{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,11]],"date-time":"2026-11-11T03:51:32Z","timestamp":1794369092754,"version":"4.9.0"},"reference-count":102,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T00:00:00Z","timestamp":1769126400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T00:00:00Z","timestamp":1769126400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1038\/s41588-025-02454-1","type":"journal-article","created":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T10:02:33Z","timestamp":1769162553000},"page":"418-433","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Single-cell atlas of the transcriptome and chromatin accessibility in the human retina"],"prefix":"10.1038","volume":"58","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8975-6776","authenticated-orcid":false,"given":"Jin","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio L.","family":"Ibarra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0678-4411","authenticated-orcid":false,"given":"Xuesen","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7464-7921","authenticated-orcid":false,"given":"Malte D.","family":"Luecken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4835-174X","authenticated-orcid":false,"given":"Jiaxiong","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aboozar","family":"Monavarfeshani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3568-4265","authenticated-orcid":false,"given":"Wenjun","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4133-0439","authenticated-orcid":false,"given":"Yiqiao","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Zuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha Lynn Zayas","family":"Colborn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Berenice Sarahi","family":"Cortez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3802-3868","authenticated-orcid":false,"given":"Leah A.","family":"Owen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brittney","family":"Wick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuan","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jongsu","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Haeussler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas M.","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karthik","family":"Shekhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8926-8836","authenticated-orcid":false,"given":"Joshua R.","family":"Sanes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Timothy","family":"Stout","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiming","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3731-142X","authenticated-orcid":false,"given":"Margaret M.","family":"DeAngelis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2419-1943","authenticated-orcid":false,"given":"Fabian J.","family":"Theis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4387-9735","authenticated-orcid":false,"given":"Rui","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,23]]},"reference":[{"key":"2454_CR1","doi-asserted-by":"crossref","first-page":"e27041","DOI":"10.7554\/eLife.27041","volume":"6","author":"A Regev","year":"2017","unstructured":"Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).","journal-title":"eLife"},{"key":"2454_CR2","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/550451a","volume":"550","author":"O Rozenblatt-Rosen","year":"2017","unstructured":"Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. & Teichmann, S. A. The Human Cell Atlas: from vision to reality. Nature 550, 451\u2013453 (2017).","journal-title":"Nature"},{"key":"2454_CR3","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1038\/s41591-023-02327-2","volume":"29","author":"L Sikkema","year":"2023","unstructured":"Sikkema, L. et al. An integrated cell atlas of the lung in health and disease. Nat. Med. 29, 1563\u20131577 (2023).","journal-title":"Nat. Med."},{"key":"2454_CR4","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41586-023-06252-9","volume":"620","author":"T Kumar","year":"2023","unstructured":"Kumar, T. et al. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 620, 181\u2013191 (2023).","journal-title":"Nature"},{"key":"2454_CR5","doi-asserted-by":"crossref","DOI":"10.1126\/science.add7046","volume":"382","author":"K Siletti","year":"2023","unstructured":"Siletti, K. et al. Transcriptomic diversity of cell types across the adult human brain. Science 382, eadd7046 (2023).","journal-title":"Science"},{"key":"2454_CR6","volume":"382","author":"NL Jorstad","year":"2023","unstructured":"Jorstad, N. L. et al. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science 382, eadf6812 (2023).","journal-title":"Science"},{"key":"2454_CR7","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/s41586-024-08172-8","volume":"635","author":"Z He","year":"2024","unstructured":"He, Z. et al. An integrated transcriptomic cell atlas of human neural organoids. Nature 635, 690\u2013698 (2024).","journal-title":"Nature"},{"key":"2454_CR8","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1038\/s41588-025-02182-6","volume":"57","author":"Q Xu","year":"2025","unstructured":"Xu, Q. et al. An integrated transcriptomic cell atlas of human endoderm-derived organoids. Nat. Genet. 57, 1201\u20131212 (2025).","journal-title":"Nat. Genet."},{"key":"2454_CR9","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2200914119","volume":"119","author":"T Van Zyl","year":"2022","unstructured":"Van Zyl, T. et al. Cell atlas of the human ocular anterior segment: tissue-specific and shared cell types. Proc. Natl Acad. Sci. USA 119, e2200914119 (2022).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2454_CR10","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2306153120","volume":"120","author":"A Monavarfeshani","year":"2023","unstructured":"Monavarfeshani, A. et al. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye. Proc. Natl Acad. Sci. USA 120, e2306153120 (2023).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2454_CR11","doi-asserted-by":"crossref","first-page":"100298","DOI":"10.1016\/j.xgen.2023.100298","volume":"3","author":"Q Liang","year":"2023","unstructured":"Liang, Q. et al. A multi-omics atlas of the human retina at single-cell resolution. Cell Genom. 3, 100298 (2023).","journal-title":"Cell Genom."},{"key":"2454_CR12","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41586-023-06638-9","volume":"624","author":"J Hahn","year":"2023","unstructured":"Hahn, J. et al. Evolution of neuronal cell classes and types in the vertebrate retina. Nature 624, 415\u2013424 (2023).","journal-title":"Nature"},{"key":"2454_CR13","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1016\/j.cell.2019.01.004","volume":"176","author":"YR Peng","year":"2019","unstructured":"Peng, Y. R. et al. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina. Cell 176, 1222\u20131237 (2019).","journal-title":"Cell"},{"key":"2454_CR14","doi-asserted-by":"crossref","first-page":"e63907","DOI":"10.7554\/eLife.63907","volume":"10","author":"M Yamagata","year":"2021","unstructured":"Yamagata, M., Yan, W. & Sanes, J. R. A cell atlas of the chick retina based on single-cell transcriptomics. eLife 10, e63907 (2021).","journal-title":"eLife"},{"key":"2454_CR15","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202\u20131214 (2015).","journal-title":"Cell"},{"key":"2454_CR16","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1016\/j.cell.2016.07.054","volume":"166","author":"K Shekhar","year":"2016","unstructured":"Shekhar, K. et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166, 1308\u20131323 (2016).","journal-title":"Cell"},{"key":"2454_CR17","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/j.neuron.2019.11.006","volume":"104","author":"NM Tran","year":"2019","unstructured":"Tran, N. M. et al. Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes. Neuron 104, 1039\u20131055 (2019).","journal-title":"Neuron"},{"key":"2454_CR18","doi-asserted-by":"crossref","first-page":"5177","DOI":"10.1523\/JNEUROSCI.0471-20.2020","volume":"40","author":"W Yan","year":"2020","unstructured":"Yan, W. et al. Mouse retinal cell atlas: molecular identification of over sixty amacrine cell types. J. Neurosci. 40, 5177\u20135195 (2020).","journal-title":"J. Neurosci."},{"key":"2454_CR19","volume":"10","author":"W Yan","year":"2020","unstructured":"Yan, W. et al. Cell atlas of the human fovea and peripheral retina. Sci. Rep. 10, 9802 (2020).","journal-title":"Sci. Rep."},{"key":"2454_CR20","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","volume":"523","author":"JD Buenrostro","year":"2015","unstructured":"Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486\u2013490 (2015).","journal-title":"Nature"},{"key":"2454_CR21","volume":"24","author":"J Wang","year":"2023","unstructured":"Wang, J. et al. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation. Genome Biol. 24, 269 (2023).","journal-title":"Genome Biol."},{"key":"2454_CR22","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-021-01336-8","volume":"19","author":"MD Luecken","year":"2022","unstructured":"Luecken, M. D. et al. Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41\u201350 (2022).","journal-title":"Nat. Methods"},{"key":"2454_CR23","unstructured":"Luecken, M. D. et al. A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. In Proc. 35th Conference on Neural Information Processing Systems Datasets and Benchmarks Track (Round 2) (NeurIPS, 2021)."},{"key":"2454_CR24","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1016\/j.cell.2020.08.013","volume":"182","author":"CS Cowan","year":"2020","unstructured":"Cowan, C. S. et al. Cell types of the human retina and its organoids at single-cell resolution. Cell 182, 1623\u20131640 (2020).","journal-title":"Cell"},{"key":"2454_CR25","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1016\/j.celrep.2019.12.082","volume":"30","author":"LD Orozco","year":"2020","unstructured":"Orozco, L. D. et al. Integration of eQTL and a single-cell atlas in the human eye identifies causal genes for age-related macular degeneration. Cell Rep. 30, 1246\u20131259 (2020).","journal-title":"Cell Rep."},{"key":"2454_CR26","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2018100811","volume":"38","author":"SW Lukowski","year":"2019","unstructured":"Lukowski, S. W. et al. A single-cell transcriptome atlas of the adult human retina. EMBO J. 38, e100811 (2019).","journal-title":"EMBO J."},{"key":"2454_CR27","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-12780-8","volume":"10","author":"M Menon","year":"2019","unstructured":"Menon, M. et al. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat. Commun. 10, 4902 (2019).","journal-title":"Nat. Commun."},{"key":"2454_CR28","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.exer.2019.05.001","volume":"184","author":"AP Voigt","year":"2019","unstructured":"Voigt, A. P. et al. Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing. Exp. Eye Res. 184, 234\u2013242 (2019).","journal-title":"Exp. Eye Res."},{"key":"2454_CR29","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/s41592-018-0229-2","volume":"15","author":"R Lopez","year":"2018","unstructured":"Lopez, R., Regier, J., Cole, M. B., Jordan, M. I. & Yosef, N. Deep generative modeling for single-cell transcriptomics. Nat. Methods 15, 1053\u20131058 (2018).","journal-title":"Nat. Methods"},{"key":"2454_CR30","doi-asserted-by":"crossref","DOI":"10.1016\/j.xops.2023.100335","volume":"3","author":"CP Santiago","year":"2023","unstructured":"Santiago, C. P. et al. Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of retinal detachment-related proliferative vitreoretinopathy. Ophthalmol. Sci. 3, 100335 (2023).","journal-title":"Ophthalmol. Sci."},{"key":"2454_CR31","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1038\/s41592-024-02191-z","volume":"21","author":"Y Rosen","year":"2024","unstructured":"Rosen, Y. et al. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat. Methods 21, 1492\u20131500 (2024).","journal-title":"Nat. Methods"},{"key":"2454_CR32","doi-asserted-by":"crossref","first-page":"e64875","DOI":"10.7554\/eLife.64875","volume":"10","author":"TE Bakken","year":"2021","unstructured":"Bakken, T. E. et al. Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans. eLife 10, e64875 (2021).","journal-title":"eLife"},{"key":"2454_CR33","unstructured":"Kolb, H., Fernandez, E. & Nelson, R. Webvision: The Organization of the Retina and Visual System (University of Utah Health Sciences Center, 1995)."},{"key":"2454_CR34","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s44330-024-00015-2","volume":"1","author":"A Liu","year":"2024","unstructured":"Liu, A. et al. Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. BMC Methods 1, 15 (2024).","journal-title":"BMC Methods"},{"key":"2454_CR35","doi-asserted-by":"crossref","first-page":"9001","DOI":"10.1073\/pnas.1922501117","volume":"117","author":"TJ Cherry","year":"2020","unstructured":"Cherry, T. J. et al. Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease. Proc. Natl Acad. Sci. USA 117, 9001\u20139012 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2454_CR36","doi-asserted-by":"crossref","first-page":"1520","DOI":"10.1101\/gr.231886.117","volume":"28","author":"AEO Hughes","year":"2018","unstructured":"Hughes, A. E. O., Myers, C. A. & Corbo, J. C. A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo. Genome Res. 28, 1520\u20131531 (2018).","journal-title":"Genome Res."},{"key":"2454_CR37","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1101\/gr.278133.123","volume":"34","author":"JL Shepherdson","year":"2024","unstructured":"Shepherdson, J. L. et al. Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res. 34, 243\u2013255 (2024).","journal-title":"Genome Res."},{"key":"2454_CR38","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41592-023-01938-4","volume":"20","author":"C Bravo Gonzalez-Blas","year":"2023","unstructured":"Bravo Gonzalez-Blas, C. et al. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat. Methods 20, 1355\u20131367 (2023).","journal-title":"Nat. Methods"},{"key":"2454_CR39","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1523\/JNEUROSCI.3145-15.2016","volume":"36","author":"J De Melo","year":"2016","unstructured":"De Melo, J. et al. Lhx2 is an essential factor for retinal gliogenesis and notch signaling. J. Neurosci. 36, 2391\u20132405 (2016).","journal-title":"J. Neurosci."},{"key":"2454_CR40","doi-asserted-by":"crossref","first-page":"E4086","DOI":"10.1073\/pnas.1405354111","volume":"111","author":"D Sapkota","year":"2014","unstructured":"Sapkota, D. et al. Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development. Proc. Natl Acad. Sci. USA 111, E4086\u2013E4095 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2454_CR41","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.neuron.2019.04.010","volume":"102","author":"BS Clark","year":"2019","unstructured":"Clark, B. S. et al. Single-cell RNA-seq analysis of retinal development identifies NFI factors as regulating mitotic exit and late-born cell specification. Neuron 102, 1111\u20131126 (2019).","journal-title":"Neuron"},{"key":"2454_CR42","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1016\/j.celrep.2019.12.072","volume":"30","author":"H Yamamoto","year":"2020","unstructured":"Yamamoto, H., Kon, T., Omori, Y. & Furukawa, T. Functional and evolutionary diversification of Otx2 and Crx in vertebrate retinal photoreceptor and bipolar cell development. Cell Rep. 30, 658\u2013671 (2020).","journal-title":"Cell Rep."},{"key":"2454_CR43","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.ydbio.2017.09.030","volume":"432","author":"LA Remez","year":"2017","unstructured":"Remez, L. A. et al. Pax6 is essential for the generation of late-born retinal neurons and for inhibition of photoreceptor-fate during late stages of retinogenesis. Dev. Biol. 432, 140\u2013150 (2017).","journal-title":"Dev. Biol."},{"key":"2454_CR44","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1093\/hmg\/ddh173","volume":"13","author":"H Cheng","year":"2004","unstructured":"Cheng, H. et al. Photoreceptor-specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors. Hum. Mol. Genet. 13, 1563\u20131575 (2004).","journal-title":"Hum. Mol. Genet."},{"key":"2454_CR45","doi-asserted-by":"crossref","first-page":"3504","DOI":"10.1002\/stem.2122","volume":"33","author":"R Kaewkhaw","year":"2015","unstructured":"Kaewkhaw, R. et al. Transcriptome dynamics of developing photoreceptors in three-dimensional retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks. Stem Cells 33, 3504\u20133518 (2015).","journal-title":"Stem Cells"},{"key":"2454_CR46","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.1038\/s41587-022-01284-4","volume":"40","author":"ZJ Cao","year":"2022","unstructured":"Cao, Z. J. & Gao, G. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding. Nat. Biotechnol. 40, 1458\u20131466 (2022).","journal-title":"Nat. Biotechnol."},{"key":"2454_CR47","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1146\/annurev-vision-100419-114940","volume":"7","author":"L Campello","year":"2021","unstructured":"Campello, L. et al. Aging of the retina: molecular and metabolic turbulences and potential interventions. Annu. Rev. Vis. Sci. 7, 633\u2013664 (2021).","journal-title":"Annu. Rev. Vis. Sci."},{"key":"2454_CR48","doi-asserted-by":"crossref","DOI":"10.1186\/s13293-021-00401-3","volume":"12","author":"IO Aninye","year":"2021","unstructured":"Aninye, I. O. et al. The roles of sex and gender in women\u2019s eye health disparities in the United States. Biol. Sex Differ. 12, 57 (2021).","journal-title":"Biol. Sex Differ."},{"key":"2454_CR49","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/s41588-018-0268-8","volume":"51","author":"SM Urbut","year":"2019","unstructured":"Urbut, S. M., Wang, G., Carbonetto, P. & Stephens, M. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nat. Genet. 51, 187\u2013195 (2019).","journal-title":"Nat. Genet."},{"key":"2454_CR50","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1006\/dbio.1996.8449","volume":"182","author":"T Nagai","year":"1997","unstructured":"Nagai, T. et al. The expression of the mouse Zic1, Zic2, and Zic3 gene suggests an essential role for Zic genes in body pattern formation. Dev. Biol. 182, 299\u2013313 (1997).","journal-title":"Dev. Biol."},{"key":"2454_CR51","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2024.109397","volume":"27","author":"B Dorgau","year":"2024","unstructured":"Dorgau, B. et al. Deciphering the spatiotemporal transcriptional and chromatin accessibility of human retinal organoid development at the single-cell level. iScience 27, 109397 (2024).","journal-title":"iScience"},{"key":"2454_CR52","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/ng.3404","volume":"47","author":"HK Finucane","year":"2015","unstructured":"Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228\u20131235 (2015).","journal-title":"Nat. Genet."},{"key":"2454_CR53","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004219","volume":"11","author":"CA De Leeuw","year":"2015","unstructured":"De Leeuw, C. A., Mooij, J. M., Heskes, T. & Posthuma, D. MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput. Biol. 11, e1004219 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"2454_CR54","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1038\/ng.3448","volume":"48","author":"LG Fritsche","year":"2016","unstructured":"Fritsche, L. G. et al. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nat. Genet. 48, 134\u2013143 (2016).","journal-title":"Nat. Genet."},{"key":"2454_CR55","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010587","volume":"19","author":"H Currant","year":"2023","unstructured":"Currant, H. et al. Sub-cellular level resolution of common genetic variation in the photoreceptor layer identifies continuum between rare disease and common variation. PLoS Genet. 19, e1010587 (2023).","journal-title":"PLoS Genet."},{"key":"2454_CR56","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-20851-4","volume":"12","author":"P Gharahkhani","year":"2021","unstructured":"Gharahkhani, P. et al. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries. Nat. Commun. 12, 1258 (2021).","journal-title":"Nat. Commun."},{"key":"2454_CR57","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/s41588-018-0126-8","volume":"50","author":"AP Khawaja","year":"2018","unstructured":"Khawaja, A. P. et al. Genome-wide analyses identify 68 new loci associated with intraocular pressure and improve risk prediction for primary open-angle glaucoma. Nat. Genet. 50, 778\u2013782 (2018).","journal-title":"Nat. Genet."},{"key":"2454_CR58","first-page":"438","volume":"26","author":"H Springelkamp","year":"2017","unstructured":"Springelkamp, H. et al. New insights into the genetics of primary open-angle glaucoma based on meta-analyses of intraocular pressure and optic disc characteristics. Hum. Mol. Genet. 26, 438\u2013453 (2017).","journal-title":"Hum. Mol. Genet."},{"key":"2454_CR59","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/s41588-020-0599-0","volume":"52","author":"PG Hysi","year":"2020","unstructured":"Hysi, P. G. et al. Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia. Nat. Genet. 52, 401\u2013407 (2020).","journal-title":"Nat. Genet."},{"key":"2454_CR60","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1038\/s41588-021-00954-4","volume":"53","author":"L Jiang","year":"2021","unstructured":"Jiang, L., Zheng, Z., Fang, H. & Yang, J. A generalized linear mixed model association tool for biobank-scale data. Nat. Genet. 53, 1616\u20131621 (2021).","journal-title":"Nat. Genet."},{"key":"2454_CR61","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1111\/rssb.12388","volume":"82","author":"G Wang","year":"2020","unstructured":"Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. A simple new approach to variable selection in regression, with application to genetic fine mapping. J. R. Stat. Soc. Series B Stat. Methodol. 82, 1273\u20131300 (2020).","journal-title":"J. R. Stat. Soc. Series B Stat. Methodol."},{"key":"2454_CR62","volume":"18","author":"Y Zou","year":"2022","unstructured":"Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. Fine-mapping from summary data with the \u2018Sum of Single Effects\u2019 model. PLoS Genet. 18, e1010299 (2022).","journal-title":"PLoS Genet."},{"key":"2454_CR63","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-33427-1","volume":"13","author":"C Marchal","year":"2022","unstructured":"Marchal, C. et al. High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci. Nat. Commun. 13, 5827 (2022).","journal-title":"Nat. Commun."},{"key":"2454_CR64","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/s41588-019-0351-9","volume":"51","author":"R Ratnapriya","year":"2019","unstructured":"Ratnapriya, R. et al. Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration. Nat. Genet. 51, 606\u2013610 (2019).","journal-title":"Nat. Genet."},{"key":"2454_CR65","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004383","volume":"10","author":"C Giambartolomei","year":"2014","unstructured":"Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).","journal-title":"PLoS Genet."},{"key":"2454_CR66","doi-asserted-by":"publisher","unstructured":"Megill, C. et al. cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.04.05.438318 (2021).","DOI":"10.1101\/2021.04.05.438318"},{"key":"2454_CR67","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1093\/bioinformatics\/btab503","volume":"37","author":"ML Speir","year":"2021","unstructured":"Speir, M. L. et al. UCSC Cell Browser: visualize your single-cell data. Bioinformatics 37, 4578\u20134580 (2021).","journal-title":"Bioinformatics"},{"key":"2454_CR68","doi-asserted-by":"publisher","unstructured":"Tarhan, L. et al. Single cell portal: an interactive home for single-cell genomics data. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.07.13.548886 (2023).","DOI":"10.1101\/2023.07.13.548886"},{"key":"2454_CR69","doi-asserted-by":"crossref","first-page":"e67403","DOI":"10.7554\/eLife.67403","volume":"10","author":"RZ Friedman","year":"2021","unstructured":"Friedman, R. Z. et al. Information content differentiates enhancers from silencers in mouse photoreceptors. eLife 10, e67403 (2021).","journal-title":"eLife"},{"key":"2454_CR70","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.cell.2016.09.025","volume":"167","author":"Y Nedelec","year":"2016","unstructured":"Nedelec, Y. et al. Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell 167, 657\u2013669 (2016).","journal-title":"Cell"},{"key":"2454_CR71","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41587-021-01001-7","volume":"40","author":"M Lotfollahi","year":"2022","unstructured":"Lotfollahi, M. et al. Mapping single-cell data to reference atlases by transfer learning. Nat. Biotechnol. 40, 121\u2013130 (2022).","journal-title":"Nat. Biotechnol."},{"key":"2454_CR72","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1167\/iovs.18-24254","volume":"60","author":"LA Owen","year":"2019","unstructured":"Owen, L. A. et al. The Utah protocol for postmortem eye phenotyping and molecular biochemical analysis. Invest. Ophthalmol. Vis. Sci. 60, 1204\u20131212 (2019).","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"2454_CR73","volume":"27","author":"J Li","year":"2024","unstructured":"Li, J. et al. Comprehensive single-cell atlas of the mouse retina. iScience 27, 109916 (2024).","journal-title":"iScience"},{"key":"2454_CR74","volume":"8","author":"GX Zheng","year":"2017","unstructured":"Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).","journal-title":"Nat. Commun."},{"key":"2454_CR75","volume":"20","author":"ATL Lun","year":"2019","unstructured":"Lun, A. T. L. et al. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 20, 63 (2019).","journal-title":"Genome Biol."},{"key":"2454_CR76","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1101\/gr.271908.120","volume":"31","author":"CN Heiser","year":"2021","unstructured":"Heiser, C. N., Wang, V. M., Chen, B., Hughey, J. J. & Lau, K. S. Automated quality control and cell identification of droplet-based single-cell data using dropkick. Genome Res. 31, 1742\u20131752 (2021).","journal-title":"Genome Res."},{"key":"2454_CR77","doi-asserted-by":"crossref","first-page":"giaa151","DOI":"10.1093\/gigascience\/giaa151","volume":"9","author":"MD Young","year":"2020","unstructured":"Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. GigaScience 9, giaa151 (2020).","journal-title":"GigaScience"},{"key":"2454_CR78","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","volume":"8","author":"CS McGinnis","year":"2019","unstructured":"McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329\u2013337 (2019).","journal-title":"Cell Syst."},{"key":"2454_CR79","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1862-5","volume":"20","author":"J Alquicira-Hernandez","year":"2019","unstructured":"Alquicira-Hernandez, J., Sathe, A., Ji, H. P., Nguyen, Q. & Powell, J. E. scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biol. 20, 264 (2019).","journal-title":"Genome Biol."},{"key":"2454_CR80","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902 (2019).","journal-title":"Cell"},{"key":"2454_CR81","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587 (2021).","journal-title":"Cell"},{"key":"2454_CR82","volume":"19","author":"FA Wolf","year":"2018","unstructured":"Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).","journal-title":"Genome Biol."},{"key":"2454_CR83","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-41695-z","volume":"9","author":"VA Traag","year":"2019","unstructured":"Traag, V. A., Waltman, L. & van Eck, N. J. From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 9, 5233 (2019).","journal-title":"Sci. Rep."},{"key":"2454_CR84","doi-asserted-by":"crossref","unstructured":"McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at https:\/\/arxiv.org\/abs\/1802.03426 (2018).","DOI":"10.21105\/joss.00861"},{"key":"2454_CR85","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/s41592-020-0825-9","volume":"17","author":"Z Miao","year":"2020","unstructured":"Miao, Z. et al. Putative cell type discovery from single-cell gene expression data. Nat. Methods 17, 621\u2013628 (2020).","journal-title":"Nat. Methods"},{"key":"2454_CR86","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/btl117","volume":"22","author":"R Suzuki","year":"2006","unstructured":"Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540\u20131542 (2006).","journal-title":"Bioinformatics"},{"key":"2454_CR87","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41588-021-00790-6","volume":"53","author":"JM Granja","year":"2021","unstructured":"Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403\u2013411 (2021).","journal-title":"Nat. Genet."},{"key":"2454_CR88","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP\u2013seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"2454_CR89","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","volume":"18","author":"T Stuart","year":"2021","unstructured":"Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Single-cell chromatin state analysis with signac. Nat. Methods 18, 1333\u20131341 (2021).","journal-title":"Nat. Methods"},{"key":"2454_CR90","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"2454_CR91","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-016-1323-z","volume":"17","author":"GE Hoffman","year":"2016","unstructured":"Hoffman, G. E. & Schadt, E. E. variancePartition: interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics 17, 483 (2016).","journal-title":"BMC Bioinformatics"},{"key":"2454_CR92","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655\u20131664 (2009).","journal-title":"Genome Res."},{"key":"2454_CR93","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/s11222-009-9166-3","volume":"21","author":"H Zhou","year":"2011","unstructured":"Zhou, H., Alexander, D. & Lange, K. A quasi-Newton acceleration for high-dimensional optimization algorithms. Stat. Comput. 21, 261\u2013273 (2011).","journal-title":"Stat. Comput."},{"key":"2454_CR94","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1038\/s41593-024-01636-0","volume":"27","author":"KJM Benjamin","year":"2024","unstructured":"Benjamin, K. J. M. et al. Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry. Nat. Neurosci. 27, 1064\u20131074 (2024).","journal-title":"Nat. Neurosci."},{"key":"2454_CR95","doi-asserted-by":"crossref","first-page":"4593","DOI":"10.1093\/bioinformatics\/btab665","volume":"37","author":"AE Murphy","year":"2021","unstructured":"Murphy, A. E., Schilder, B. M. & Skene, N. G. MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics. Bioinformatics 37, 4593\u20134596 (2021).","journal-title":"Bioinformatics"},{"key":"2454_CR96","doi-asserted-by":"crossref","DOI":"10.3389\/fnins.2016.00016","volume":"10","author":"NG Skene","year":"2016","unstructured":"Skene, N. G. & Grant, S. G. Identification of vulnerable cell types in major brain disorders using single cell transcriptomes and expression weighted cell type enrichment. Front. Neurosci. 10, 16 (2016).","journal-title":"Front. Neurosci."},{"key":"2454_CR97","doi-asserted-by":"crossref","first-page":"3847","DOI":"10.1093\/bioinformatics\/btv470","volume":"31","author":"SG Coetzee","year":"2015","unstructured":"Coetzee, S. G., Coetzee, G. A. & Hazelett, D. J. motifbreakR: an R\/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics 31, 3847\u20133849 (2015).","journal-title":"Bioinformatics"},{"key":"2454_CR98","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1009440","volume":"17","author":"C Wallace","year":"2021","unstructured":"Wallace, C. A more accurate method for colocalisation analysis allowing for multiple causal variants. PLoS Genet. 17, e1009440 (2021).","journal-title":"PLoS Genet."},{"key":"2454_CR99","doi-asserted-by":"publisher","unstructured":"Li, J. & Wang, J. RCHENLAB\/HRCA_reproducibility: manuscript release. Zenodo https:\/\/doi.org\/10.5281\/zenodo.17265527 (2025).","DOI":"10.5281\/zenodo.17265527"},{"key":"2454_CR100","doi-asserted-by":"publisher","unstructured":"Li, J. lijinbio\/cellqc: initial release. Zenodo https:\/\/doi.org\/10.5281\/zenodo.8137510 (2023).","DOI":"10.5281\/zenodo.8137510"},{"key":"2454_CR101","doi-asserted-by":"publisher","unstructured":"Ibarra, I. theislab\/HRCA-reproducibility: manuscript release. Zenodo https:\/\/doi.org\/10.5281\/zenodo.17412073 (2025).","DOI":"10.5281\/zenodo.17412073"},{"key":"2454_CR102","doi-asserted-by":"publisher","unstructured":"Li, J., & Chen, R. Human Retina Cell Atlas reference model. Zenodo https:\/\/doi.org\/10.5281\/zenodo.14014720 (2024).","DOI":"10.5281\/zenodo.14014720"}],"updated-by":[{"DOI":"10.1038\/s41588-026-02545-7","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:00:00Z","timestamp":1771372800000}}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41588-025-02454-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-025-02454-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-025-02454-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T21:03:45Z","timestamp":1771535025000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41588-025-02454-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,23]]},"references-count":102,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["2454"],"URL":"https:\/\/doi.org\/10.1038\/s41588-025-02454-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-3471275\/v1","asserted-by":"object"}]},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,23]]},"assertion":[{"value":"20 October 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 February 2026","order":5,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":6,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A Correction to this paper has been published:","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1038\/s41588-026-02545-7","URL":"https:\/\/doi.org\/10.1038\/s41588-026-02545-7","order":8,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"F.J.T. consults for Immunai, CytoReason, Cellarity and Omniscope, and owns interests in Dermagnostix GmbH and Cellarity. M.D.L. has received research contracts from the CZI and speaker fees from Pfizer and Janssen Pharmaceuticals. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}