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Bioinformatics (Oxford, England)|September 29, 2020
Swan: a library for the analysis and visualization of long-read transcriptomesFairlie Reese, Ali MortazaviGenome Biology|July 20, 2023
L-GIREMI uncovers RNA editing sites in long-read RNA-seqZhiheng Liu, Giovanni Quinones-Valdez, Ting Fu, et al.Genome Research|December 24, 2021
Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue typesJill E Moore, Xiao-Ou Zhang, Shaimae I Elhajjajy, et al.Genome Biology|October 8, 2021
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seqElisabeth Rebboah, Fairlie Reese, Katherine Williams, et al.Biorxiv : the Preprint Server for Biology|March 11, 2024
Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of ADNarges Rezaie, Elisabeth Rebboah, Brian A Williams, et al.RNA (New York, N.Y.)|September 27, 2019
Exon size and sequence conservation improves identification of splice-altering nucleotidesMaliheh Movassat, Elmira Forouzmand, Fairlie Reese, et al.Cell Reports Methods|July 10, 2023
hdWGCNA identifies co-expression networks in high-dimensional transcriptomics dataSamuel Morabito, Fairlie Reese, Negin Rahimzadeh, et al.Nature Immunology|August 23, 2012
Technical considerations for functional sequencing assaysWeihua Zeng, Ali MortazaviBiorxiv : the Preprint Server for Biology|June 12, 2025
Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modificationsElnaz Abdollahzadeh, Ali MortazaviBriefings in Functional Genomics|March 27, 2018
Integrating ChIP-seq with other functional genomics dataShan Jiang, Ali MortazaviPageof 21