{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T11:51:31Z","timestamp":1773489091746,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T00:00:00Z","timestamp":1661817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Australia National Health and Medical Research Council (NHMRC) Investigator Grant","award":["APP1173469"],"award-info":[{"award-number":["APP1173469"]}]},{"name":"AIR@innoHK programme of the Innovation and Technology Commission of Hong Kong"},{"name":"Australia NHMRC Career Developmental Fellowship","award":["APP1111338"],"award-info":[{"award-number":["APP1111338"]}]},{"name":"Australian Research Council Discovery Early Career Researcher Award","award":["DE200100944"],"award-info":[{"award-number":["DE200100944"]}]},{"DOI":"10.13039\/100015539","name":"Australian Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015539","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Training Program Tuition Fee Offset and University of Sydney Postgraduate Award Stipend Scholarship"},{"name":"Research Training Program Tuition Fee Offset and Stipend Scholarship and Chen Family Research Scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>With the recent surge of large-cohort scale single cell research, it is of critical importance that analytical methods can fully utilize the comprehensive characterization of cellular systems that single cell technologies produce to provide insights into samples from individuals. Currently, there is little consensus on the best ways to compress information from the complex data structures of these technologies to summary statistics that represent each sample (e.g. individuals).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present scFeatures, an approach that creates interpretable cellular and molecular representations of single-cell and spatial data at the sample level. We demonstrate that summarizing a broad collection of features at the sample level is both important for understanding underlying disease mechanisms in different experimental studies and for accurately classifying disease status of individuals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>scFeatures is publicly available as an R package at https:\/\/github.com\/SydneyBioX\/scFeatures. All data used in this study are publicly available with accession ID reported in the Section 2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac590","type":"journal-article","created":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T09:25:51Z","timestamp":1661851551000},"page":"4745-4753","source":"Crossref","is-referenced-by-count":17,"title":["scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2356-4031","authenticated-orcid":false,"given":"Yue","family":"Cao","sequence":"first","affiliation":[{"name":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"School of Mathematics and Statistics, The University of Sydney , Sydney, NSW 2006, Australia"}]},{"given":"Yingxin","family":"Lin","sequence":"additional","affiliation":[{"name":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"School of Mathematics and Statistics, The University of Sydney , Sydney, NSW 2006, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5253-4747","authenticated-orcid":false,"given":"Ellis","family":"Patrick","sequence":"additional","affiliation":[{"name":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"School of Mathematics and Statistics, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"Computational Systems Biology Group, Children\u2019s Medical Research Institute , Westmead, NSW 2145, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1098-3138","authenticated-orcid":false,"given":"Pengyi","family":"Yang","sequence":"additional","affiliation":[{"name":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"School of Mathematics and Statistics, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"Computational Systems Biology Group, Children\u2019s Medical Research Institute , Westmead, NSW 2145, Australia"}]},{"given":"Jean Yee Hwa","family":"Yang","sequence":"additional","affiliation":[{"name":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"School of Mathematics and Statistics, The University of Sydney , Sydney, NSW 2006, Australia"},{"name":"Laboratory of Data Discovery for Health Limited (D24H), Science Park , Hong Kong SAR, China"}]}],"member":"286","published-online":{"date-parts":[[2022,8,30]]},"reference":[{"key":"2022101415192481500_btac590-B1","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/s13059-019-1795-z","article-title":"A comparison of automatic cell identification methods for single-cell RNA sequencing data","volume":"20","author":"Abdelaal","year":"2019","journal-title":"Genome Biol"},{"key":"2022101415192481500_btac590-B2","doi-asserted-by":"crossref","first-page":"eaba1983","DOI":"10.1126\/sciadv.aba1983","article-title":"Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis","volume":"6","author":"Adams","year":"2020","journal-title":"Sci. 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