{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:56Z","timestamp":1753875836068,"version":"3.41.2"},"reference-count":92,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T00:00:00Z","timestamp":1745193600000},"content-version":"vor","delay-in-days":51,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Center for Intelligent Drug Systems and Smart Bio-devices"},{"name":"Cancer and Immunology Research Center","award":["114W031101"],"award-info":[{"award-number":["114W031101"]}]},{"name":"Featured Areas Research Center Program"},{"name":"Higher Education Sprout Project and Yushan Young Fellow Program","award":["113C51N055"],"award-info":[{"award-number":["113C51N055"]}]},{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["NSTC 113-2740-B-400-005","113-2321-B-A49-025","113-2634-F-039-001","113-2221-E-A49-160-MY3"],"award-info":[{"award-number":["NSTC 113-2740-B-400-005","113-2321-B-A49-025","113-2634-F-039-001","113-2221-E-A49-160-MY3"]}],"id":[{"id":"10.13039\/100020595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004737","name":"National Health Research Institutes","doi-asserted-by":"publisher","award":["NHRI-EX113-11320BI","NHRI-EX114-11320BI"],"award-info":[{"award-number":["NHRI-EX113-11320BI","NHRI-EX114-11320BI"]}],"id":[{"id":"10.13039\/501100004737","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Encoding spatially resolved transcriptomics (SRT) data serves to identify the biological semantics of RNA expression within the tissue while preserving spatial characteristics. Depending on the analytical scenario, one may focus on different contextual structures of tissues. For instance, anatomical regions reveal consistent patterns by focusing on spatial homogeneity, while elucidating complex tumor micro-environments requires more expression heterogeneity. However, current spatial encoding methods lack consideration of the tissue context. Meanwhile, most developed SRT technologies are still limited in providing exact patterns of intact tissues due to limitations such as low resolution or missed measurements. Here, we propose STForte, a novel pairwise graph autoencoder-based approach with cross-reconstruction and adversarial distribution matching, to model the spatial homogeneity and expression heterogeneity of SRT data. STForte extracts interpretable latent encodings, enabling downstream analysis by accurately portraying various tissue contexts. Moreover, STForte allows spatial imputation using only spatial consistency to restore the biological patterns of unobserved locations or low-quality cells, thereby providing fine-grained views to enhance the SRT analysis. Extensive evaluations of datasets under different scenarios and SRT platforms demonstrate that STForte is a scalable and versatile tool for providing enhanced insights into spatial data analysis.<\/jats:p>","DOI":"10.1093\/bib\/bbaf174","type":"journal-article","created":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T03:57:20Z","timestamp":1745207840000},"source":"Crossref","is-referenced-by-count":0,"title":["STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6778-7034","authenticated-orcid":false,"given":"Yuxuan","family":"Pang","sequence":"first","affiliation":[{"name":"Division of Health Medical Intelligence , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]},{"name":"The University of Tokyo , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]}]},{"given":"Chunxuan","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Data Science, The Chinese University of Hong Kong , Shenzhen (CUHK-Shenzhen), 2001 Longxiang Road, Longgang, Shenzhen, 518172 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5598-2521","authenticated-orcid":false,"given":"Yao-zhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Division of Health Medical Intelligence , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]},{"name":"The University of Tokyo , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7076-8432","authenticated-orcid":false,"given":"Zhuo","family":"Wang","sequence":"additional","affiliation":[{"name":"Warshel Institute for Computational Biology , School of Medicine, , Shenzhen (CUHK-Shenzhen), 2001 Longxiang Road, Longgang, Shenzhen, 518172 ,","place":["China"]},{"name":"The Chinese University of Hong Kong , School of Medicine, , Shenzhen (CUHK-Shenzhen), 2001 Longxiang Road, Longgang, Shenzhen, 518172 ,","place":["China"]},{"name":"School of Medicine, The Chinese University of Hong Kong , Shenzhen (CUHK-Shenzhen), 2001 Longxiang Road, Longgang, Shenzhen, 518172 ,","place":["China"]}]},{"given":"Seiya","family":"Imoto","sequence":"additional","affiliation":[{"name":"Division of Health Medical Intelligence , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]},{"name":"The University of Tokyo , Human Genome Center, The Institute of Medical Science, , 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639 ,","place":["Japan"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0283-7712","authenticated-orcid":false,"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University , No. 75 Bo-Ai Street, Hsinchu 300 ,","place":["Taiwan"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,21]]},"reference":[{"key":"2025042023564379600_ref1","doi-asserted-by":"publisher","first-page":"e2003243","DOI":"10.1371\/journal.pbio.2003243","article-title":"60 years ago, Francis crick changed the logic of biology","volume":"15","author":"Cobb","year":"2017","journal-title":"PLoS Biol"},{"key":"2025042023564379600_ref2","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41592-020-01033-y","article-title":"Method of the year: Spatially resolved transcriptomics","volume":"18","author":"Marx","year":"2021","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref3","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","article-title":"Museum of spatial transcriptomics","volume":"19","author":"Moses","year":"2022","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref4","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","article-title":"Exploring tissue architecture using spatial transcriptomics","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"2025042023564379600_ref5","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/nbt.4260","article-title":"Identification of spatially associated subpopulations by combining scrnaseq and sequential fluorescence in situ hybridization data","volume":"36","author":"Zhu","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025042023564379600_ref6","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial transcriptomics at subspot resolution with bayesspace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2025042023564379600_ref7","doi-asserted-by":"publisher","first-page":"7203","DOI":"10.1038\/s41467-022-34879-1","article-title":"Spatially aware dimension reduction for spatial transcriptomics","volume":"13","author":"Shang","year":"2022","journal-title":"Nat Commun"},{"key":"2025042023564379600_ref8","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13073-024-01283-x","article-title":"Unsupervised spatially embedded deep representation of spatial transcriptomics","volume":"16","author":"Xu","year":"2024","journal-title":"Genome Med"},{"key":"2025042023564379600_ref9","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41592-021-01255-8","article-title":"Spagcn: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network","volume":"18","author":"Hu","year":"2021","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref10","doi-asserted-by":"publisher","first-page":"e131","DOI":"10.1093\/nar\/gkac901","article-title":"DeepST: Identifying spatial domains in spatial transcriptomics by deep learning","volume":"50","author":"Xu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025042023564379600_ref11","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1038\/s41467-022-29439-6","article-title":"Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder","volume":"13","author":"Dong","year":"2022","journal-title":"Nat Commun"},{"key":"2025042023564379600_ref12","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41467-023-36796-3","article-title":"Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with graphst","volume":"14","author":"Long","year":"2023","journal-title":"Nat Commun"},{"key":"2025042023564379600_ref13","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1038\/s41592-024-02215-8","article-title":"Benchmarking spatial clustering methods with spatially resolved transcriptomics data","volume":"21","author":"Yuan","year":"2024","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref14","doi-asserted-by":"publisher","first-page":"026583","DOI":"10.1101\/cshperspect.a026583","article-title":"Spatial heterogeneity in the tumor microenvironment","volume":"6","author":"Yuan","year":"2016","journal-title":"Cold Spring Harb Perspect Med"},{"key":"2025042023564379600_ref15","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s40164-022-00277-y","article-title":"Heterogeneity of the tumor immune microenvironment and its clinical relevance","volume":"11","author":"Jia","year":"2022","journal-title":"Exp Hematol Oncol"},{"key":"2025042023564379600_ref16","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/s41698-022-00272-w","article-title":"Tumor microenvironment heterogeneity an important mediator of prostate cancer progression and therapeutic resistance","volume":"6","author":"Ge","year":"2022","journal-title":"npj Precis Oncol"},{"key":"2025042023564379600_ref17","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1038\/s41587-021-01182-1","article-title":"Spatial components of molecular tissue biology","volume":"40","author":"Palla","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025042023564379600_ref18","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1038\/s41592-019-0548-y","article-title":"High-definition spatial transcriptomics for in situ tissue profiling","volume":"16","author":"Vickovic","year":"2019","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref19","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1126\/science.aaw1219","article-title":"Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution","volume":"363","author":"Rodriques","year":"2019","journal-title":"Science"},{"key":"2025042023564379600_ref20","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using dna nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"2025042023564379600_ref21","doi-asserted-by":"publisher","first-page":"3953","DOI":"10.1016\/j.cell.2024.05.055","article-title":"Open-st: High-resolution spatial transcriptomics in 3d","volume":"187","author":"Schott","year":"2024","journal-title":"Cell"},{"key":"2025042023564379600_ref23","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"Stahl","year":"2016","journal-title":"Science"},{"key":"2025042023564379600_ref24","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1038\/s41596-018-0045-2","article-title":"Barcoded solid-phase rna capture for spatial transcriptomics profiling in mammalian tissue sections","volume":"13","author":"Salm\u00e9n","year":"2018","journal-title":"Nat Protoc"},{"key":"2025042023564379600_ref25","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1038\/s41587-021-01075-3","article-title":"Super-resolved spatial transcriptomics by deep data fusion","volume":"40","author":"Bergenstr\u00e5hle","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025042023564379600_ref26","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1038\/s41587-023-02019-9","article-title":"Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology","volume":"42","author":"Zhang","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2025042023564379600_ref27","doi-asserted-by":"publisher","first-page":"013","DOI":"10.1093\/bib\/bbad013","article-title":"DIST: Spatial transcriptomics enhancement using deep learning","volume":"24","author":"Zhao","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025042023564379600_ref28","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkad169","article-title":"The spatial landscape of gene expression isoforms in tissue sections","volume":"51","author":"Lebrigand","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025042023564379600_ref29","doi-asserted-by":"crossref","first-page":"289","DOI":"10.32614\/RJ-2016-021","article-title":"Mclust 5: Clustering, classification and density estimation using gaussian finite mixture models","volume":"8","author":"Scrucca","year":"2016","journal-title":"The R journal"},{"key":"2025042023564379600_ref30","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1620\/tjem.214.213","article-title":"Fatty acid binding protein: Localization and functional significance in the brain","volume":"214","author":"Owada","year":"2008","journal-title":"Tohoku J Exp Med"},{"key":"2025042023564379600_ref31","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/S0169-328X(97)00023-5","article-title":"A newly identified membrane protein localized exclusively in intracellular organelles of neurons","volume":"46","author":"Kadota","year":"1997","journal-title":"Mol Brain Res"},{"key":"2025042023564379600_ref32","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1016\/S0306-4522(01)00003-3","article-title":"Neuronal bc1 rna: Co-expression with growth-associated protein-43 messenger rna","volume":"103","author":"Lin","year":"2001","journal-title":"Neuroscience"},{"key":"2025042023564379600_ref33","doi-asserted-by":"publisher","first-page":"6449","DOI":"10.1523\/JNEUROSCI.3076-20.2021","article-title":"I.: Generation and characterization of a cell type-specific, inducible cre-driver line to study olfactory processing","volume":"41","author":"Koldaeva","year":"2021","journal-title":"J Neurosci"},{"key":"2025042023564379600_ref34","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1007\/s10735-007-9115-4","article-title":"Molecular identity of olfactory bulb interneurons: Transcriptional codes of periglomerular neuron subtypes","volume":"38","author":"Allen","year":"2007","journal-title":"J Mol Histol"},{"key":"2025042023564379600_ref35","doi-asserted-by":"publisher","first-page":"1197","DOI":"10.1038\/s41598-022-26434-1","article-title":"Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell rna-seq data","volume":"13","author":"Hsu","year":"2023","journal-title":"Sci Rep"},{"key":"2025042023564379600_ref36","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1002\/stem.1137","article-title":"Roles of planar cell polarity signaling in maturation of neuronal precursor cells in the postnatal mouse olfactory bulb","volume":"30","author":"Hirota","year":"2012","journal-title":"Stem Cells"},{"key":"2025042023564379600_ref37","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1007\/BF00305720","article-title":"Parvalbumin-immunoreactive structures in the hippocampus of the human adult","volume":"264","author":"Braak","year":"1991","journal-title":"Cell Tissue Res"},{"key":"2025042023564379600_ref38","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nn.2536","article-title":"Chordin-induced lineage plasticity of adult svz neuroblasts after demyelination","volume":"13","author":"Jablonska","year":"2010","journal-title":"Nat Neurosci"},{"key":"2025042023564379600_ref39","doi-asserted-by":"publisher","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From louvain to Leiden: Guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci Rep"},{"key":"2025042023564379600_ref40","doi-asserted-by":"publisher","first-page":"1881","DOI":"10.1007\/s13277-013-1253-6","article-title":"Human kallikrein 2 (klk2) promotes prostate cancer cell growth via function as a modulator to promote the ara70-enhanced androgen receptor transactivation","volume":"35","author":"Shang","year":"2014","journal-title":"Tumor Biology"},{"key":"2025042023564379600_ref41","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s00439-012-1229-4","article-title":"Hoxb13 is a susceptibility gene for prostate cancer: Results from the international consortium for prostate cancer genetics (icpcg)","volume":"132","author":"Xu","year":"2013","journal-title":"Hum Genet"},{"key":"2025042023564379600_ref42","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1056\/NEJMoa1110000","article-title":"Germline mutations in hoxb13 and prostate-cancer risk","volume":"366","author":"Ewing","year":"2012","journal-title":"N Engl J Med"},{"key":"2025042023564379600_ref43","doi-asserted-by":"publisher","first-page":"2119","DOI":"10.1016\/j.ajpath.2019.07.007","article-title":"Prostate cancer: The role of inflammation and chemokines","volume":"189","author":"Rani","year":"2019","journal-title":"Am J Pathol"},{"key":"2025042023564379600_ref44","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1093\/cei\/uxab039","article-title":"Does CCL19 act as a double-edged sword in cancer development?","volume":"207","author":"Gowhari Shabgah","year":"2021","journal-title":"Clin Exp Immunol"},{"key":"2025042023564379600_ref45","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1083\/jcb.132.3.299","article-title":"Role of CD3 gamma in T cell receptor assembly","volume":"132","author":"Dietrich","year":"1996","journal-title":"J Cell Biol"},{"key":"2025042023564379600_ref46","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1002\/j.1460-2075.1991.tb08023.x","article-title":"The cd3\u2013gamma and cd3\u2013delta subunits of the t cell antigen receptor can be expressed within distinct functional tcr\/cd3 complexes","volume":"10","author":"Alarc\u00f3n","year":"1991","journal-title":"EMBO J"},{"key":"2025042023564379600_ref47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2012\/925135","article-title":"Cd4$^+$t cells: Differentiation and functions","volume":"2012","author":"Camara","year":"2012","journal-title":"Clin Dev Immunol"},{"key":"2025042023564379600_ref48","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1093\/intimm\/2.10.973","article-title":"Distribution of the CD68 macrophage\/myeloid associated antigen","volume":"2","author":"Pulford","year":"1990","journal-title":"Int Immunol"},{"key":"2025042023564379600_ref49","doi-asserted-by":"publisher","first-page":"6786","DOI":"10.1073\/pnas.1805542115","article-title":"Critical role of integrin cd11c in splenic dendritic cell capture of missing-self cd47 cells to induce adaptive immunity","volume":"115","author":"Wu","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"2025042023564379600_ref50","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2017.00563","article-title":"A unique cellular and molecular microenvironment is present in tertiary lymphoid organs of patients with spontaneous prostate cancer regression","volume":"8","author":"Garc\u00eda-Hern\u00e1ndez","year":"2017","journal-title":"Front Immunol"},{"key":"2025042023564379600_ref51","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/s41568-019-0144-6","article-title":"Tertiary lymphoid structures in the era of cancer immunotherapy","volume":"19","author":"Saut\u00e8s-Fridman","year":"2019","journal-title":"Nat Rev Cancer"},{"key":"2025042023564379600_ref52","doi-asserted-by":"publisher","first-page":"1871","DOI":"10.1126\/science.294.5548.1871","article-title":"Prostaglandins and leukotrienes: Advances in eicosanoid biology","volume":"294","author":"Funk","year":"2001","journal-title":"Science"},{"key":"2025042023564379600_ref53","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/0014-5793(88)80847-0","article-title":"Primary structure of sheep prostaglandin endoperoxide synthase deduced from cdna sequence","volume":"231","author":"Yokoyama","year":"1988","journal-title":"FEBS Lett"},{"key":"2025042023564379600_ref54","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1016\/j.cell.2015.08.015","article-title":"Cyclooxygenase-dependent tumor growth through evasion of immunity","volume":"162","author":"Zelenay","year":"2015","journal-title":"Cell"},{"key":"2025042023564379600_ref55","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1124\/pr.59.3.1","article-title":"Membrane prostaglandin e synthase-1: A novel therapeutic target","volume":"59","author":"Samuelsson","year":"2007","journal-title":"Pharmacol Rev"},{"key":"2025042023564379600_ref56","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/s13148-015-0110-4","article-title":"Epigenetics override pro-inflammatory ptgs transcriptomic signature towards selective hyperactivation of pge2 in colorectal cancer","volume":"7","author":"Cebola","year":"2015","journal-title":"Clin Epigenetics"},{"key":"2025042023564379600_ref57","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41586-022-04918-4","article-title":"Single-cell roadmap of human gonadal development","volume":"607","author":"Garcia-Alonso","year":"2022","journal-title":"Nature"},{"key":"2025042023564379600_ref58","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41592-022-01728-4","article-title":"Screening cell\u2013cell communication in spatial transcriptomics via collective optimal transport","volume":"20","author":"Cang","year":"2023","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref59","doi-asserted-by":"publisher","first-page":"5239","DOI":"10.1111\/bph.13331","article-title":"Prostaglandin e2 and the ep receptors in malignancy: Possible therapeutic targets?","volume":"172","author":"O\u2019Callaghan","year":"2015","journal-title":"Br J Pharmacol"},{"key":"2025042023564379600_ref60","doi-asserted-by":"publisher","first-page":"5029","DOI":"10.1038\/s41467-023-40271-4","article-title":"Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response","volume":"14","author":"Arora","year":"2023","journal-title":"Nat Commun"},{"key":"2025042023564379600_ref61","doi-asserted-by":"crossref","first-page":"10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"J Stat Mech: Theory Exp"},{"volume-title":"Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD \u201816","author":"","key":"2025042023564379600_ref62","doi-asserted-by":"publisher","DOI":"10.1145\/2939672.2939785"},{"key":"2025042023564379600_ref63","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1159\/000095110","article-title":"Myelin-associated Oligodendrocytic basic protein: A family of abundant CNS myelin proteins in search of a function","volume":"28","author":"Montague","year":"2006","journal-title":"Dev Neurosci"},{"key":"2025042023564379600_ref64","doi-asserted-by":"publisher","first-page":"1713","DOI":"10.1111\/j.1471-4159.1986.tb13079.x","article-title":"Distribution of glial fibrillary acidic protein in gliosed human white matter","volume":"47","author":"Newcombe","year":"1986","journal-title":"J Neurochem"},{"key":"2025042023564379600_ref65","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1016\/j.brainres.2004.02.003","article-title":"Interlaminar astroglia of the cerebral cortex: A marker of the primate brain","volume":"1006","author":"Colombo","year":"2004","journal-title":"Brain Res"},{"key":"2025042023564379600_ref66","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1016\/j.neuron.2018.09.027","article-title":"Neonatal tbr1 dosage controls cortical layer 6 connectivity","volume":"100","author":"Fazel Darbandi","year":"2018","journal-title":"Neuron"},{"key":"2025042023564379600_ref67","doi-asserted-by":"publisher","first-page":"3272","DOI":"10.1002\/cne.22399","article-title":"Molecular analysis of neocortical layer structure in the ferret","volume":"518","author":"Rowell","year":"2010","journal-title":"J Comp Neurol"},{"key":"2025042023564379600_ref68","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/j.cell.2012.02.052","article-title":"Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures","volume":"149","author":"Zeng","year":"2012","journal-title":"Cell"},{"key":"2025042023564379600_ref69","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1097\/nen.0b013e3180301c06","article-title":"Layer-specific markers as probes for neuron type identity in human neocortex and malformations of cortical development","volume":"66","author":"Hevner","year":"2007","journal-title":"J Neuropathol Exp Neurol"},{"key":"2025042023564379600_ref70","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/j.neulet.2014.07.031","article-title":"Reln-expressing neuron density in layer i of the superior temporal lobe is similar in human brains with autism and in age-matched controls","volume":"579","author":"Camacho","year":"2014","journal-title":"Neurosci Lett"},{"key":"2025042023564379600_ref71","doi-asserted-by":"publisher","first-page":"7826","DOI":"10.1523\/JNEUROSCI.1866-06.2006","article-title":"Expression and function of snap-25 as a universal snare component in gabaergic neurons","volume":"26","author":"Tafoya","year":"2006","journal-title":"J Neurosci"},{"key":"2025042023564379600_ref72","first-page":"1124","article-title":"Partial alignment of multislice spatially resolved transcriptomics data","volume":"33","author":"Liu","year":"2023","journal-title":"Genome Res"},{"key":"2025042023564379600_ref73","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2025042023564379600_ref74","doi-asserted-by":"publisher","first-page":"D996","DOI":"10.1093\/nar\/gks1042","article-title":"Allen brain atlas: An integrated spatio-temporal portal for exploring the central nervous system","volume":"41","author":"Sunkin","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025042023564379600_ref75","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2015.00114","article-title":"Diverse subtypes of astrocytes and their development during corticogenesis","volume":"9","author":"Tabata","year":"2015","journal-title":"Front Neurosci"},{"key":"2025042023564379600_ref76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0002525","article-title":"Cortical layer 1 and layer 2\/3 astrocytes exhibit distinct calcium dynamics in vivo","volume":"3","author":"Takata","year":"2008","journal-title":"PloS One"},{"key":"2025042023564379600_ref77","doi-asserted-by":"publisher","DOI":"10.3389\/fnana.2021.791015","article-title":"Axonal and dendritic morphology of excitatory neurons in layer 2\/3 mouse barrel cortex imaged through whole-brain two-photon tomography and registered to a digital brain atlas","volume":"15","author":"Liu","year":"2022","journal-title":"Front Neuroanat"},{"key":"2025042023564379600_ref78","doi-asserted-by":"publisher","first-page":"52370","DOI":"10.7554\/eLife.52370","article-title":"Cortical ror $\\beta $ is required for layer 4 transcriptional identity and barrel integrity","volume":"9","author":"Clark","year":"2020","journal-title":"eLife"},{"key":"2025042023564379600_ref79","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1002\/cne.23875","article-title":"Fezf2 expression in layer 5 projection neurons of mature mouse motor cortex","volume":"524","author":"Tantirigama","year":"2016","journal-title":"J Comp Neurol"},{"key":"2025042023564379600_ref80","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1002\/cne.25539","article-title":"A multifaceted architectural framework of the mouse claustrum complex","volume":"531","author":"Grimstvedt","year":"2023","journal-title":"J Comp Neurol"},{"key":"2025042023564379600_ref81","doi-asserted-by":"publisher","DOI":"10.3389\/fnana.2019.00016","article-title":"Genetic elimination of connective tissue growth factor in the forebrain affects subplate neurons in the cortex and oligodendrocytes in the underlying white matter","volume":"13","author":"Yu","year":"2019","journal-title":"Front Neuroanat"},{"key":"2025042023564379600_ref82","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1111\/j.1601-183X.2008.00420.x","article-title":"Behavioral characterization of p311 knockout mice","volume":"7","author":"Taylor","year":"2008","journal-title":"Genes Brain Behav"},{"key":"2025042023564379600_ref83","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1111\/j.1471-4159.2004.02738.x","article-title":"P311 accelerates nerve regeneration of the axotomized facial nerve","volume":"91","author":"Fujitani","year":"2004","journal-title":"J Neurochem"},{"key":"2025042023564379600_ref84","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/j.jpba.2017.03.062","article-title":"Molecular fingerprinting of principal neurons in the rodent hippocampus: A neuroinformatics approach","volume":"144","author":"Hamilton","year":"2017","journal-title":"J Pharm Biomed Anal"},{"key":"2025042023564379600_ref85","doi-asserted-by":"publisher","first-page":"11794","DOI":"10.1073\/pnas.0812608106","article-title":"Genomic-anatomic evidence for distinct functional domains in hippocampal field ca1","volume":"106","author":"Dong","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"2025042023564379600_ref86","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1186\/1741-7007-11-106","article-title":"Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice","volume":"11","author":"Schmouth","year":"2013","journal-title":"BMC Biol"},{"key":"2025042023564379600_ref87","doi-asserted-by":"publisher","first-page":"12343","DOI":"10.1523\/JNEUROSCI.6108-08.2009","article-title":"Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons","volume":"29","author":"Molyneaux","year":"2009","journal-title":"J Neurosci"},{"key":"2025042023564379600_ref88","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1109\/TPAMI.2020.3032189","article-title":"Learning on attribute-missing graphs","volume":"44","author":"Chen","year":"2020","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"volume-title":"Proceedings of the Web Conference 2021. WWW \u201821","author":"","key":"2025042023564379600_ref89","doi-asserted-by":"publisher","DOI":"10.1145\/3442381.3449882"},{"volume-title":"Proceedings of the First Learning on Graphs Conference","author":"","key":"2025042023564379600_ref90"},{"key":"2025042023564379600_ref91","first-page":"37","article-title":"Autoencoders, unsupervised learning, and deep architectures","volume-title":"Proceedings of ICML Workshop on Unsupervised and Transfer Learning. Proceedings of Machine Learning Research","author":"Baldi","year":"2012"},{"volume-title":"Workshop Track of International Conference on Learning Representations (ICLR)","author":"","key":"2025042023564379600_ref92"},{"key":"2025042023564379600_ref93","article-title":"Generative adversarial nets","volume":"27","author":"Goodfellow","year":"2014","journal-title":"Advances in neural information processing systems"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/2\/bbaf174\/62958281\/bbaf174.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/2\/bbaf174\/62958281\/bbaf174.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T03:57:24Z","timestamp":1745207844000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf174\/8116686"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":92,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf174","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,3]]},"article-number":"bbaf174"}}