updating TSS annotations for 20% of GENCODE genes and identifying new GWAS candidate genes.

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

The paper introduces LR-Split-seq, a long-read single-cell RNA-seq method, to study differential RNA isoform expression and validates it using mouse myoblast differentiation data.

Swan: a library for the analysis and visualization of long-read transcriptomes

Swan is a Python library for analyzing and visualizing long-read transcriptomes, identifying differentially expressed transcripts and novel splicing events.

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

TALON annotates and counts full-length reads from PacBio or Nanopore in one framework; in mouse brain, 422 genes showed more novel-isoform reads than annotated ones.