Author

Paul Allegakoen

University of California, San Francisco

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:scRNA-seq· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Franklin W. HuangiD· 2 shared Aaron M. KershneriD· 1 shared Aaron McGeeveriD· 1 shared Aditi AgrawaliD· 1 shared Ahmad Al‐MoujahediD· 1 shared Ahmad N. NabhaniD· 1 shared Alina A. Alam· 1 shared Ankit S. BagheliD· 1 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersCancer Biology

Franklin W. HuangORCID

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Author profile →

3 papers

Recent·Most cited

Histologic variants in bladder cancer harbor aggressive molecular features including TM4SF1 expression and a CA125+ cell state

Heiko Yang, Hanbing Song, Elizabeth Yip, Timothy Gilpatrick, Kevin Chang, Paul Allegakoen, Kevin L. Lu, Keliana S F Hui, Julia H. Pham, Corynn Kasap, Vipul Kumar, Janae Gayle, Bradley A. Stohr, Chien‐Kuang Cornelia Ding, Arun P. Wiita, , Franklin W. Huang

Single cell RNA sequencing of bladder cancer subtypes identified a CA125+ cell state linked to aggressive features and TM4SF1 as a therapeutic target.

Nature Communications · Jun 17, 2025Peer-reviewedCancer Biology

Actionable biological programs to enhance EGFR-targeted therapy response unveiled by single-cell lineage tracing in clinically relevant lung cancer models

Beatrice Gini, Whitney Tamaki, Johnny X. Yu, Dora Barbosa, Wei Wu, Yashar Pourmoghadam, Paul Allegakoen, Donghwa Kim, Sohit Miglani, Sarah Elmes, Victor R. Olivas, Hani Goodarzi, Trever Grant Bivona

This study uses single-cell lineage tracing and RNAseq to identify pre-existing resistant tumor subclones in lung cancer models and their transcriptional programs, revealing mechanisms of therapy resistance.

bioRxiv · May 19, 2025 · PreprintCancer Biology

Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets

Jia Zhao, Gefei Wang, Jingsi Ming, Zhixiang Lin, Yang Wang, Snigdha Agarwal, Aditi Agrawal, Ahmad Al‐Moujahed, Alina A. Alam, Megan A. Albertelli, Paul Allegakoen, Thomas H. Ambrosi, Jane Antony, Steven E. Artandi, Fabienne Aujard, , Patricia Kim Phuong Nguyen

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

Nature Computational Science · May 30, 2022Peer-reviewedBioinformatics