Author

Karen W. Cheng

Chan Zuckerberg Biohub San FranciscoORCID 0000-0002-9501-5605Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 1 Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:human· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell signaling & trafficking· 1 Assay:CRISPR screen· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Amy L. KistleriD· 2 shared Duo PengiD· 2 shared Joshua Eric EliasiD· 2 shared Leah C. DormaniD· 2 shared Alan R. LoweiD· 1 shared Alexander Lin· 1 shared Alexander V. HillsleyiD· 1 shared Andreas S. PuschnikiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersMicrobiology

Amy L. KistlerORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

Chad Liu, Alexander V. Hillsley, Madhurya Sekhar, Cassidy Jones, Gabriel Sturm, Taihei Fujimori, Diane M. Wiener, Karen W. Cheng, Talon Chandler, Alexander Lin, Duo Peng, Max Frank, Leah C. Dorman, Ilakkiyan Jeyakumar, Ivan E. Ivanov, , Manuel D. Leonetti

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

bioRxiv · Aug 25, 2026 · PreprintSystems Biology

Replicating without stress: a dengue replicon model reveals distinct host rewiring to accommodate persistence

Karen W. Cheng, Damian Kim, Frank McCarthy, Kuo‐Feng Weng, Leah C. Dorman, Joshua Eric Elias, Amy L. Kistler, Ranen Aviner

This study uses a dengue replicon model to show how host pathways are rewired to support persistent RNA replication without stress responses.

bioRxiv · Sep 27, 2025 · PreprintMicrobiology

Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication

Karen W. Cheng, Madhura Bhave, Andrew L. Markhard, Duo Peng, Karan D. Bhatt, Katherine A. Travisano, Josette V. Medicielo, Sanae Lembirik, Leila Njoya, Manu Anantpadma, Jens H. Kuhn, Andreas S. Puschnik, Amy L. Kistler

This paper develops a CRISPR knockout screening method using viral replicons to identify host factors essential for viral replication, successfully identifying known and novel genes for dengue, chikungunya, and Ebola viruses.

bioRxiv · Jan 9, 2025 · PreprintGenomics