Fairlie Reese

发表

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

Barbara J. Wold, Diane Trout, Stefania Forner, 2019, bioRxiv.

Exon size and sequence conservation improves identification of splice-altering nucleotides

K. J. Hertel, Fairlie Reese, Maliheh Movassat, 2019, RNA.

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

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types

Z. Weng, Jill E. Moore, Henry E. Pratt, 2021, Genome research.

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

V. Swarup, Samuel J Morabito, Emily Miyoshi, 2022, bioRxiv.

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

A. Mortazavi, B. Wold, Diane Trout, 2021, Genome Biology.

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

A. Mortazavi, X. Xiao, Ting Fu, 2022, bioRxiv.

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

Ali Mortazavi, Fairlie Reese, A. Mortazavi, 2020, bioRxiv.

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

Z. Weng, A. Mortazavi, Jill E. Moore, 2021, bioRxiv.

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, bioRxiv.

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

Michael A. Beer, M. Gerstein, Z. Weng, 2023, bioRxiv.

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

A. Mortazavi, Fairlie Reese, Narges Rezaie, 2022, bioRxiv.

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

V. Swarup, Samuel J Morabito, Emily Miyoshi, 2023, Cell reports methods.

Long-Term Patterns of Noise From Underwater Explosions and Their Relation to Fisheries in Southern California

H. Schnitzler, J. Ryan, S. Wiggins, 2021, Frontiers in Marine Science.

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

A. Mortazavi, B. Wold, Diane Trout, 2021, Genome Biology.

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

Caden M. Henningfield, Vanessa M. Scarfone, V. Swarup, 2023, bioRxiv.

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, Research square.

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

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2023, bioRxiv.

Systematic assessment of long-read RNA-seq methods for transcript identi cation and quanti cation

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, Research square.

Deciphering the impact of genomic variation on function.

William H. Majoros, Neva C. Durand, Alan F. Rubin, 2024, Nature.

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

G. Carvill, I. Scheffer, H. Mefford, 2023, bioRxiv.

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

A. Mortazavi, Diane Trout, L. Reinholdt, 2024, bioRxiv.

Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice

D. Matheos, R. Campbell, Fairlie Reese, 2024, Cell reports.