{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T03:16:22Z","timestamp":1773544582882,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The developmental stage of a cell can be determined by cellular morphology or various other observable indicators. Such classical markers could be complemented with modern surrogates, like whole-genome transcription profiles, that can encode the state of the entire organism and provide increased quantitative resolution. Recent findings suggest that such profiles provide sufficient information to reliably predict the cell's developmental stage.<\/jats:p>\n               <jats:p>Results: We use whole-genome transcription data and several data projection methods to infer differentiation stage prediction models for embryonic cells. Given a transcription profile of an uncharacterized cell, these models can then predict its developmental stage. In a series of experiments comprising 14 datasets from the Gene Expression Omnibus, we demonstrate that the approach is robust and has excellent prediction ability both within a specific cell line and across different cell lines.<\/jats:p>\n               <jats:p>Availability: Model inference and computational evaluation procedures in the form of Python scripts and accompanying datasets are available at http:\/\/www.biolab.si\/supp\/stagerank.<\/jats:p>\n               <jats:p>Contact: \u00a0blaz.zupan@fri.uni-lj.si<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr422","type":"journal-article","created":{"date-parts":[[2011,7,16]],"date-time":"2011-07-16T02:00:39Z","timestamp":1310781639000},"page":"2546-2553","source":"Crossref","is-referenced-by-count":16,"title":["Stage prediction of embryonic stem cell differentiation from genome-wide expression data"],"prefix":"10.1093","volume":"27","author":[{"given":"Lan","family":"Zagar","sequence":"first","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Mulas","sequence":"additional","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Garagna","sequence":"additional","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maurizio","family":"Zuccotti","sequence":"additional","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Bellazzi","sequence":"additional","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Blaz","family":"Zupan","sequence":"additional","affiliation":[{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"1 Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia, 2Centre for Tissue Engineering, University of Pavia, Pavia, 3Dipartimento di Biologia Animale, Laboratorio di Biologia dello Sviluppo, University of Pavia, Pavia, 4Sezione di Istologia ed Embriologia, Dipartimento di Medicina Sperimentale, University of Parma, Parma, 5Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, Italy and 6Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, 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