{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T17:40:10Z","timestamp":1745948410219,"version":"3.40.4"},"publisher-location":"Cham","reference-count":50,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783031829895","type":"print"},{"value":"9783031829901","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"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":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-3-031-82990-1_8","type":"book-chapter","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T15:49:19Z","timestamp":1745941759000},"page":"163-172","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Computational Approaches in Spatial Transcriptomics for the Study of Mammalian Spermatogenesis"],"prefix":"10.1007","author":[{"given":"Deina","family":"Bossa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melanie","family":"Evans","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shreya","family":"Rajachandran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiqi","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiqi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,4,30]]},"reference":[{"key":"8_CR1","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/978-3-319-53298-1_3","volume-title":"Male Hypogonadism: Basic, Clinical and Therapeutic Principles","author":"H Chen","year":"2017","unstructured":"Chen, H., et al.: Human spermatogenesis and its regulation. In: Winters, S.J., Huhtaniemi, I.T. (eds.) Male Hypogonadism: Basic, Clinical and Therapeutic Principles, pp. 49\u201372. Springer International Publishing, Cham (2017)"},{"key":"8_CR2","doi-asserted-by":"crossref","unstructured":"Hale, D.W.: Mammalian spermatogenesis. In: Verma, R.S. (ed.) Advances in Genome Biology, pp. 249\u2013304. Amsterdam, The Netherlands, JAI (1996)","DOI":"10.1016\/S1067-5701(96)80011-8"},{"key":"8_CR3","first-page":"91","volume":"61","author":"PT Saunders","year":"2003","unstructured":"Saunders, P.T.: Germ cell-somatic cell interactions during spermatogenesis. Reprod. Suppl. 61, 91\u2013101 (2003)","journal-title":"Reprod. Suppl."},{"key":"8_CR4","first-page":"271","volume":"182","author":"IB Fritz","year":"1994","unstructured":"Fritz, I.B.: Somatic cell-germ cell relationships in mammalian testes during development and spermatogenesis. Ciba Found. Symp. 182, 271\u2013274 (1994).; discussion 274\u201381","journal-title":"Ciba Found. Symp."},{"issue":"6","key":"8_CR5","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1093\/humupd\/dmad017","volume":"29","author":"X Zhang","year":"2023","unstructured":"Zhang, X., et al.: Dissecting mammalian reproduction with spatial transcriptomics. Hum. Reprod. Update. 29(6), 794\u2013810 (2023)","journal-title":"Hum. Reprod. Update"},{"issue":"6","key":"8_CR6","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/s41587-022-01448-2","volume":"41","author":"L Tian","year":"2023","unstructured":"Tian, L., Chen, F., Macosko, E.Z.: The expanding vistas of spatial transcriptomics. Nat. Biotechnol. 41(6), 773\u2013782 (2023)","journal-title":"Nat. Biotechnol."},{"issue":"5","key":"8_CR7","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","volume":"19","author":"L Moses","year":"2022","unstructured":"Moses, L., Pachter, L.: Museum of spatial transcriptomics. Nat. Methods. 19(5), 534\u2013546 (2022)","journal-title":"Nat. Methods"},{"issue":"5","key":"8_CR8","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109915","volume":"37","author":"H Chen","year":"2021","unstructured":"Chen, H., et al.: Dissecting mammalian spermatogenesis using spatial transcriptomics. Cell Rep. 37(5), 109915 (2021)","journal-title":"Cell Rep."},{"issue":"3","key":"8_CR9","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1038\/s41587-020-0739-1","volume":"39","author":"RR Stickels","year":"2021","unstructured":"Stickels, R.R., et al.: Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol. 39(3), 313\u2013319 (2021)","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"8_CR10","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","volume":"20","author":"C Hafemeister","year":"2019","unstructured":"Hafemeister, C., Satija, R.: Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20(1), 296 (2019)","journal-title":"Genome Biol."},{"issue":"1","key":"8_CR11","doi-asserted-by":"publisher","first-page":"7739","DOI":"10.1038\/s41467-023-43120-6","volume":"14","author":"D Pham","year":"2023","unstructured":"Pham, D., et al.: Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues. Nat. Commun. 14(1), 7739 (2023)","journal-title":"Nat. Commun."},{"issue":"7","key":"8_CR12","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112737","volume":"42","author":"S Rajachandran","year":"2023","unstructured":"Rajachandran, S., et al.: Dissecting the spermatogonial stem cell niche using spatial transcriptomics. Cell Rep. 42(7), 112737 (2023)","journal-title":"Cell Rep."},{"issue":"1","key":"8_CR13","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1038\/s41467-021-27729-z","volume":"13","author":"GC Linderman","year":"2022","unstructured":"Linderman, G.C., et al.: Zero-preserving imputation of single-cell RNA-seq data. Nat. Commun. 13(1), 192 (2022)","journal-title":"Nat. Commun."},{"issue":"7","key":"8_CR14","doi-asserted-by":"publisher","first-page":"1873","DOI":"10.1016\/j.cell.2019.05.006","volume":"177","author":"JD Welch","year":"2019","unstructured":"Welch, J.D., et al.: Single-cell multi-omic integration compares and contrasts features of brain cell identity. Cell. 177(7), 1873\u20131887 e17 (2019)","journal-title":"Cell"},{"issue":"7","key":"8_CR15","doi-asserted-by":"publisher","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(7), 1888\u20131902 e21 (2019)","journal-title":"Cell"},{"issue":"Suppl_1","key":"8_CR16","doi-asserted-by":"publisher","first-page":"i299","DOI":"10.1093\/bioinformatics\/btab298","volume":"37","author":"C Shengquan","year":"2021","unstructured":"Shengquan, C., et al.: stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. Bioinformatics. 37(Suppl_1), i299\u2013i307 (2021)","journal-title":"Bioinformatics"},{"issue":"12","key":"8_CR17","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","volume":"19","author":"M Pachitariu","year":"2022","unstructured":"Pachitariu, M., Stringer, C.: Cellpose 2.0: how to train your own model. Nat. Methods. 19(12), 1634\u20131641 (2022)","journal-title":"Nat. Methods"},{"issue":"1","key":"8_CR18","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","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(1), 15 (2018)","journal-title":"Genome Biol."},{"issue":"11","key":"8_CR19","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","volume":"39","author":"E Zhao","year":"2021","unstructured":"Zhao, E., et al.: Spatial transcriptomics at subspot resolution with BayesSpace. Nat. Biotechnol. 39(11), 1375\u20131384 (2021)","journal-title":"Nat. Biotechnol."},{"issue":"11","key":"8_CR20","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41592-021-01255-8","volume":"18","author":"J Hu","year":"2021","unstructured":"Hu, J., et al.: SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network. Nat. Methods. 18(11), 1342\u20131351 (2021)","journal-title":"Nat. Methods"},{"issue":"1","key":"8_CR21","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13073-024-01283-x","volume":"16","author":"H Xu","year":"2024","unstructured":"Xu, H., et al.: Unsupervised spatially embedded deep representation of spatial transcriptomics. Genome Med. 16(1), 12 (2024)","journal-title":"Genome Med."},{"issue":"4","key":"8_CR22","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1038\/s41587-021-00830-w","volume":"40","author":"DM Cable","year":"2022","unstructured":"Cable, D.M., et al.: Robust decomposition of cell type mixtures in spatial transcriptomics. Nat. Biotechnol. 40(4), 517\u2013526 (2022)","journal-title":"Nat. Biotechnol."},{"issue":"9","key":"8_CR23","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab043","volume":"49","author":"M Elosua-Bayes","year":"2021","unstructured":"Elosua-Bayes, M., et al.: SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. Nucleic Acids Res. 49(9), e50 (2021)","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"8_CR24","doi-asserted-by":"publisher","first-page":"1352","DOI":"10.1038\/s41592-021-01264-7","volume":"18","author":"T Biancalani","year":"2021","unstructured":"Biancalani, T., et al.: Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nat. Methods. 18(11), 1352\u20131362 (2021)","journal-title":"Nat. Methods"},{"issue":"5","key":"8_CR25","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/s41587-021-01139-4","volume":"40","author":"V Kleshchevnikov","year":"2022","unstructured":"Kleshchevnikov, V., et al.: Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40(5), 661\u2013671 (2022)","journal-title":"Nat. Biotechnol."},{"issue":"11","key":"8_CR26","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.1038\/s41587-023-01697-9","volume":"41","author":"MR Vahid","year":"2023","unstructured":"Vahid, M.R., et al.: High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE. Nat. Biotechnol. 41(11), 1543\u20131548 (2023)","journal-title":"Nat. Biotechnol."},{"issue":"1","key":"8_CR27","doi-asserted-by":"publisher","first-page":"7930","DOI":"10.1038\/s41467-023-43600-9","volume":"14","author":"Z Zhou","year":"2023","unstructured":"Zhou, Z., et al.: Spatial transcriptomics deconvolution at single-cell resolution using Redeconve. Nat. Commun. 14(1), 7930 (2023)","journal-title":"Nat. Commun."},{"issue":"2","key":"8_CR28","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/s41592-019-0701-7","volume":"17","author":"S Sun","year":"2020","unstructured":"Sun, S., Zhu, J., Zhou, X.: Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies. Nat. Methods. 17(2), 193\u2013200 (2020)","journal-title":"Nat. Methods"},{"issue":"17","key":"8_CR29","doi-asserted-by":"publisher","first-page":"2644","DOI":"10.1093\/bioinformatics\/btab164","volume":"37","author":"A Andersson","year":"2021","unstructured":"Andersson, A., Lundeberg, J.: Sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling. Bioinformatics. 37(17), 2644\u20132650 (2021)","journal-title":"Bioinformatics"},{"key":"8_CR30","doi-asserted-by":"crossref","unstructured":"Zhu, J., Sabatti, C.: Integrative spatial single-cell analysis with graph-based feature learning. bioRxiv, 2020: p. 2020.08.12.248971","DOI":"10.1101\/2020.08.12.248971"},{"issue":"39","key":"8_CR31","doi-asserted-by":"publisher","first-page":"19490","DOI":"10.1073\/pnas.1912459116","volume":"116","author":"C Xia","year":"2019","unstructured":"Xia, C., et al.: Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl. Acad. Sci. USA. 116(39), 19490\u201319499 (2019)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"1","key":"8_CR32","doi-asserted-by":"publisher","first-page":"4847","DOI":"10.1038\/s41598-018-22297-7","volume":"8","author":"G Wang","year":"2018","unstructured":"Wang, G., Moffitt, J.R., Zhuang, X.: Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci. Rep. 8(1), 4847 (2018)","journal-title":"Sci. Rep."},{"issue":"7751","key":"8_CR33","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/s41586-019-1049-y","volume":"568","author":"CL Eng","year":"2019","unstructured":"Eng, C.L., et al.: Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature. 568(7751), 235\u2013239 (2019)","journal-title":"Nature"},{"issue":"9","key":"8_CR34","doi-asserted-by":"publisher","first-page":"1076","DOI":"10.1038\/s41592-022-01575-3","volume":"19","author":"DM Cable","year":"2022","unstructured":"Cable, D.M., et al.: Cell type-specific inference of differential expression in spatial transcriptomics. Nat. Methods. 19(9), 1076\u20131087 (2022)","journal-title":"Nat. Methods"},{"issue":"1","key":"8_CR35","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s13059-023-03159-6","volume":"25","author":"K Mason","year":"2024","unstructured":"Mason, K., et al.: Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome Biol. 25(1), 14 (2024)","journal-title":"Genome Biol."},{"issue":"5457","key":"8_CR36","doi-asserted-by":"publisher","first-page":"1489","DOI":"10.1126\/science.287.5457.1489","volume":"287","author":"X Meng","year":"2000","unstructured":"Meng, X., et al.: Regulation of cell fate decision of undifferentiated spermatogonia by GDNF. Science. 287(5457), 1489\u20131493 (2000)","journal-title":"Science"},{"issue":"3","key":"8_CR37","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/j.stemcr.2015.01.010","volume":"4","author":"S Takashima","year":"2015","unstructured":"Takashima, S., et al.: Functional differences between GDNF-dependent and FGF2-dependent mouse spermatogonial stem cell self-renewal. Stem Cell Rep. 4(3), 489\u2013502 (2015)","journal-title":"Stem Cell Rep."},{"issue":"1","key":"8_CR38","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1095\/biolreprod.115.135145","volume":"94","author":"JT Busada","year":"2016","unstructured":"Busada, J.T., Geyer, C.B.: The role of retinoic acid (RA) in spermatogonial differentiation. Biol. Reprod. 94(1), 10 (2016)","journal-title":"Biol. Reprod."},{"issue":"1","key":"8_CR39","doi-asserted-by":"publisher","first-page":"btac775","DOI":"10.1093\/bioinformatics\/btac775","volume":"39","author":"MSB Raredon","year":"2023","unstructured":"Raredon, M.S.B., et al.: Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics. 39(1), btac775 (2023)","journal-title":"Bioinformatics"},{"issue":"1","key":"8_CR40","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s13059-021-02286-2","volume":"22","author":"R Dries","year":"2021","unstructured":"Dries, R., et al.: Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol. 22(1), 78 (2021)","journal-title":"Genome Biol."},{"issue":"1","key":"8_CR41","doi-asserted-by":"publisher","first-page":"4429","DOI":"10.1038\/s41467-022-32111-8","volume":"13","author":"X Shao","year":"2022","unstructured":"Shao, X., et al.: Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat. Commun. 13(1), 4429 (2022)","journal-title":"Nat. Commun."},{"issue":"12","key":"8_CR42","doi-asserted-by":"publisher","first-page":"1698","DOI":"10.1038\/s41588-021-00972-2","volume":"53","author":"L Garcia-Alonso","year":"2021","unstructured":"Garcia-Alonso, L., et al.: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat. Genet. 53(12), 1698\u20131711 (2021)","journal-title":"Nat. Genet."},{"issue":"1","key":"8_CR43","doi-asserted-by":"publisher","first-page":"2084","DOI":"10.1038\/s41467-020-15968-5","volume":"11","author":"Z Cang","year":"2020","unstructured":"Cang, Z., Nie, Q.: Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nat. Commun. 11(1), 2084 (2020)","journal-title":"Nat. Commun."},{"issue":"2","key":"8_CR44","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41592-022-01728-4","volume":"20","author":"Z Cang","year":"2023","unstructured":"Cang, Z., et al.: Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nat. Methods. 20(2), 218\u2013228 (2023)","journal-title":"Nat. Methods"},{"issue":"8","key":"8_CR45","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1016\/j.str.2023.05.017","volume":"31","author":"M Castelli","year":"2023","unstructured":"Castelli, M., et al.: How aberrant N-glycosylation can alter protein functionality and ligand binding: an atomistic view. Structure. 31(8), 987\u20131004.e8 (2023)","journal-title":"Structure"},{"issue":"12","key":"8_CR46","doi-asserted-by":"publisher","first-page":"dev170506","DOI":"10.1242\/dev.170506","volume":"146","author":"S Tritschler","year":"2019","unstructured":"Tritschler, S., et al.: Concepts and limitations for learning developmental trajectories from single cell genomics. Development. 146(12), dev170506 (2019)","journal-title":"Development"},{"issue":"1","key":"8_CR47","doi-asserted-by":"publisher","first-page":"7603","DOI":"10.1038\/s41467-023-43220-3","volume":"14","author":"H Xu","year":"2023","unstructured":"Xu, H., et al.: SPACEL: deep learning-based characterization of spatial transcriptome architectures. Nat. Commun. 14(1), 7603 (2023)","journal-title":"Nat. Commun."},{"key":"8_CR48","doi-asserted-by":"publisher","first-page":"2588","DOI":"10.1016\/j.csbj.2021.04.060","volume":"19","author":"N Adossa","year":"2021","unstructured":"Adossa, N., et al.: Computational strategies for single-cell multi-omics integration. Comput. Struct. Biotechnol. J. 19, 2588\u20132596 (2021)","journal-title":"Comput. Struct. Biotechnol. J."},{"issue":"2","key":"8_CR49","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.tig.2021.08.012","volume":"38","author":"P Rautenstrauch","year":"2022","unstructured":"Rautenstrauch, P., et al.: Intricacies of single-cell multi-omics data integration. Trends Genet. 38(2), 128\u2013139 (2022)","journal-title":"Trends Genet."},{"issue":"7993","key":"8_CR50","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/s41586-023-06837-4","volume":"625","author":"AJC Russell","year":"2024","unstructured":"Russell, A.J.C., et al.: Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature. 625(7993), 101\u2013109 (2024)","journal-title":"Nature"}],"container-title":["Advances in Experimental Medicine and Biology","Molecular Male Reproductive Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-82990-1_8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T17:04:28Z","timestamp":1745946268000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-82990-1_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"ISBN":["9783031829895","9783031829901"],"references-count":50,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-82990-1_8","relation":{},"ISSN":["0065-2598","2214-8019"],"issn-type":[{"value":"0065-2598","type":"print"},{"value":"2214-8019","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]},"assertion":[{"value":"30 April 2025","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}