Author

Benjamin A. Nanes

The University of Texas Southwestern Medical CenterORCID 0000-0001-9686-1611Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:benchmarking· 1 Organism:human· 1 Assay:imaging· 1 Research Focus:perturbation response prediction· 1 Assay:scRNA-seq· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Andrew D. WeemsiD· 1 shared Andrew R. JamiesoniD· 1 shared Bo-Jui ChangiD· 1 shared Clarence YappiD· 1 shared Edward M. JenkinsiD· 1 shared Felix ZhouiD· 1 shared Gabriel Muhire GihanaiD· 1 shared Galen T SquiersiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Andrew D. WeemsORCID

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2 papers

Recent·Most cited

Perturb-seq resolves physiologic programs and bidirectional regulation of non-canonical NF-κB signaling in epidermal organoids

Galen T Squiers, Benjamin A. Nanes, Maggie M. Balas, Joshua J. Lingo, L H Wang, Huan Zhao, Sabahat Munawar, Mpathi Nzima, Gary C. Hon, Jason C. Klein

The paper uses Perturb-seq in epidermal organoids to study non-canonical NF-κB signaling's role in keratinocyte differentiation.

bioRxiv · Jul 23, 2026 · PreprintGenomics

Universal consensus 3D segmentation of cells from 2D segmented stacks

Felix Zhou, Zach Marin, Clarence Yapp, Qiongjing Zou, Benjamin A. Nanes, Stephan Daetwyler, Andrew R. Jamieson, Md Torikul Islam, Edward M. Jenkins, Gabriel Muhire Gihana, Jinlong Lin, Hazel M. Borges, Bo-Jui Chang, Andrew D. Weems, Sean J. Morrison, , Gaudenz M. Danuser

The paper introduces u-Segment3D, a tool that converts 2D cell segmentations into 3D consensus segmentations without training data, demonstrating effectiveness across diverse datasets.

Nature Methods · Nov 1, 2025Peer-reviewedBioinformatics