Hallou, A., He, R., Simons, B. D., & Dumitrascu, B. (2025). A computational pipeline for spatial mechano-transcriptomics. Nature Methods. https://doi.org/10.1038/s41592-025-02618-1

Börner, K., Blood, P. D., Silverstein, J. C., Ruffalo, M., Satija, R., Teichmann, S. A., Pryhuber, G. J., Misra, R. S., Purkerson, J. M., Fan, J., Hickey, J. W., Molla, G., Xu, C., Zhang, Y., Weber, G. M., Jain, Y., Qaurooni, D., Kong, Y., … Herr, B. W. (2025). Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods. https://doi.org/10.1038/s41592-024-02563-5

Shafighi, S., Geras, A., Jurzysta, B., Sahaf Naeini, A., Filipiuk, I., Ra̧czkowska, A., Toosi, H., Koperski, Ł., Thrane, K., Engblom, C., Mold, J. E., Chen, X., Hartman, J., Nowis, D., Carbone, A., Lagergren, J., & Szczurek, E. (2024). Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-53374-3

Gu, J., Iyer, A., Wesley, B., Taglialatela, A., Leuzzi, G., Hangai, S., Decker, A., Gu, R., Klickstein, N., Shuai, Y., Jankovic, K., Parker-Burns, L., Jin, Y., Zhang, J. Y., Hong, J., Niu, X., Costa, J. A., Pezet, M. G., Chou, J., … Gaublomme, J. T. (2024). Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap. Nature Biotechnology. https://doi.org/10.1038/s41587-024-02386-x

Shannon, M. J., Eisman, S. E., Lowe, A. R., Sloan, T. F. W., & Mace, E. M. (2024). cellPLATO – an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data. Journal of Cell Science, 137(20). https://doi.org/10.1242/jcs.261887

Nemzow, L., Boehringer, T., Mayenburg, J., Beaton-Green, L. A., Wilkins, R. C., & Turner, H. C. (2024). Interlaboratory comparison of high-throughput protein biomarker assay quantifications for radiation exposure classification. PLOS ONE, 19(4), e0301418. https://doi.org/10.1371/journal.pone.0301418

Li, X., Liu, H., Song, X., Marboe, C. C., Brott, B. C., Litovsky, S. H., & Gan, Y. (2024). Structurally constrained and pathology-aware convolutional transformer generative adversarial network for virtual histology staining of human coronary optical coherence tomography images. Journal of Biomedical Optics, 29(03). https://doi.org/10.1117/1.jbo.29.3.036004

Hatton, I. A., Galbraith, E. D., Merleau, N. S. C., Miettinen, T. P., Smith, B. M., & Shander, J. A. (2023). The human cell count and size distribution. Proceedings of the National Academy of Sciences, 120(39). https://doi.org/10.1073/pnas.2303077120

Feldmann, C., Schänzler, M., Ben-Johny, M., & Wahl-Schott, C. (2023). Protocol for deriving proximity, affinity, and stoichiometry of protein interactions using image-based quantitative two-hybrid FRET. STAR Protocols, 4(3), 102459. https://doi.org/10.1016/j.xpro.2023.102459

Chen, Z., Zhang, B., Gong, F., Wan, L., & Ma, L. (2023). RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data. Frontiers in Genetics, 14. https://doi.org/10.3389/fgene.2023.1110899

Paquelet, G. E., Carrion, K., Lacefield, C. O., Zhou, P., Hen, R., & Miller, B. R. (2023). Protocol for in vivo imaging and analysis of brainstem neuronal activity in the dorsal raphe nucleus of freely behaving mice. STAR Protocols, 4(1), 102074. https://doi.org/10.1016/j.xpro.2023.102074

Lin, J., Cheng, Z., Yang, G., & Cui, M. (2022). Optical gearbox enabled versatile multiscale high-throughput multiphoton functional imaging. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-34472-6

Lin, B. (2022). Topological Data Analysis in Time Series: Temporal Filtration and Application to Single-Cell Genomics. Algorithms, 15(10), 371. https://doi.org/10.3390/a15100371