hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

Samuel Morabito, Fairlie Reese, Negin Rahimzadeh, +2

Cell Reports Methods

EngineeringGeneticsPresent HdwgcnaMultiomicsTranscriptomics Technology +20

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

Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, +13

GeneticsNovel IsoformsRna SplicingMolecular BiologyTranscriptomics Technology +21

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

Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, +84

Nature Methods

The ENCODE Uniform Analysis Pipelines

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, +57

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease

Emily Miyoshi, Samuel Morabito, Caden M. Henningfield, +23

Nature Genetics

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

Elisabeth Rebboah, Fairlie Reese, Katherine Williams, +7

Genome biology

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

Fairlie Reese, Brian A. Williams, Gabriela Balderrama-Gutierrez, +42

EngineeringGeneticsMolecular BiologyTranscriptomics TechnologyMolecular Genetics +19

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

Francisco J. Pardo-Palacios, Fairlie Reese, Sílvia Carbonell Sala, +34

EngineeringLibrary PreparationGeneticsTranscriptomics TechnologyGenomics +21

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

Samuel Morabito, Fairlie Reese, Negin Rahimzadeh, +2

EngineeringNeurogenomicsGeneticsPresent HdwgcnaTranscriptomics Technology +25

The ENCODE Uniform Analysis Pipelines

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, +59