{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T14:21:46Z","timestamp":1789395706262,"version":"build-2803163510"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T00:00:00Z","timestamp":1787443200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62072210"],"award-info":[{"award-number":["62072210"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Natural Science Foundation of Jilin Province","award":["20260102286JC"],"award-info":[{"award-number":["20260102286JC"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Rice blast caused by Magnaporthe oryzae (M. oryzae) is a dynamic cross-kingdom infection process involving rapid transcriptional reprogramming and spatial tissue remodeling across successive stages. Although single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) provide complementary information, most integration methods analyze stages independently and ignore temporal continuity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed the Plant Spatio-Temporal Integration Network (PSTN), which jointly learns stage-specific cell-to-space mappings through expression reconstruction and bidirectional maximum-similarity temporal regularization. Applied to matched rice scRNA-seq and ST data at 0, 12, and 24\u2009h, PSTN outperformed Tangram, SpaGE, cell2location, and DestVI across three gene-set sizes. At 4000 highly variable genes (HVGs), mean squared error (MSE) remained below 0.09 at all stages, with high gene-wise and spot-wise correlations. Mapping-structure and marker-based analyses recovered tissue-associated spatial and temporal patterns. Gene-permutation controls markedly reduced performance, demonstrating reliance on correct cross-modal gene correspondence. An independent mouse-cortex benchmark supported the static reconstruction component across systems. PSTN enables temporally coupled single-cell and spatial integration in dynamic host\u2013pathogen systems.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>PSTN is available at https:\/\/github.com\/zhuyuheng111\/PSTN. The Zenodo DOI for the repository is 10.5281\/zenodo.21365720.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag637","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T11:44:26Z","timestamp":1787312666000},"source":"Crossref","is-referenced-by-count":0,"title":["Plant Spatio-Temporal Integration Network (PSTN): a framework for dynamic single-cell and spatial transcriptomics in fungal\u2013plant interactions"],"prefix":"10.1093","volume":"42","author":[{"given":"Yuheng","family":"Zhu","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Jilin University , Jilin 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2058-7123","authenticated-orcid":false,"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University , Jilin 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Plant Protection, China Agricultural University , Beijing 100193,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enshuang","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University , Jilin 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinfei","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University , Jilin 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanbo","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University , Jilin 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