Student Tracker Search

Poorna R, Chen WW, Qiu P, Cicerone MT. Toward Gene-Correlated Spatially Resolved Metabolomics with Fingerprint Coherent Raman Imaging. J Phys Chem B. 2023 Jun 29;127(25):5576-5587. doi: 10.1021/acs.jpcb.3c01446. Epub 2023 Jun 13. Erratum in: J Phys Chem B. 2023 Aug 24;127(33):7416. PMID: 37311254; PMCID: PMC10316396.

• Zijun Gao, Keyi Han, Xuanwen Hua, Wenhao Liu, Shu Jia, "hydroSIM: super-resolution speckle illumination microscopy with a hydrogel diffuser," Biomed. Opt. Express 15, 3574 (2024)

• Huang, Xinyuan, Xiujuan Gao, and Ling Fu. "BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images." Bioinformatics 40.2 (2024): btae052.
• Tadesse, Kidan, et al. "Three-dimensional multifocal scanning microscopy for super-resolution cell and tissue imaging." Optics Express 31.23 (2023): 38550-38559.
• Lim, Sumin, et al. "Multiphoton super-resolution imaging via virtual structured illumination." arXiv preprint arXiv:2404.11849 (2024).
• WANG, GUAN, et al. "Grating-free autofocus for single-pixel microscopic imaging."

Weiss DA*, Borsa AM*, Pala A, Sederberg AJ, Stanley GB. A machine learning approach for real-time cortical state estimation. J Neural Eng. 2024 Feb 1;21(1):10.1088/1741-2552/ad1f7b. doi: 10.1088/1741-2552/ad1f7b. PMID: 38232377; PMCID: PMC10868597.

1. S. Dembowitz, F. G. Rivera Moctezuma, N. Zhang, A. Venkataraman, and A. F.
Coskun, “Untangling the fusion of spatial omics and mechanobiology,” Progress in
Biomedical Engineering, vol. 8, no. 1, p. 012009, 2026.
2. J. Li, N. Zhang, S. Sirigireddy, L. Ramanan, D. Vijay, M. Thapa, A. Grakoui, and A.
F. Coskun, “Spatially resolved multiplex protein profiling reveals DNA methylation-
dependent microenvironmental remodeling in liver fibrosis,” PNAS Nexus, p. pgag047,
2026.
3. 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, vol. 25, no. 20, pp. 5379–5392, 2025.
4. 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, vol. 20,
no. 11, p. e0336917, 2025.
5. 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, vol. 8, no. 4, p. 046108, 2024.
6. 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.-T. 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,
pp. 1–23, 2024.
7. N. Zhang, S. Cai, M. Wang, T. Hu, F. Schneider, S.-Y. Sun, and A. F. Coskun,
169
“Graph-based spatial proximity of super-resolved protein–protein interactions pre-
dicts cancer drug responses in single cells,” Cellular and Molecular Bioengineering,
vol. 17, pp. 467–490, 2024.
8. 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 bio-
materials, microfluidics, and spatial omics,” npj Aging, vol. 10, no. 1, pp. 1–27,
2024.
9. H. E. Grossniklaus, N. Zhang, C. Morote Garcia, A. Coskun, J. T. Sellers, Y. Yan,
K. Bostwick, and H. Yang, “The role of macrophages in vascular formation in uveal
melanoma,” Investigative Ophthalmology & Visual Science, vol. 64, no. 8, p. 900,
2023.
10. 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, vol. 13, no. 7, pp. 691–693, 2023.
11. Z. Fang, A. J. Ford, T. Hu, N. Zhang, A. Mantalaris, and A. F. Coskun, “Subcel-
lular spatially resolved gene neighborhood networks in single cells,” Cell Reports
Methods, vol. 3, no. 5, p. 100476, 2023.
12. N. Zhang, D. Ohlstrom, S. Pang, N. S. Bharadwaj, A. Qu, H. Grossniklaus, and A. F.
Coskun, “Tissue spatial omics dissects organoid biomimicry,” GEN Biotechnology,
vol. 2, no. 5, pp. 372–383, 2023.
13. M. Venkatesan, N. Zhang, B. Marteau, Y. Yajima, N. Ortiz De Zarate 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, vol. 13, no. 1, p.
5374, 2023.

Ehrlich S, VandeLoo AD, Badawy M, Gonzalez MM, Stockslager M, Yang A, Sinha S, Bracha S, Park D, Magondu B, Yang B, Boyden ES, Forest CR. Screening channelrhodopsins using robotic intracellular electrophysiology and single cell sequencing. J Neurosci Methods. 2026 Apr;428:110663. doi: 10.1016/j.jneumeth.2025.110663. Epub 2025 Dec 18. PMID: 41421605.

Ehrlich S, VandeLoo AD, Magondu B, Chien A, Sinha S, Boyden ES, Forest CR. Mutation E300 recommended by protein language models gives ChrimsonR amplified photocurrent response. bioRxiv [Preprint]. 2026 May 17:2026.05.13.725064. doi: 10.64898/2026.05.13.725064. PMID: 42182401; PMCID: PMC13192664.

VandeLoo AD, Malta NJ, Sanganeriya S, Aponte E, van Zyl C, Xu D, Forest C. SAMCell: Generalized label-free biological cell segmentation with segment anything. PLoS One. 2025 Sep 8;20(9):e0319532. doi: 10.1371/journal.pone.0319532. PMID: 40920883; PMCID: PMC12416835.