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Works (15)

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

Nature Methods
2024-07 | Journal article
Contributors: Francisco J. Pardo-Palacios; Dingjie Wang; Fairlie Reese; Mark Diekhans; Sílvia Carbonell-Sala; Brian Williams; Jane E. Loveland; Maite De María; Matthew S. Adams; Gabriela Balderrama-Gutierrez et al.
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Crossref

Long-read sequencing transcriptome quantification with lr-kallisto

2024-07-19 | Preprint
Contributors: Rebekah K. Loving; Delaney K. Sullivan; A. Sina Booeshagi; Fairlie Reese; Elisabeth Rebboah; Jasmine Sakr; Narges Rezaie; Heidi Y. Liang; Ghassan Filimban; Shimako Kawauchi et al.
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The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states

2024-06-14 | Preprint
Contributors: Elisabeth Rebboah; Narges Rezaie; Brian A. Williams; Annika K. Weimer; Minyi Shi; Xinqiong Yang; Heidi Yahan Liang; Louise A. Dionne; Fairlie Reese; Diane Trout et al.
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Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD

2024-02-29 | Preprint
Contributors: Narges Rezaie; Elisabeth Rebboah; Brian A. Williams; Heidi Yahan Liang; Fairlie Reese; Gabriela Balderrama-Gutierrez; Louise A. Dionne; Laura Reinholdt; Diane Trout; Barbara J. Wold et al.
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Crossref

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

Bioinformatics
2023-07-01 | Journal article
Contributors: Narges Rezaie; Farilie Reese; Ali Mortazavi; Anthony Mathelier
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Crossref

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

2023-05-16 | Preprint
Contributors: Fairlie Reese; Brian Williams; Gabriela Balderrama-Gutierrez; Dana Wyman; Muhammed Hasan Çelik; Elisabeth Rebboah; Narges Rezaie; Diane Trout; Milad Razavi-Mohseni; Yunzhe Jiang et al.
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Crossref

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

2022-08-23 | Preprint
Contributors: Narges Rezaie; Fairlie Reese; Ali Mortazavi
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Crossref

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

2022-03-27 | Preprint
Contributors: Zhiheng Liu; Giovanni Quinones-Valdez; Ting Fu; Mudra Choudhury; Fairlie Reese; Ali Mortazavi; Xinshu Xiao
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Crossref

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

Genome Research
2022-02 | Journal article
Contributors: Jill E. Moore; Xiao-Ou Zhang; Shaimae I. Elhajjajy; Kaili Fan; Henry E. Pratt; Fairlie Reese; Ali Mortazavi; Zhiping Weng
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Crossref

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

2021-08 | Preprint
Contributors: Pardo-Palacios F; Reese F; Carbonell-Sala S; Diekhans M; Liang C; Wang D; Williams B; Adams M; Behera A; Lagarde J et al.
Source: Self-asserted source
Fairlie Reese via Europe PubMed Central

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

Bioinformatics
2021-06-09 | Journal article
Contributors: Fairlie Reese; Ali Mortazavi; Inanc Birol
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Crossref

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

2021-05-13 | Other
Contributors: Jill E. Moore; Xiao-Ou Zhang; Shaimae I. Elhajjajy; Kaili Fan; Fairlie Reese; Ali Mortazavi; Zhiping Weng
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Crossref

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

2021-04-27 | Preprint
Contributors: Elisabeth Rebboah; Fairlie Reese; Katherine Williams; Gabriela Balderrama-Gutierrez; Cassandra McGill; Diane Trout; Isaryhia Rodriguez; Heidi Liang; Barbara J. Wold; Ali Mortazavi
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Crossref

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

2020-06-10 | Preprint
Contributors: Fairlie Reese; Ali Mortazavi
Source: check_circle
Crossref

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

2019-06-18 | Other
Contributors: Dana Wyman; Gabriela Balderrama-Gutierrez; Fairlie Reese; Shan Jiang; Sorena Rahmanian; Stefania Forner; Dina Matheos; Weihua Zeng; Brian Williams; Diane Trout et al.
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Crossref

Peer review (2 reviews for 2 publications/grants)

Review activity for Nature communications (1)
Review activity for PloS one. (1)