| hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data S Morabito, F Reese, N Rahimzadeh, E Miyoshi, V Swarup Cell reports methods 3 (6), 2023 | 245* | 2023 |
| A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. bioRxiv 672931 D Wyman, G Balderrama-Gutierrez, F Reese, S Jiang, S Rahmanian, ... Preprint, 2020 | 136* | 2020 |
| Systematic assessment of long-read RNA-seq methods for transcript identification and quantification FJ Pardo-Palacios, D Wang, F Reese, M Diekhans, S Carbonell-Sala, ... Nature methods, 1-15, 2024 | 87 | 2024 |
| The ENCODE uniform analysis pipelines BC Hitz, L Jin-Wook, O Jolanki, MS Kagda, K Graham, P Sud, I Gabdank, ... Biorxiv, 2023 | 68 | 2023 |
| Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq E Rebboah, F Reese, K Williams, G Balderrama-Gutierrez, C McGill, ... Genome biology 22, 1-28, 2021 | 46 | 2021 |
| Exon size and sequence conservation improves identification of splice-altering nucleotides M Movassat, E Forouzmand, F Reese, KJ Hertel RNA 25 (12), 1793-1805, 2019 | 37 | 2019 |
| PyWGCNA: a Python package for weighted gene co-expression network analysis N Rezaie, F Reese, A Mortazavi Bioinformatics 39 (7), btad415, 2023 | 29 | 2023 |
| Swan: a library for the analysis and visualization of long-read transcriptomes F Reese, A Mortazavi Bioinformatics 37 (9), 1322-1323, 2021 | 24 | 2021 |
| The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity F Reese, B Williams, G Balderrama-Gutierrez, D Wyman, MH Çelik, ... bioRxiv, 2023 | 22 | 2023 |
| L-GIREMI uncovers RNA editing sites in long-read RNA-seq Z Liu, G Quinones-Valdez, T Fu, E Huang, M Choudhury, F Reese, ... Genome Biology 24 (1), 171, 2023 | 19 | 2023 |
| Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s Disease E Miyoshi, S Morabito, CM Henningfield, S Das, N Rahimzadeh, ... Nature Genetics, 1-14, 2024 | 15 | 2024 |
| Deciphering the impact of genomic variation on function Code of Conduct Committee (alphabetical by last name) Cody Sarah 33 Farrell ... Nature 633 (8028), 47-57, 2024 | 11 | 2024 |
| Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types JE Moore, XO Zhang, SI Elhajjajy, K Fan, HE Pratt, F Reese, A Mortazavi, ... Genome Research 32 (2), 389-402, 2022 | 11 | 2022 |
| Long-read sequencing and profiling of RNA-binding proteins reveals the pathogenic mechanism of aberrant splicing of an SCN1A poison exon in epilepsy HC Happ, PN Schneider, JH Hong, E Goes, M Bandouil, CG Biar, ... bioRxiv, 2023.05. 04.538282, 2023 | 2 | 2023 |
| Long-term patterns of noise from underwater explosions and their relation to fisheries in Southern California A Krumpel, A Rice, KE Frasier, F Reese, JS Trickey, AE Simonis, JP Ryan, ... Frontiers in Marine Science 8, 796849, 2021 | 2 | 2021 |
| Long-read sequencing transcriptome quantification with lr-kallisto RK Loving, DK Sullivan, F Reese, E Rebboah, J Sakr, N Rezaie, ... bioRxiv, 2024 | 1 | 2024 |
| The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states E Rebboah, N Rezaie, BA Williams, AK Weimer, M Shi, X Yang, HY Liang, ... bioRxiv, 2024 | 1 | 2024 |
| Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice JE Childs, S Morabito, S Das, C Santelli, V Pham, K Kusche, VA Vera, ... Cell reports 43 (3), 2024 | 1 | 2024 |
| Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD N Rezaie, E Rebboah, BA Williams, HY Liang, F Reese, ... bioRxiv, 2024 | 1 | 2024 |
| Relapse to Cocaine Self-Administration is Regulated by Medial Habenula Nr4a2 J Childs, S Morabito, S Das, C Santelli, K Kusche, VA Vera, F Reese, ... NEUROPSYCHOPHARMACOLOGY 48, 413-414, 2023 | | 2023 |
Ali MortazaviProfessor of Developmental and Cell Biology, University of California, IrvineAdresse e-mail validée de uci.edu
