Author

Sebnem Ece Eksi

Oregon Health & Science UniversityORCID 0000-0003-1012-5571Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Assay:spatial transcriptomics· 2 Approach:statistical model· 2 Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Approach:deep learning· 1

Frequent Co-Authors

Kaoutar Ait-AhmadiD· 3 shared Young Hwan ChangiD· 3 shared Çiğdem AkiD· 2 shared Gordon Brent MillsiD· 2 shared Zachary SimsiD· 2 shared Eric M. CrameriD· 1 shared Guillaume ThibaultiD· 1 shared Jessica X. YuiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Kaoutar Ait-AhmadORCID

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3 papers

Recent·Most cited

miniMTI: minimal multiplex tissue imaging enhances biomarker expression prediction from histology

Young Hwan Chang, Zachary Sims, Sandhya Govindarajan, Kaoutar Ait-Ahmad, Çiğdem Ak, Marigold Kuykendall, Gordon Brent Mills, Sebnem Ece Eksi

miniMTI reduces the number of molecular markers needed for multiplex tissue imaging by combining H&E with a few measured markers, preserving biological and clinical information.

bioRxiv · Jan 23, 2026 · PreprintBioinformatics

UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging

Kunlun Wang, Kaoutar Ait-Ahmad, Sam Kupp, Zachary Sims, Eric M. Cramer, Zeynep Sayar, Jessica X. Yu, Melissa H. Y. Wong, Gordon Brent Mills, Sebnem Ece Eksi, Young Hwan Chang

UniFORM normalizes multiplex tissue imaging data by aligning negative populations and preserving positive variation, outperforming existing methods in batch effect mitigation and downstream analysis.

Cell Reports Methods · Sep 1, 2025Peer-reviewedBioinformatics

AxonFinder: Automated segmentation of tumor innervating neuronal fibers

Kaoutar Ait-Ahmad, Çiğdem Ak, Guillaume Thibault, Young Hwan Chang, Sebnem Ece Eksi

AxonFinder segments axons in prostate tumor microenvironments using deep learning, showing correlation between axon density and cancer risk.

Heliyon · Dec 14, 2024Peer-reviewedSystems Biology