Publications

Wang, K. Ait-Ahmad, K., Kupp, S., Eksi, S.E.^, Chang, Y.H.^

UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging.

Cell Reports Methods Volume 5, Issue 9, 101172 (2025).

Kupp, S.D., VanGordon, I.A., Gönen, M., Esener, S., Eksi, S.E., Ak, C^.

Interpretable and integrative analysis of single-cell multiomics with scMKL.

Commun Biol 8, 1160 (2025).

doi.org/10.1038/s42003-025-08533-7

Sims, Z., Govindarajan, S., Mills, G.B., Eksi, S.E., Chang, Y.H.

Language of Stains: Tokenization Enhances Multiplex Immunofluorescence and Histology Image Synthesis.

Medical Image Computing and Computer Assisted Intervention (MICCAI 2025).

Fredrikson, J.P., Roth, D.M., Cosgrove, J.A., Sener, G., Crow, L.A., Eckenstein, K., Wu, L., Hosseini, M., Thomas, G., Eksi, S.E., Bertassoni, L.^

Engineering Neuronal Networks in Jammed Microgels to Innervate Bioprinted Cancer Organoids On-a-Chip.

Lab on a Chip (2025).

doi: 10.1039/d5lc00134j

Sattler, A, Korzun, T, Gupta, K., Diba, P., Kyprianou, N., Eksi, S.E.^

Sympathetic nerve signaling rewires the tumor microenvironment; a shift in 'microenvironmental-ity'.

Cancer and Metastasis Rev 44, 25 (2025).

doi: 10.1007/s10555-025-10241-x

Ait-Ahmad, K., Ak, C., Thibault, G., Chang, Y.H., Eksi, S. E.^

Axonfinder: Automated Segmentation of Tumor Innervating Neuronal Fibers.

Heliyon (2025).

doi: 10.2139/ssrn.4931895

Ak, C., Sayar, Z., Thibault, G., Burlingame, E., Kuykendall, M.J., Eng, J., Chitsazan, A., Adey, A., Boniface, C., Spellman, P., Thomas, G.T., Ryan, P., Chan, Y.H., Demir, E., Stavrinides, V. Eksi, S.E.^

Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in microenvironment.

iScience (2024).

doi.org/10.1016/j.isci.2024

Gustafson, K., Sayar, Z., Le, Hillary, Gower, A., Civitci, F., Ibsen, S., Modestino, A., Heller, M., Esener, S., Eksi, S.E.^

Oligo-tagged antibodies enable multiplex protein detection in liquid biopsy assays for prostate cancer patient stratification.

Electrophoresis (2024).

doi: 10.1002/elps.202400088

Stavrinides, V.^, Eksi, S.E., Finn, R., Texeira-Mendes, L., Rana, S., Trahearn, N., Grey, A., Giganti, F., Huet, E., Fiard, G., Freeman, A., Haider, A., Allen, C., Kirkham, A., Cole, A.P., Punwani, S., Pashayan, N., Emberton, M., Moore, C.M., Orczyk, C.

MRI follow up of targeted biopsy-negative prostate lesions.

European Urology Focus (2023).

doi.org/10.1016/j.euf.2023.03.011

Gustafson, K., Sayar, Z., Le, Hillary, Gower, A., Ibsen, S., Modestino, A., Heller, M., Esener, S.^, Eksi, S.E.^

Cyc-DEP: Cyclic immunofluorescence profiling of particles collected using dielectrohoresis.

Electrophoresis (2022).

doi: 10.1002/elps.202200001. PMID: 35753078.

Eksi, S.E.^, Chitsazan, A., Sayar, Z., Thomas, G., Fields, A., Kopp, R., Spellman, P., Adey, A.^

Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

Nat Commun 12, 7292 (2021).

doi.org/10.1038/s41467-021-27615-8

Eksi, S.E., Saldivar, J.C.

Cohesin is out for stalled replication stress.

Developmental Cell. Volume 52, Issue 6, P675-676 (2020).

Schau, G., Sayar, Z., Burlingame, E.A., Eng, J., Eksi, S.E., Gray, J.W., Chang, Y.H.^

Estimating Mutual Information Content of Biomedical Data Modalities through Self-Supervised Domain Translation in Prostate Cancer.

Learning Meaningful Representation of Life (NeurIPS) (2019).

Eksi, S.E., Barmina, O., McCallough, C.L., Kopp, A., Orenic, T.V.^

A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila.

PLoS Genetics 14(4): e1007320 (2018).