Single cell biotechnology and spatial omics

    Publications

    Refereed Book Chapters

    * T. Hu, N. Zhang, M. Venkatesan, C. M. Schürch, G. P. Nolan, and A. F. Coskun, “High-Definition CODEX for 3D Multiplex Cell Spatial Phenotyping” in Revealing Uncharted Biology with Single-Cell Proteomic Technologies: Current Available Platforms, W. Fantl Ed. Elsevier Inc., 191-216, 2024.

    * A. Kumar, S. Cai, M. Allam, S. Henderson, M. Ozbeyler, L. Saiontz, and A. F. Coskun, “Single Cell and Spatial Analysis of Emergent Organoid Platforms” in Cancer Systems and Integrative Biology Edition, U. Kasid and R. Clarke Eds; Springer Nature, 311–344, 2023.

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    Published and Accepted Journal Articles

    Sater S et al. “Society for Immunotherapy of Cancer: Standards for Reporting of Multiplex Immunohistochemistry/Immunofluorescence Assays (STORMI),” Journal for ImmunoTherapy of Cancer. 13:e012280 (2025). LINK

    * S. Dembowitz, F. Rivera Moctezuma, N. Zhang, A. Venkataraman, and A. F. Coskun, “Untangling the fusion of spatial omics and mechanobiology,” Prog. Biomed. Eng. 8 012009 DOI 10.1088/2516-1091/ae16f2 (2026). [Link]

    * H. Torres, E. Ozturk, Z. Fang, N. Zhang, S. Cai, N. Sarkar, and A. F. Coskun, “What is a “Good” figure: Scoring of biomedical data visualization,” PLoS One 20(11): e0336917. https://doi.org/10.1371/journal.pone.0336917, (2025). [Link]

    * E. Ozturk, F. G. Rivera Moctezuma, and A. F. Coskun, “MetaboFM: A Foundation Model for Spatial Metabolomics,” BioRxiv, 2025. [Link]

    * N. Zhang, Z. Fang, P. Kadakia, J. Guo, D. Vijay, M. Thapa, S. Dembowitz, A. Grakoui, and A. F. Coskun, “Modular, Open-Sourced Multiplexing for Democratizing Spatial Omics,” Lab on a Chip, 2025. [Link]

    * Z. Fang, K. Krusen, H. Priest, M. Wang, S. Kim, A. Sriram, A. Yellaki, A. Singh, E. Horwitz, A. F. Coskun, “Graph-based 3D spatial gene neighborhood networks of single cells in gels and tissues,” BME Frontiers (Science Partner Journal), 6, 0110, 2025 [Link]

    * R. Ringquist, E. Bhatia, P. Chatterjee, D. Maniar, Z. Fang, P. Franz, L. Kramer, D. Ghoshal, N. Sonthi, E. Downey, J. Canlas, A. Ochal, S. Agarwal, V. Cuellar, G. Harrigan, A. F. Coskun, A. Singh, K. Roy, “Modeling the Human Immune Response to Severe Influenza Infection in an Immunocompetent Lung-on-Chip,” Nature Biomedical Engineering, 2025. https://doi.org/10.1038/s41551-025-01491-9 [Link]

    * Y. Qiu, J. Lin, A. Wang, Z. Fang, Y. Sakurai, H. Choi, E. K. Williams, E. T. Hardy, K. Maher, A. F. Coskun, G. Woods, W. A. Lam, “Clinically relevant clot resolution via a thromboinflammation-on-a-chip,” Nature, 2025. [Link]

    * D. Ghoshal, I. Petersen, R. Ringquist, L. Kramer, E. Bhatia, T. Hu , A. Richard, R. Park, J. Corbin, S. Agarwal, A. Thomas, S. Ramirez, J. Tharayil, E. Downey, F. Ketchum, A. Ochal, N. Sonthi, S. Lonial, J.N. Kochenderfer, R. Tran, M. Zhu, W.A. Lam, A.F. Coskun, K. Roy, “Multi-niche human bone marrow on-a-chip for studying the interactions of adoptive CAR-T cell therapies with multiple myeloma,” Biomaterials, May; 316:123016, 2025. [Link]

    * A. Venkataraman, I. Kordic, J. Li, N. Zhang, N. S. Bharadwaj, Z. Fang, S. Das, and A. F. Coskun, “Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics,” npj Aging 10, 57, 2024 [Link]

    * N. Zhang, M. Wang, D. Nambiar, S. Iyer, P. Kadakia, Q. Luo, S. Pang, A. Qu, N. S. Bharadwaj, P. Qiu, and A. F. Coskun, “High cell throughput, programmable fixation reveals the RNA and protein co-regulation with spatially resolved NFκB pseudo-signaling,” APL Bioengineering. 8 (4): 046108, 2024. [Link]

    * E. Ozturk, A. Venkataraman, F. G. Rivera Moctezuma, A. F. Coskun, “Super Resolved Single-Cell Spatial Metabolomics from Multimodal Mass Spectrometry Imaging guided by Imaging Mass Cytometry,” BioRxiv, 2024. [Link]

    * S. Cai, T. Hu, A. Venkataraman, F.  G. Rivera Moctezuma, E. Ozturk, N. Zhang, M. Wang, T. Zvidzai, S. Das, A. Pillai, F. Schneider, S. S. Ramalingam, Y. Oh, S.Y. Sun, and A. F. Coskun, “’Spatially resolved subcellular protein–protein interactomics in drug-perturbed lung-cancer cultures and tissues,” Nature Biomedical Engineering, doi: 10.1038/s41551-024-01271-x, 2024. [Link]

    * N. Zhang, S. Cai, M. Wang, T. Hu, F. Schneider, S.Y. Sun, and A. F. Coskun, “Graph-based spatial proximity of super-resolved protein-protein interactions predicts cancer drug responses in single cells,” Cellular and Molecular Bioengineering, Young Innovator, doi: 10.1007/s12195-024-00822-1, 2024. [Link]

    * Z. Zhong, M. Quiñones-Pérez, Z. Dai, V. M. Juarez, E. Bhatia, C. R. Carlson, S. B. Shah, A. Patel, Z. Fang, T. Hu, M. Allam, S. L. Hicks, M. Gupta, S. L. Gupta, E. Weeks, S. D. Vagelos, A. Molina, A. Mulero-Russe, A. Mora-Boza, D. J. Joshi, R. P. Sekaly, T. Sulchek, S. L. Goudy, J. Wrammert, K. Roy, J. M. Boss, A. F. Coskun, C. D. Scharer, A. J. García, J. L. Koff, and A. Singh, “Human immune organoids to decode B cell response in healthy donors and patients with lymphoma,” Nature Materials, doi: 10.1038/s41563-024-02037-1, 2024. [Link]

    * M Allam and A F Coskun, “Combining spatial metabolomics and proteomics profiling of single cells,” Nature Reviews Immunology, 24, 701, 2024. [Link]

    * M Allam, T Hu, Z Fang, A Singh**, A F Coskun**, “Spatial Immunophenotyping using Multiplexed Imaging of Immune Follicles in Secondary Lymphoid Tissues,” PNAS Nexus, 3, 8, pgae285, 2024. [Link]

    * T. Hu, Allam, S. Cai, W. Henderson, B. Yueh, A. Garipcan, A. Ievlev, M. Afkarian, S. Beyaz, and A. F Coskun, “Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology,” Nature Communications, 14, 8260, 2023. [Link]

    * N. Zhang, D. Ohlstrom, S. Pang, N. Bharadwaj, A. Qu, H. Grossniklaus, and A. F. Coskun, “Tissue Spatial Omics Dissects Organoid Biomimicry,” GEN Biotechnology, 2:5, 372-383, 2023.

    * D. Li, Z.  Fang, Q. Shi, N. Zhang, B. Gong, W. Tong, A. F. Coskun, and J. Xu, “Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application,” Journal of Pharmaceutical Analysis, 13(7): 691-693, 2023.

    * Z. Fang, A. Ford, T. Hu, N. Zhang, A. Mantalaris, and A.  F. Coskun, “Subcellular spatially resolved gene neighborhood networks in single cells,” Cell Reports Methods, 100476, 2023.

    * M. Venkatesan, N. Zhang, B. Marteau, Y. Yajima, N. Garcia, Z. Fang, T. Hu, S. Cai, A. Ford, H. Olszewski, A. Borst, and A. F. Coskun, “Spatial subcellular organelle networks in single cells,” Scientific Reports, 13, 5374, 2023.

    * S. Shah, C. Carlson, K. Lai, Z. Zhong, G. Marsico, K. Lee, N. Félix-Velez, E. Abeles, M. Allam, T. Hu, L. Walter, K. Martin, K. Gandhi, S. Butler, R. Puri, A. McCleary-Wheeler, W. Tam, O. Elemento, K. Takata, C. Steidl, D. Scott, L. Fontan, H. Ueno, B. Cosgrove, G. Inghirami, A. García, A. F. Coskun, J. Koff, A. Melnick, and A. Singh, “Combinatorial Targeting of Aberrant Signaling Pathways in Lymphomas Rescues Lymphoid Tumor Microenvironment-mediated attenuation of MALT1 inhibitors,” Nature Materials, vol. 22, no. 511–523. 2023.

    * Yanai, E.J. Fertig, M. Li, F. Coscia, J. Klughammer, Q. Nie, J. Chen, and A. F. Coskun, “What do you most hope spatial molecular profiling will help us understand? Part 2,” Cell Systems, vol. 14, no. 7, p. 543–546, 2023.

    * M. Allam, T. Hu, J. Lee, J. Aldrich, S. Badve, Y. Polar, M. Bhave, S. Ramalingam, F. Schneider, and A. F. Coskun, “Spatially variant immune infiltration scoring in human cancer tissues,” npj Precision Oncology, 6, no. 1, p. 60, 2022.

    * S. Cai, Hu, M. Venkatesan, M. Allam, F. Schneider, S. S. Ramalingam, S.Y. Sun, and A. F. Coskun, “Multiplexed protein profiling reveals spatial subcellular signaling networks,” iScience, vol. 25, no. 9, p. 104980, 2022.

    * J. Mosquera, S. Kim, R. Bareja, Z. Fang, S. Cai, H. Pan, M. Asad, M.L. Martin, M. Sigouros, F. M. Rowdo, S. Ackermann, J. Capuano, J. Bernheim, C. Cheung, A. Doane, N. Brady, R. Singh, D. S. Rickman, V. Prabhu, J.E. Allen, L. Puca, A.F. Coskun, M.A. Rubin, H. Beltran, J. M. Mosquera, O. Elemento, A. Singh, “Extracellular Matrix in Synthetic Hydrogel-Based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 Inhibitors,” Advanced Materials, vol. 34, no. 2, p. e2100096, 2022.

    * S. Ganesh, T. Hu, Woods, M. Allam, S. Cai, W. Henderson, and A. F. Coskun, “Spatially resolved 3D metabolomic profiling in tissues,” Science Advances, vol. 7, no. 5, p. eabd0957, 2021.

    * Allam, T. Hu, S. Cai, K. Laxminarayanan, R. B. Hughley, and A. F. Coskun, “Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease,” Commun. Biol., vol. 4, no. 1, p. 632, 2021.

    * Y. Guo, H. Lee, Z. Fang, A. Velalopoulou, J. Kim, M.B. Thomas, J. Liu, R.G. Abramowitz, Y. Kim, A.F. Coskun, D.P. Krummel, S. Sengupta, T.J. MacDonald, and C. Arvanitis, “Single-cell analysis reveals effective siRNA delivery in brain tumors with microbubble-enhanced ultrasound and cationic nanoparticles,” Science Advances, vol. 7, no. 18, p. eabf7390, 2021.

    * A. F. Coskun, G. Han, S. Ganesh, S.Y. Chen, X.R. Clavé, S. Harmsen, S. Jiang, C.M. Schürch, Y. Bai, C. Hitzman, and G.P. Nolan. “Nanoscopic subcellular imaging enabled by ion beam tomography,” Nature Communications, vol. 12, no. 1, p. 789, 2021.

    X. Rovira-Clavé, S. Jiang, Y. Bai, B. Zhu, G. Barlow, S. Bhate, A.F. Coskun, G. Han, C.K. Ho, C. Hitzman, S.Y. Chen, F.A. Bava,and G.P. Nolan. “Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging,” Nature Communications, vol. 12, no. 1, p. 4628, 2021.

    * M. Venkatesan, H. Mohan, J.R. Ryan, C.M. Schürch, G.P. Nolan, D.H. Frakes, and A.F. Coskun. “Virtual and augmented reality for biomedical applications,” Cell Reports Medicine, vol. 2, no. 7, p. 100348, 2021.

    * S. Ganesh, B. Utebay, J. Heit, and A. F. Coskun, “Cellular sociology regulates the hierarchical spatial patterning and organization of cells in organisms,” Open Biology, vol. 10, no. 12, p. 200300, 2020,

    * M. Allam, S. Cai, and A. F. Coskun, “Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics,” npj Precision Oncology, vol. 4, p. 11, 2020.

    * S. Cai, M. Allam, and A. F. Coskun, “Multiplex Spatial Bioimaging for Combination Therapy Design,” Trends Cancer, vol. 6, no. 10, pp. 813–818, 2020.

    * M. Allam, S. Cai, S. Ganesh, M. Venkatesan, S. Doodhwala, Z. Song, T. Hu, A. Kumar, J. Heit, COVID-19 Study group, A.F. Coskun, “COVID-19 Diagnostics, Tools, and Prevention,” Diagnostics, vol. 10, no. 6, p. E409, 2020.

    * S. Harmsen, A. F. Coskun, S. Ganesh, G. P. Nolan, and S. S. Gambhir, “Isotopically Encoded Nanotags for Multiplexed Ion Beam Imaging,” Advanced Materials Technologies, vol. 5, no. 7, p. 2000098, 2020.

    * M. Venkatesan and A. F. Coskun, “Digital posters for interactive cellular media and bioengineering education,” Communications Biology, vol. 2, p. 455, 2019.

    A. F. Coskun, S. N. Topkaya, A. K. Yetisen, and A. E. Cetin, “Portable Multiplex Optical Assays,” Advanced Optical Materials vol. 7, p. 1801109, 2019.

    S. Knowlton, A. Joshi, P. Syrrist, A. F. Coskun, and S. Tasoglu, “3D-printed smartphone-based point of care tool for fluorescence- and magnetophoresis-based cytometry,” Lab. Chip, vol. 17, no. 16, pp. 2839–2851, 2017.

    A. F. Coskun, U. Eser, and S. Islam, “Cellular identity at the single-cell level,” Mol. Biosyst., vol. 12, no. 10, pp. 2965–2979, 2016.

    A. F. Coskun and L. Cai, “Dense transcript profiling in single cells by image correlation decoding,” Nat. Methods, vol. 13, no. 8, pp. 657–660, 2016.

    A. K. Yetisen, A. F. Coskun, G. England, S. Cho, H. Butt, J. Hurwitz, M. Kolle, A. Khademhosseini, A. J. Hart, A. Folch, S. H. Yun, “Art on the Nanoscale and Beyond,” Advanced Materials, vol. 28, no. 9, pp. 1724–1742, 2016.

    A. K. Yetisen, J. Davis, A. F. Coskun, G. M. Church, and S. H. Yun, “Bioart,” Trends Biotechnol., vol. 33, no. 12, pp. 724–734, 2015.

    A. K. Yetisen, L. R. Volpatti, A. F. Coskun, S. Cho, E. Kamrani, H. Butt, A. Khademhosseini, and S. H. Yun, “Entrepreneurship,” Lab. Chip, vol. 15, no. 18, pp. 3638–3660, 2015.

    E. Lubeck, A. F. Coskun, T. Zhiyentayev, M. Ahmad, and L. Cai, “Single-cell in situ RNA profiling by sequential hybridization,” Nat. Methods, vol. 11, no. 4, pp. 360–361, 2014.

    A. F. Coskun, A. E. Cetin, B. C. Galarreta, D. A. Alvarez, H. Altug, and A. Ozcan, “Lensfree optofluidic plasmonic sensor for real-time and label-free monitoring of molecular binding events over a wide field-of-view,” Sci. Rep., vol. 4, p. 6789, 2014.

    A. F. Coskun and A. Ozcan, “Computational imaging, sensing and diagnostics for global health applications,” Curr. Opin. Biotechnol., vol. 25, pp. 8–16, 2014.

    I. Sencan, A. F. Coskun, U. Sikora, and A. Ozcan, “Spectral demultiplexing in holographic and fluorescent on-chip microscopy,” Sci. Rep., vol. 4, p. 3760, 2014.

    A. Cetin, A.F. Coskun, B. Galarreta, M. Huang, D. Herman, A. Ozcan, and H. Altug, “Handheld high-throughput plasmonic biosensor using computational on-chip imaging,” Light Sci Appl vol. 3, p. e122, 2014.

    O. Mudanyali, E. McLeod, W. Luo, A. Greenbaum, A. F. Coskun, Y. Hennequin, C. P. Allier, and A. Ozcan, “Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses,” Nat. Photonics, vol. 7, no. 3, 2013.

    A. F. Coskun, R. Nagi, K. Sadeghi, S. Phillips, and A. Ozcan, “Albumin testing in urine using a smart-phone,” Lab. Chip, vol. 13, no. 21, pp. 4231–4238, 2013.

    I. Navruz, A. F. Coskun, J. Wong, S. Mohammad, D. Tseng, R. Nagi, S. Phillips, and A. Ozcan, “Smart-phone based computational microscopy using multi-frame contact imaging on a fiber-optic array,” Lab. Chip, vol. 13, no. 20, pp. 4015–4023, 2013.

    A. F. Coskun, J. Wong, D. Khodadadi, R. Nagi, A. Tey, and A. Ozcan, “A personalized food allergen testing platform on a cellphone,” Lab. Chip, vol. 13, no. 4, pp. 636–640, 2013.

    A. Greenbaum, W. Luo, B. Khademhosseinieh, T. W. Su, A. F. Coskun, and A. Ozcan, “Increased space-bandwidth product in pixel super-resolved lensfree on-chip microscopy,” Scientific Reports vol. 3, p. 1717, 2013.

    S. A. Arpali, C. Arpali, A. F. Coskun, H.-H. Chiang, and A. Ozcan, “High-throughput screening of large volumes of whole blood using structured illumination and fluorescent on-chip imaging,” Lab. Chip, vol. 12, no. 23, pp. 4968–4971, 2012.

    S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, “Giga-pixel lensfree holographic microscopy and tomography using color image sensors,” PloS One, vol. 7, no. 9, p. e45044, 2012.

    A. Greenbaum, W. Luo, T. W. Su, Z. Göröcs, L. Xue, S. O. Isikman, A. F Coskun, O. Mudanyali, and A. Ozcan, “Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy,” Nat. Methods, vol. 9, no. 9, pp. 889–895, 2012.

    A. F. Coskun, T.-W. Su, I. Sencan, and A. Ozcan, “Lensless fluorescent microscopy on a chip,” J. Vis. Exp. JoVE, no. 54, p. 3181, 2011.

    Q. Zhu, S. Mavandadi, A. F. Coskun, O. Yaglidere, and A. Ozcan, “Optofluidic fluorescent imaging cytometry on a cell phone,” Anal. Chem., vol. 83, no. 17, pp. 6641–6647, 2011.

    A. F. Coskun, I. Sencan, T.-W. Su, and A. Ozcan, “Wide-field lensless fluorescent microscopy using a tapered fiber-optic faceplate on a chip,” The Analyst, vol. 136, no. 17, pp. 3512–3518, 2011.

    A. F. Coskun, I. Sencan, T.-W. Su, and A. Ozcan, “Lensfree fluorescent on-chip imaging of transgenic Caenorhabditis elegans over an ultra-wide field-of-view,” PloS One, vol. 6, no. 1, p. e15955, 2011.

    B. Khademhosseinieh, G. Biener, I. Sencan, T.-W. Su, A. F. Coskun, and A. Ozcan, “Lensfree sensing on a microfluidic chip using plasmonic nanoapertures,” Appl. Phys. Lett., vol. 97, no. 22, p. 221107, 2010.

    W. Bishara, T.-W. Su, A. F. Coskun, and A. Ozcan, “Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution,” Opt. Express, vol. 18, no. 11, pp. 11181–11191, 2010.

    A. F. Coskun, I. Sencan, T.-W. Su, and A. Ozcan, “Lensless wide-field fluorescent imaging on a chip using compressive decoding of sparse objects,” Opt. Express, vol. 18, no. 10, pp. 10510–10523, 2010.

    A. F. Coskun, T.-W. Su, I. Sencan, and A. Ozcan, “Lensfree Fluorescent On-Chip Imaging using Compressive Sampling,” Opt. Photonics News, vol. 21, no. 12, p. 27, 2010.

    B. Khademhosseinieh, I. Sencan, G. Biener, T. W. Su, A. F. Coskun, D. Tseng, and A. Ozcan, “Lensfree on-chip imaging using nanostructured surfaces,” Appl. Phys. Lett., vol. 96, no. 17, p. 171106, Apr. 2010.

    A. F. Coskun, T.-W. Su, and A. Ozcan, “Wide field-of-view lens-free fluorescent imaging on a chip,” Lab. Chip, vol. 10, no. 7, pp. 824–827, Apr. 2010, doi: 10.1039/b926561a.

    A. Sennaroglu, A. F. Coskun, and U. Demirbas, “Analysis of solid-state saturable absorbers with temperature dependent absorption cross-sections,” Opt. Mater., vol. 31, no. 4, pp. 598–603, 2009.

    A. Kiraz, Y. Karadağ, and A. F. Coskun, “Spectral tuning of liquid microdroplets standing on a superhydrophobic surface using electrowetting,” Appl. Phys. Lett., vol. 92, no. 19, p. 191104, 2008.