Author

Rebecca Raphael

University of Pittsburgh

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· 1 Cell Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:human· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:clustering· 1 Research Focus:development & morphogenesis· 1

Frequent Co-Authors

Aatur Dilip SinghiiD· 2 shared Shikhar UttamiD· 2 shared Akram S. ShalabyiD· 1 shared Angela EnriqueziD· 1 shared Benjamin Raymond· 1 shared Bogdan KochetoviD· 1 shared Brenda B. DiergaardeiD· 1 shared Brian J. LeibowitziD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersSystems Biology

Aatur Dilip SinghiORCID

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Author profile →

3 papers

Recent·Most cited

SpaReg: sparsity-based 3D reconstruction of tissue microenvironments at native resolution across morphological and spatial molecular modalities

Rajdeep Pawar, Thomas Jacob, Rebecca Raphael, Elaine Byrnes, Simon C. Watkins, Thing Rinda Soong, Aatur Dilip Singhi, Shikhar Uttam

SpaReg reconstructs 3D tissue microenvironments from histology, spatial proteomics, and spatial transcriptomics data, preserving morphology and enabling accurate classification and disease modeling.

bioRxiv · Sep 29, 2026 · PreprintSystems Biology

Evolution and instability of human centromeres are accelerated by heterochromatin boundary loss and CENP-A overexpression

Megan A. Mahlke, Angela Enriquez, Lior Lumerman, Poulomi Nath, Cy Chittenden, Savannah J. Hoyt, Jonas Koeppel, Yuan Xu, Rebecca Raphael, Kylie Zaffina, Paul W. Hook, Winston Timp, Karen H. Miga, Peter J. Campbell, Rachel J. O’Neill, , Yael Nechemia‐Arbely

The paper shows that human centromeres and neocentromeres evolve epigenetically, with instability linked to loss of heterochromatin boundaries and CENP-A overexpression.

Cell Reports · Aug 1, 2026Peer-reviewedCell Biology

UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples

Bogdan Kochetov, Phoenix D. Bell, Paulo S. Garcia, Akram S. Shalaby, Rebecca Raphael, Benjamin Raymond, Brian J. Leibowitz, Karen Elizabeth Schoedel, Rhonda M. Brand, Randall E. Brand, Jian Yu, Lin Zhang, Brenda B. Diergaarde, Robert E. Schoen, Aatur Dilip Singhi, Shikhar Uttam

UNSEG provides an unsupervised method for segmenting cells and their nuclei in complex tissue samples without training data, outperforming deep learning methods in generalization and consistency.

Communications Biology · Aug 30, 2024Peer-reviewedBioinformatics