Author

Timothy Shaw

University of California San DiegoORCID 0000-0002-2484-5724Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Molecular Biology· 3 Pharmacology & Toxicology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Research Focus:differential expression· 3 Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:cell-cell communication· 1 Approach:experimental assay· 1

Frequent Co-Authors

Jens Lykke‐AnderseniD· 3 shared Amit FulzeleiD· 1 shared Anastasia Pimentel· 1 shared Blake SkrableiD· 1 shared Cody OcheltreeiD· 1 shared David PekkeriD· 1 shared Eric J. BennettiD· 1 shared Gene Wei-Ming YeoiD· 1 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersMolecular Biology

Jens Lykke‐AndersenORCID

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4 papers

Recent·Most cited

Molecular BiologyThe EMBO JournalPeer-reviewedDec 5, 2025

Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates

Cody Ocheltree, Blake Skrable, Anastasia Pimentel…·Jens Lykke‐Andersen

The paper investigates human sncRNA 3' end processing, revealing two types of adenylation that influence maturation or degradation.

DOI 10.1038/s44318-025-00655-2

humanbulk RNA-seq

𝕏 PostBluesky

Molecular BiologyRNAPeer-reviewedMay 29, 2025

Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor

Timothy Shaw, Megan E. Dowdle, Yasmeen Ajaj…·Jens Lykke‐Andersen

The paper identifies Angel1 as a key factor in non-stop mRNA decay by showing its role in destabilizing mRNAs lacking stop codons.

5 citations

𝕏 PostBluesky

Pharmacology & ToxicologybioRxivPreprintMay 28, 2024

A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

David Pekker, Steven Kuntz, Monica McArthur…·Swagatam Mukhopadhyay

The paper develops a dose-response model and analysis tool to accurately quantify gene knockdown effects of oligonucleotide-based medicines using next-generation sequencing data.

DOI 10.1101/2024.05.28.596270

bulk RNA-seqstatistical model

𝕏 PostBluesky

Molecular BiologyRNAPeer-reviewedFeb 18, 2022

Tailer: A Pipeline for Sequencing-Based Analysis of Non-Polyadenylated RNA 3' End Processing

Timothy Shaw, Jens Lykke‐Andersen

Tailer quantifies and analyzes RNA 3' end tailing from sequencing data, showing accurate and reproducible results across studies.

3 citations

bulk RNA-seqstatistical model

𝕏 PostBluesky