{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T14:27:56Z","timestamp":1790173676800,"version":"4.1.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T00:00:00Z","timestamp":1706832000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Ministry of Education and Research","award":["01KD2208A"],"award-info":[{"award-number":["01KD2208A"]}]},{"name":"International Max Planck Research School for Genome Science"},{"name":"G\u00f6ttingen Graduate Center for Neurosciences, Biophysics, und Molecular Biosciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Novel hypotheses in biomedical research are often developed or validated in model organisms such as mice and zebrafish and thus play a crucial role. However, due to biological differences between species, translating these findings into human applications remains challenging. Moreover, commonly used orthologous gene information is often incomplete and entails a significant information loss during gene-id conversion. To address these issues, we present a novel methodology for species-agnostic transfer learning with heterogeneous domain adaptation. We extended the cross-domain structure-preserving projection toward out-of-sample prediction. Our approach not only allows knowledge integration and translation across various species without relying on gene orthology but also identifies similar GO among the most influential genes composing the latent space for integration. Subsequently, during the alignment of latent spaces, each composed of species-specific genes, it is possible to identify functional annotations of genes missing from public orthology databases. We evaluated our approach with four different single-cell sequencing datasets focusing on cell-type prediction and compared it against related machine-learning approaches. In summary, the developed model outperforms related methods working without prior knowledge when predicting unseen cell types based on other species\u2019 data. The results demonstrate that our novel approach allows knowledge transfer beyond species barriers without the dependency on known gene orthology but utilizing the entire gene sets.<\/jats:p>","DOI":"10.1093\/bib\/bbae004","type":"journal-article","created":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T07:32:40Z","timestamp":1705563160000},"source":"Crossref","is-referenced-by-count":21,"title":["Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9963-7014","authenticated-orcid":false,"given":"Youngjun","family":"Park","sequence":"first","affiliation":[{"name":"Department of Medical Informatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen, Germany"},{"name":"International Max Planck Research Schools for Genome Science, Georg-August-Universit\u00e4t G\u00f6ttingen G\u00f6ttingen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils P","family":"Muttray","sequence":"additional","affiliation":[{"name":"Applied Statistics, Georg-August-Universit\u00e4t G\u00f6ttingen G\u00f6ttingen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Christin","family":"Hauschild","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen, Germany"},{"name":"Campus-Institute Data Science (CIDAS), Georg-August-Universit\u00e4t G\u00f6ttingen G\u00f6ttingen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,2,1]]},"reference":[{"issue":"1","key":"2024020211573592100_ref1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nrg1250","article-title":"The age of model organisms","volume":"5","author":"Davis","year":"2004","journal-title":"Nat Rev 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