Author

Benjamin W. Herken

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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Genomics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Assay:bulk RNA-seq· 1 Approach:diffusion model· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Organism:mouse· 1 Research Focus:perturbation response prediction· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Adam Barner· 1 shared Adam J. LittermaniD· 1 shared Ann HuangiD· 1 shared Anusuya Arjavalingam· 1 shared Bárbara González‐TerániD· 1 shared Bo WangiD· 1 shared Byron J. Smith· 1 shared Chloe WangiD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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1 shared paperSystems Biology

Adam Barner

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Author profile →

2 papers

Recent·Most cited

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

Chloe Wang, Mehran Karimzadeh, Neal G. Ravindra, Lexi R. Bounds, Nader Alerasool, Ann Huang, Shihao Ma, Daniel R. Gulbranson, Haotian Cui, Yongju Lee, Anusuya Arjavalingam, Elliot J. MacKrell, Matthew S. Wilken, Jieming Chen, Benjamin W. Herken, , Bo Wang

X-Cell predicts causal perturbation responses across diverse cellular contexts using a diffusion language model trained on a large CRISPRi Perturb-seq dataset.

bioRxiv · Mar 20, 2026 · PreprintSystems Biology

Environmental challenge rewires functional connections among human genes

Benjamin W. Herken, Garrett T. Wong, Thomas M. Norman, Luke A. Gilbert

The paper quantifies how human gene functional connections change under environmental stress, revealing large-scale rewiring of genetic interactions across different conditions.

bioRxiv · Aug 9, 2023 · PreprintGenomics