{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T08:44:26Z","timestamp":1775119466316,"version":"3.50.1"},"reference-count":87,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T00:00:00Z","timestamp":1721260800000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2022YFA1106000"],"award-info":[{"award-number":["2022YFA1106000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2020YFA0113200"],"award-info":[{"award-number":["2020YFA0113200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32222026"],"award-info":[{"award-number":["32222026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170660"],"award-info":[{"award-number":["32170660"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92168205"],"award-info":[{"award-number":["92168205"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62088101"],"award-info":[{"award-number":["62088101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2021SHZDZX0100"],"award-info":[{"award-number":["2021SHZDZX0100"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The burgeoning generation of single-cell or spatial multiomic data allows for the characterization of gene regulation networks (GRNs) at an unprecedented resolution. However, the accurate reconstruction of GRNs from sparse and noisy single-cell or spatial multiomic data remains challenging.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present SCRIPro, a comprehensive computational framework that robustly infers GRNs for both single-cell and spatial multiomics data. SCRIPro first improves sample coverage through a density clustering approach based on multiomic and spatial similarities. Additionally, SCRIPro scans transcriptional regulator (TR) importance by performing chromatin reconstruction and in silico deletion analyses using a comprehensive reference covering 1292 human and 994 mouse TRs. Finally, SCRIPro combines TR-target importance scores derived from multiomic data with TR-target expression levels to ensure precise GRN reconstruction. We benchmarked SCRIPro on various datasets, including single-cell multiomic data from human B-cell lymphoma, mouse hair follicle development, Stereo-seq of mouse embryos, and Spatial-ATAC-RNA from mouse brain. SCRIPro outperforms existing motif-based methods and accurately reconstructs cell type-specific, stage-specific, and region-specific GRNs. Overall, SCRIPro emerges as a streamlined and fast method capable of reconstructing TR activities and GRNs for both single-cell and spatial multiomic data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SCRIPro is available at https:\/\/github.com\/wanglabtongji\/SCRIPro.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae466","type":"journal-article","created":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T11:53:14Z","timestamp":1721303594000},"source":"Crossref","is-referenced-by-count":10,"title":["Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro"],"prefix":"10.1093","volume":"40","author":[{"given":"Zhanhe","family":"Chang","sequence":"first","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"},{"name":"Frontier Science Center for Stem Cell Research, Tongji University , Shanghai, China"},{"name":"Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University , Shanghai, China"}]},{"given":"Yunfan","family":"Xu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"},{"name":"Frontier Science Center for Stem Cell Research, Tongji University , Shanghai, China"}]},{"given":"Xin","family":"Dong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"},{"name":"Frontier Science Center for Stem Cell Research, Tongji University , Shanghai, China"}]},{"given":"Yawei","family":"Gao","sequence":"additional","affiliation":[{"name":"Frontier Science Center for Stem Cell Research, Tongji University , Shanghai, China"},{"name":"Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University , Shanghai, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7573-3768","authenticated-orcid":false,"given":"Chenfei","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200092, China"},{"name":"Frontier Science Center for Stem Cell Research, Tongji University , Shanghai, China"},{"name":"National Key Laboratory of Autonomous Intelligent Unmanned Systems, Tongji University , Shanghai 200120, China"},{"name":"Frontier Science Center for Intelligent Autonomous Systems, Tongji University , Shanghai 200120, China"}]}],"member":"286","published-online":{"date-parts":[[2024,7,18]]},"reference":[{"key":"2024073019312383800_btae466-B1","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat Methods"},{"issue":"1","key":"2024073019312383800_btae466-B2","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.202302415","article-title":"MICA: a multi-omics method to predict gene regulatory networks in early human embryos","volume":"7","author":"Alanis-Lobato","year":"2024","journal-title":"Life Sci 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