{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,26]],"date-time":"2026-04-26T08:42:20Z","timestamp":1777192940733,"version":"3.51.4"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T00:00:00Z","timestamp":1552608000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Commission of a H2020","award":["675743"],"award-info":[{"award-number":["675743"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore the full heterogeneity of a biological sample at the single-cell level is currently limited by the number of markers measured simultaneously on a single panel.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To extend the number of markers per cell, we propose an in silico method to integrate CyTOF datasets measured using multiple panels that share a set of markers. Additionally, we present an approach to select the most informative markers from an existing CyTOF dataset to be used as a shared marker set between panels. We demonstrate the feasibility of our methods by evaluating the quality of clustering and neighborhood preservation of the integrated dataset, on two public CyTOF datasets. We illustrate that by computationally extending the number of markers we can further untangle the heterogeneity of mass cytometry data, including rare cell-population detection.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Implementation is available on GitHub (https:\/\/github.com\/tabdelaal\/CyTOFmerge).<\/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\/btz180","type":"journal-article","created":{"date-parts":[[2019,3,14]],"date-time":"2019-03-14T20:29:22Z","timestamp":1552595362000},"page":"4063-4071","source":"Crossref","is-referenced-by-count":31,"title":["CyTOFmerge: integrating mass cytometry data across multiple panels"],"prefix":"10.1093","volume":"35","author":[{"given":"Tamim","family":"Abdelaal","sequence":"first","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Delft, The Netherlands"},{"name":"Leiden Computational Biology Center, Leiden University Medical Center , ZC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"H\u00f6llt","sequence":"additional","affiliation":[{"name":"Leiden Computational Biology Center, Leiden University Medical Center , ZC Leiden, The Netherlands"},{"name":"Computer Graphics and Visualization Group, Delft University of Technology , XE Delft, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"van Unen","sequence":"additional","affiliation":[{"name":"Department of Immunohematology and Blood Transfusion"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boudewijn P F","family":"Lelieveldt","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Delft, The Netherlands"},{"name":"Leiden Computational Biology Center, Leiden University Medical Center , ZC Leiden, The Netherlands"},{"name":"Department of Radiology, Leiden University Medical Center , ZA Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frits","family":"Koning","sequence":"additional","affiliation":[{"name":"Department of Immunohematology and Blood Transfusion"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcel J T","family":"Reinders","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Delft, The Netherlands"},{"name":"Leiden Computational Biology Center, Leiden University Medical Center , ZC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmed","family":"Mahfouz","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Delft, The Netherlands"},{"name":"Leiden Computational Biology Center, Leiden University Medical Center , ZC Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,15]]},"reference":[{"key":"2023013108270946400_btz180-B1","first-page":"1","article-title":"Predicting cell populations in single cell mass cytometry data","author":"Abdelaal","year":"2019","journal-title":"Cytom. 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