{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T18:39:38Z","timestamp":1791052778195,"version":"4.1.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biotechnology and Biological Sciences Research 610 Council"},{"name":"Fly Cell Atlas","award":["BB\/T014563\/1"],"award-info":[{"award-number":["BB\/T014563\/1"]}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Core Capability","award":["BB\/CCG2220\/1"],"award-info":[{"award-number":["BB\/CCG2220\/1"]}]},{"name":"Earlham Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Basic biological processes are shared across animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell-type gene expression between species reveals conserved and divergent cellular functions. However, as phylogenetic distance increases, gene-based comparisons become less informative. The gene ontology (GO) knowledgebase offers a solution by serving as the most comprehensive resource of gene functions across a vast diversity of species, providing a bridge for distant species comparisons.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present scGOclust, a computational tool that constructs de novo cellular functional profiles using GO terms, facilitating systematic and robust comparisons within and across species. We applied scGOclust to analyse and compare the heart, gut, and kidney between mouse and fly, and whole-body data from Caenorhabditis elegans and Hydra vulgaris. We show that scGOclust effectively recapitulates the function spectrum of different cell types, characterizes functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Additionally, we identified subpopulations within the fly crop that show circadian rhythm-regulated secretory properties and hypothesize an analogy between fly principal cells from different segments and distinct mouse kidney tubules. We envision scGOclust as an effective tool for uncovering functionally analogous cell types or organs across distant species, offering fresh perspectives on evolutionary and functional biology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ScGOclust is publicly available on CRAN: https:\/\/cran.r-project.org\/web\/packages\/scGOclust\/index.html and development versions are available on GitHub: github.com\/Papatheodorou-Group\/scGOclust\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf195","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:03:20Z","timestamp":1752584600000},"page":"i571-i579","source":"Crossref","is-referenced-by-count":3,"title":["ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9738-9726","authenticated-orcid":false,"given":"Yuyao","family":"Song","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory , Wellcome Genome Campus , Hinxton, CB10 1SD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1494-1402","authenticated-orcid":false,"given":"Yanhui","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9595-5146","authenticated-orcid":false,"given":"Julian","family":"Dow","sequence":"additional","affiliation":[{"name":"School of Molecular Biosciences, University of Glasgow , Glasgow G12 8QQ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7542-472X","authenticated-orcid":false,"given":"Norbert","family":"Perrimon","sequence":"additional","affiliation":[{"name":"Department of Genetics, Harvard Medical School , Boston, MA 02115,","place":["United States"]},{"name":"Howard Hughes Medical Institute , Chevy Chase, MD 20815,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7270-5470","authenticated-orcid":false,"given":"Irene","family":"Papatheodorou","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory , Wellcome Genome Campus , Hinxton, CB10 1SD,","place":["United Kingdom"]},{"name":"Earlham Institute , Norwich Research Park , Norwich, NR4 7UZ,","place":["United Kingdom"]},{"name":"Norwich Medical School, University of East Anglia , Norwich NR4 7UA,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,15]]},"reference":[{"key":"2025071509031565500_btaf195-B1","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1242\/dmm.003970","article-title":"Drosophila melanogaster as a model for human intestinal infection and pathology","volume":"4","author":"Apidianakis","year":"2011","journal-title":"Dis Model Mech"},{"key":"2025071509031565500_btaf195-B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. 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