References

If you used zoom in your research, please cite the following study:

This study has not been published yet

If you use zoom.prepare.abagen_ctx for the processing of AHBA dataset, please also cite:

[1] Markello, R. D., Arnatkeviciute, A., Poline, J. B., Fulcher, B. D., Fornito, A. & Misic, B. Standardizing workflows in imaging transcriptomics with the abagen toolbox. Elife 10, e72129 (2021).

[2] Dear, R. et al. Cortical gene expression architecture links healthy neurodevelopment to the imaging, transcriptomics and genetics of autism and schizophrenia. Nat. Neurosci. 27, 1075-1086 (2024).

If you used zoom.prepare.process_SBP to perform Alexander-Bloch’s spatial permutation model, please also cite:

[1] Markello, R. D. et al. Neuromaps: structural and functional interpretation of brain maps. Nat. Methods 19, 1472-1479 (2022).

[2] Alexander-Bloch, A. F. et al. On testing for spatial correspondence between maps of human brain structure and function. Neuroimage 178, 540-551 (2018).

If you used zoom.sc_tool.compute_gss to get gene specificity scores, please also cite:

Song, L., Chen, W., Hou, J., Guo, M. & Yang, J. Spatially resolved mapping of cells associated with human complex traits. Nature 641 932-941 (2025).

If you ZOOM or ZOOM_SC object to perform imaging-transcriptomics analysis, please also cite:

Wang, Y. et al. Spatio-molecular profiles shape the human cerebellar hierarchy along the sensorimotor-association axis. Cell Rep. 43, 113770 (2024).

And the idea and methodology used for single-cell scoring were adopted from:

[1] Zhang, M. J. et al. Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nat. Genet. 54, 1572-1580 (2022).

[2] Fulcher, B. D., Arnatkeviciute, A. & Fornito, A. Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data. Nat. Commun. 12, 2669 (2021).