Author

Stephanie A. Nevins

Stanford Medicine

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· 4 Cancer Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 6 Approach:experimental assay· 4 Approach:statistical model· 4 Research Focus:cell type annotation· 3 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Assay:ATAC-seq· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Michael P. SnyderiD· 6 shared Aaron M. HorningiD· 5 shared Edward D. EspliniD· 5 shared William James GreenleafiD· 5 shared Annika K K WeimeriD· 4 shared James M. FordiD· 4 shared Roxanne ChiuiD· 4 shared Teri A. LongacreiD· 4 shared

Activity by Year

2021-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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6 shared papersGenomics

Michael P. SnyderORCID

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Author profile →

6 papers

Recent·Most cited

Polyclonal origins of human premalignant colorectal lesions

Debra Van Egeren, Ryan O. Schenck, Aziz Khan, Aaron M. Horning, Shanlan Mo, Clemens L. Weiß, Edward D. Esplin, Winston R. Becker, Si Wu, Casey Ryan Hanson, Nasim Bararpour, Lihua Jiang, Kévin Contrepois, Hayan Lee, Stephanie A. Nevins, , Christina N. Curtis

This study shows that many premalignant colorectal polyps contain multiple genetic lineages, indicating polyclonal origins rather than single-cell expansion.

Nature · Nov 25, 2025Peer-reviewedCancer Biology

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis

Yizhou Zhu, Hayan Lee, Shannon M. White, Annika K K Weimer, Emma Monte, Aaron M. Horning, Stephanie A. Nevins, Edward D. Esplin, Kristina Paul, Gat Krieger, Zohar Shipony, Roxanne Chiu, Rozelle Laquindanum, Thomas V. Karathanos, Melissa W. Y. Chua, , Michael P. Snyder

This study shows that early colorectal cancer loses promoter-enhancer connectivity, leading to gene expression changes and a two-phase model of transcriptional regulation.

Nature Cancer · Oct 30, 2024Peer-reviewedGenomics

Ultra high-throughput whole-genome methylation sequencing reveals trajectories in precancerous polyps to early colorectal adenocarcinoma

Hayan Lee, Gat Krieger, Tyson A. Clark, Aziz Khan, Casey Ryan Hanson, Yizhou Zhu, Nasim Bararpour, Aaron M. Horning, Edward D. Esplin, Stephanie A. Nevins, Annika K K Weimer, Eti Meiri, Shlomit Gilad, Sima Benjamin, Danit Lebanony, , Michael P. Snyder

The paper uses ultra high-throughput methylation sequencing to study DNA methylation changes during colorectal cancer progression from normal tissue to adenocarcinoma.

bioRxiv · May 30, 2022 · PreprintGenomics

High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron M. Horning, Almudena Espín-Pérez, Roxanne Chiu, Derek C. Chen, Daniel J. Cotter, Edward D. Esplin, Annika K K Weimer, Chiara Caraccio, Vishal Gautham Venkataraaman, Christian M. Schürch, Sarah Black, Maria Brbić, , Michael P. Snyder

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.

bioRxiv · Nov 25, 2021 · PreprintGenomics

Integration and comparison of multi-omics profiles of NGLY1 deficiency plasma and cellular models to identify clinically relevant molecular phenotypes

Songjie Chen, Guangwen Wang, Xiaotao Shen, Daniel Hornburg, Shannon M. Rego, Rene Hoffman, Stephanie A. Nevins, Xun Cheng, Michael P. Snyder

This study integrates metabolomics and proteomics data from NGLY1 deficiency patient samples and cellular models to identify molecular phenotypes linked to immune activation and metabolic disturbances.

bioRxiv · May 28, 2021 · PreprintSystems Biology

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Winston R. Becker, Stephanie A. Nevins, Derek C. Chen, Roxanne Chiu, Aaron M. Horning, Rozelle Laquindanum, Meredith A. Mills, Hassan Chaı̈b, Uri Ladabaum, Teri A. Longacre, Jeanne Shen, Edward D. Esplin, Anshul Bharat Kundaje, James M. Ford, Christina N. Curtis, , William James Greenleaf

The paper uses single-cell data to show a continuum of cell state and composition changes from polyps to colorectal cancer, identifying stem-like cells and regulatory markers.

bioRxiv · Mar 24, 2021 · PreprintGenomics