{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T10:59:59Z","timestamp":1776164399919,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2222003"],"award-info":[{"award-number":["T2222003"]}],"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":["32170849"],"award-info":[{"award-number":["32170849"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Science and Technology of China","award":["2022YFA1105400"],"award-info":[{"award-number":["2022YFA1105400"]}]},{"name":"Guangdong Province Science and Technology Program","award":["2023B1212060050"],"award-info":[{"award-number":["2023B1212060050"]}]},{"name":"Guangdong Province Science and Technology Program","award":["2020B1212060052"],"award-info":[{"award-number":["2020B1212060052"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Transcriptomic analysis across species is increasingly used to reveal conserved gene regulations which implicate crucial regulators. Cross-species analysis of single-cell RNA sequencing (scRNA-seq) data provides new opportunities to identify the cellular and molecular conservations, especially for cell types and cell type-specific gene regulations. However, few methods have been developed to analyze cross-species scRNA-seq data to uncover both molecular and cellular conservations. Here, we built a tool called CACIMAR, which can perform cross-species analysis of cell identities, markers, regulations, and interactions using scRNA-seq profiles. Based on the weighted sum models of the conserved features, we developed different conservation scores to measure the conservation of cell types, regulatory networks, and intercellular interactions. Using publicly available scRNA-seq data on retinal regeneration in mice, zebrafish, and chick, we demonstrated four main functions of CACIMAR. First, CACIMAR allows to identify conserved cell types even in evolutionarily distant species. Second, the tool facilitates the identification of evolutionarily conserved or species-specific marker genes. Third, CACIMAR enables the identification of conserved intracellular regulations, including cell type-specific regulatory subnetworks and regulators. Lastly, CACIMAR provides a unique feature for identifying conserved intercellular interactions. Overall, CACIMAR facilitates the identification of evolutionarily conserved cell types, marker genes, intracellular regulations, and intercellular interactions, providing insights into the cellular and molecular mechanisms of species evolution.<\/jats:p>","DOI":"10.1093\/bib\/bbae283","type":"journal-article","created":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T12:40:08Z","timestamp":1717072808000},"source":"Crossref","is-referenced-by-count":4,"title":["CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data"],"prefix":"10.1093","volume":"25","author":[{"given":"Junyao","family":"Jiang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"School of Life Sciences , Westlake University, No. 600 Dunyu Road, Xihu District, Hangzhou, 310030 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinlian","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sunan","family":"Huang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fan","family":"Jiang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanran","family":"Liang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xueli","family":"Xu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7491-7001","authenticated-orcid":false,"given":"Jie","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Regenerative Biology , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangdong Provincial Key Laboratory of Biocomputing, , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"},{"name":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 , China"},{"name":"China-New Zealand Joint Laboratory on Biomedicine and Health , No. 190 Kaiyuan Road, Huangpu District, Guangzhou 510530 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,6,10]]},"reference":[{"key":"2024061011482997800_ref1","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1016\/j.cell.2019.11.010","article-title":"Cross-species single-cell analysis reveals divergence of the primate microglia program","volume":"179","author":"Geirsdottir","year":"2019","journal-title":"Cell"},{"key":"2024061011482997800_ref2","doi-asserted-by":"crossref","first-page":"eabb8598","DOI":"10.1126\/science.abb8598","article-title":"Gene regulatory networks controlling vertebrate retinal regeneration","volume":"370","author":"Hoang","year":"2020","journal-title":"Science"},{"key":"2024061011482997800_ref3","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1038\/s41588-022-01197-7","article-title":"Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types","volume":"54","author":"Li","year":"2022","journal-title":"Nat Genet"},{"key":"2024061011482997800_ref4","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41586-021-03465-8","article-title":"Comparative cellular analysis of motor cortex in human, marmoset and mouse","volume":"598","author":"Bakken","year":"2021","journal-title":"Nature"},{"key":"2024061011482997800_ref5","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1146\/annurev-cellbio-100616-060818","article-title":"How single-cell genomics is changing evolutionary and developmental biology","volume":"33","author":"Marioni","year":"2017","journal-title":"Annu Rev Cell Dev Biol"},{"key":"2024061011482997800_ref6","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/nrg3229","article-title":"Comparative studies of gene expression and the evolution of gene regulation","volume":"13","author":"Romero","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2024061011482997800_ref7","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/s41559-021-01580-3","article-title":"Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts","volume":"6","author":"Shafer","year":"2022","journal-title":"Nat Ecol Evol"},{"key":"2024061011482997800_ref8","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.66747","article-title":"Mapping single-cell atlases throughout Metazoa unravels cell type evolution","volume":"10","author":"Tarashansky","year":"2021","journal-title":"Elife"},{"key":"2024061011482997800_ref9","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024061011482997800_ref10","doi-asserted-by":"crossref","first-page":"6495","DOI":"10.1038\/s41467-023-41855-w","article-title":"Benchmarking strategies for cross-species integration of single-cell RNA sequencing data","volume":"14","author":"Song","year":"2023","journal-title":"Nat Commun"},{"key":"2024061011482997800_ref11","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1101\/gr.276868.122","article-title":"Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network","volume":"33","author":"Liu","year":"2023","journal-title":"Genome Res"},{"key":"2024061011482997800_ref12","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1093\/ilar\/ilx013","article-title":"Mouse genome informatics (MGI) resource: genetic, genomic, and biological knowledgebase for the laboratory mouse","volume":"58","author":"Eppig","year":"2017","journal-title":"ILAR J"},{"key":"2024061011482997800_ref13","doi-asserted-by":"crossref","first-page":"3041","DOI":"10.1093\/molbev\/msy194","article-title":"Two methods for mapping and visualizing associated data on phylogeny using Ggtree","volume":"35","author":"Yu","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2024061011482997800_ref14","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2022.105359","article-title":"IReNA: integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles","volume":"25","author":"Jiang","year":"2022","journal-title":"iScience"},{"key":"2024061011482997800_ref15","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024061011482997800_ref16","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/978-1-60761-987-1_18","article-title":"Cytoscape: software for visualization and analysis of biological networks","volume":"696","author":"Kohl","year":"2011","journal-title":"Methods Mol Biol"},{"key":"2024061011482997800_ref17","doi-asserted-by":"crossref","first-page":"3224","DOI":"10.1038\/s41467-022-30755-0","article-title":"Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data","volume":"13","author":"Dimitrov","year":"2022","journal-title":"Nat Commun"},{"key":"2024061011482997800_ref18","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa183","article-title":"SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics","volume":"48","author":"Cabello-Aguilar","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024061011482997800_ref19","article-title":"sankeyD3: D3 JavaScript Sankey graphs from","author":"Breitwieser","year":"2016"},{"key":"2024061011482997800_ref20","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","article-title":"Circlize implements and enhances circular visualization in R","volume":"30","author":"Gu","year":"2014","journal-title":"Bioinformatics"},{"key":"2024061011482997800_ref21","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: Elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"2024061011482997800_ref22","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.exer.2010.02.001","article-title":"Pax6a and Pax6b are required at different points in neuronal progenitor cell proliferation during zebrafish photoreceptor regeneration","volume":"90","author":"Thummel","year":"2010","journal-title":"Exp Eye Res"},{"key":"2024061011482997800_ref23","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nrn3783","article-title":"Retinal bipolar cells: elementary building blocks of vision","volume":"15","author":"Euler","year":"2014","journal-title":"Nat Rev Neurosci"},{"key":"2024061011482997800_ref24","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nrn3723","article-title":"M\u00fcller glial cell reprogramming and retina regeneration","volume":"15","author":"Goldman","year":"2014","journal-title":"Nat Rev Neurosci"},{"key":"2024061011482997800_ref25","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":"2024061011482997800_ref26","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.1093\/nar\/gkac276","article-title":"Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms","volume":"50","author":"Crow","year":"2022","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/4\/bbae283\/58180427\/bbae283.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/4\/bbae283\/58180427\/bbae283.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,10]],"date-time":"2024-06-10T07:49:07Z","timestamp":1718005747000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae283\/7690342"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,23]]},"references-count":26,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,5,23]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae283","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.01.23.576964","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7]]},"published":{"date-parts":[[2024,5,23]]},"article-number":"bbae283"}}