Author

Zachary Hemminger

University of California, Los Angeles

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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Bioinformatics· 2 Genomics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:mouse· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Research Focus:dimensionality reduction· 2 Research Focus:gene regulatory network inference· 2 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2

Frequent Co-Authors

Roy WollmaniD· 4 shared Jingyi Jessica LiiD· 3 shared Dongyuan SongiD· 2 shared Fangming XieiD· 2 shared Haley De Ocampo· 2 shared Aihui WangiD· 1 shared Douglas V. ArnesoniD· 1 shared Fernando Gómez‐PinillaiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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4 shared papersBioinformatics

Roy WollmanORCID

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Author profile →

4 papers

Recent·Most cited

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

Zachary Hemminger, Gabriela Sanchez-Tam, Haley De Ocampo, Aihui Wang, Thomas J Underwood, Fangming Xie, Qiuying Zhao, Dongyuan Song, Jingyi Jessica Li, Hong‐Wei Dong, Roy Wollman

The paper introduces ATLAS, a method to map transcriptional differences across genetic backgrounds in mouse brains, revealing significant cell type distribution changes between sexes and genetic models.

Nature Methods · Oct 30, 2026Peer-reviewedGenomics

CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments

Zachary Hemminger, Haley De Ocampo, Fangming Xie, Zhiqian Zhai, Jingyi Jessica Li, Roy Wollman

CIPHER optimizes aggregate spatial transcriptomics experiments by jointly designing gene signatures and cell embeddings, improving decoding accuracy and experimental reliability.

PLoS Computational Biology · Jun 4, 2026Peer-reviewedBioinformatics

JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics

Russell Littman, Zachary Hemminger, Robert Foreman, Douglas V. Arneson, Guanglin Zhang, Fernando Gómez‐Pinilla, Xia Yang, Roy Wollman

JSTA improves spatial transcriptomics accuracy by jointly segmenting cells and annotating their types, revealing detailed spatial gene expression patterns in mouse hippocampus.

Molecular Systems Biology · May 31, 2021Peer-reviewedSystems Biology

scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li

scPNMF selects informative genes from scRNA-seq data to improve cell type distinction and enable alignment with targeted gene profiling data.

Bioinformatics · Apr 23, 2021Peer-reviewedBioinformatics