{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041325,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"Supplement_2","license":[{"start":{"date-parts":[[2020,12,31]],"date-time":"2020-12-31T00:00:00Z","timestamp":1609372800000},"content-version":"vor","delay-in-days":30,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006447","name":"University of Zurich","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006447","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University Hospital Zurich and University Hospital Basel"},{"name":"Tumor Profiler Consortium"},{"DOI":"10.13039\/501100022491","name":"Max Planck ETH Center for Learning Systems","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100022491","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/ratschlab\/scim.<\/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\/btaa843","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T07:44:22Z","timestamp":1600069462000},"page":"i919-i927","source":"Crossref","is-referenced-by-count":58,"title":["SCIM: universal single-cell matching with unpaired feature sets"],"prefix":"10.1093","volume":"36","author":[{"given":"Stefan G","family":"Stark","sequence":"first","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine , 8057 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanna","family":"Ficek","sequence":"additional","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine , 8057 Z\u00fcrich, Switzerland"},{"name":"Max Planck Institute for Intelligent Systems, Empirical Inference Department , 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Locatello","sequence":"additional","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Center for Learning Systems , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Department of Quantitative Biomedicine, University of Z\u00fcrich , 8057 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ximena","family":"Bonilla","sequence":"additional","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine , 8057 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phane","family":"Chevrier","sequence":"additional","affiliation":[{"name":"University Hospital Z\u00fcrich , 8091 Z\u00fcrich, Switzerl"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Franziska","family":"Singer","sequence":"additional","affiliation":[{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"University Hospital Z\u00fcrich , 8091 Z\u00fcrich Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Tumor Profiler Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudolf","family":"Aebersold","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faisal S","family":"Al-Quaddoomi","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas","family":"Albinus","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilaria","family":"Alborelli","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonali","family":"Andani","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Per-Olof","family":"Attinger","sequence":"additional","affiliation":[{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina","family":"Bacac","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Zurich , Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"},{"name":", Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Baumhoer","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beatrice","family":"Beck-Schimmer","sequence":"additional","affiliation":[{"name":"University of Zurich, VP Medicine , K\u00fcnstlergasse 15, 8001 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Beisel","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lara","family":"Bernasconi","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Clinical Trials Center , R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"},{"name":", R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Bertolini","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernd","family":"Bodenmiller","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ximena","family":"Bonilla","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruben","family":"Casanova","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phane","family":"Chevrier","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalia","family":"Chicherova","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maya","family":"D'Costa","sequence":"additional","affiliation":[{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esther","family":"Danenberg","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie","family":"Davidson","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica-Andreea Dr\u0103","family":"gan","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reinhard","family":"Dummer","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefanie","family":"Engler","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Erkens","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katja","family":"Eschbach","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cinzia","family":"Esposito","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Fedier","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro","family":"Ferreira","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanna","family":"Ficek","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anja L","family":"Frei","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruno","family":"Frey","sequence":"additional","affiliation":[{"name":"Roche Diagnostics GmbH , Nonnenwald 2, 82377 Penzberg , \u00a0 Germany"},{"name":", Nonnenwald 2, 82377 Penzberg , \u00a0 Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Goetze","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda","family":"Grob","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Gut","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Detlef","family":"G\u00fcnther","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 1-5\/10, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martina","family":"Haberecker","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pirmin","family":"Haeuptle","sequence":"additional","affiliation":[{"name":"Cantonal Hospital Baselland, Medical University Clinic , Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"},{"name":", Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viola","family":"Heinzelmann-Schwarz","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"},{"name":"University Hospital Basel, Gynecological Cancer Center , Spitalstrasse 21, 4031 Basel , \u00a0 Switzerland"},{"name":", Spitalstrasse 21, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvia","family":"Herter","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Zurich , Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"},{"name":", Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rene","family":"Holtackers","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tamara","family":"Huesser","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Zurich , Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"},{"name":", Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anja","family":"Irmisch","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francis","family":"Jacob","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Jacobs","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim M","family":"Jaeger","sequence":"additional","affiliation":[{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katharina","family":"Jahn","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alva R","family":"James","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip M","family":"Jermann","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Kahles","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdullah","family":"Kahraman","sequence":"additional","affiliation":[{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viktor H","family":"Koelzer","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Werner","family":"Kuebler","sequence":"additional","affiliation":[{"name":"University Hospital Basel , Spitalstrasse 21\/Petersgraben 4, 4031 Basel , \u00a0 Switzerland"},{"name":", Spitalstrasse 21\/Petersgraben 4, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack","family":"Kuipers","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian P","family":"Kunze","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Department of Information- and Communication Technology , Spitalstrasse 26, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Kurzeder","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Brustzentrum , Spitalstrasse 21, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kjong-Van","family":"Lehmann","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mitchell","family":"Levesque","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Lugert","sequence":"additional","affiliation":[{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerd","family":"Maass","sequence":"additional","affiliation":[{"name":"Roche Diagnostics GmbH , Nonnenwald 2, 82377 Penzberg , \u00a0 Germany"},{"name":", Nonnenwald 2, 82377 Penzberg , \u00a0 Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Manz","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Department of Medical Oncology and Hematology , R\u00e4mistrasse 100, 8091 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philipp","family":"Markolin","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julien","family":"Mena","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrike","family":"Menzel","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julian M","family":"Metzler","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Department of Gynecology , Frauenklinikstrasse 10, 8091 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicola","family":"Miglino","sequence":"additional","affiliation":[{"name":"Cantonal Hospital Baselland, Medical University Clinic , Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"},{"name":", Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuela S","family":"Milani","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Holger","family":"Moch","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Muenst","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Murri","sequence":"additional","affiliation":[{"name":"University of Zurich, Services and Support for Science IT , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlotte KY","family":"Ng","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":"University of Bern, Department of BioMedical Research , Murtenstrasse 35, 3008 Bern , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Nicolet","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Nowak","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick GA","family":"Pedrioli","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucas","family":"Pelkmans","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salvatore","family":"Piscuoglio","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"},{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Prummer","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathilde","family":"Ritter","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Rommel","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda L","family":"Rosano-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natascha","family":"Santacroce","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacobo Sarabia del","family":"Castillo","sequence":"additional","affiliation":[{"name":"University of Zurich, Institute of Molecular Life Sciences , Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"},{"name":", Winterthurerstrasse 190, 8057 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramona","family":"Schlenker","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, Roche Diagnostics GmbH , Nonnenwald 2, 82377 Penzberg , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petra C","family":"Schwalie","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Severin","family":"Schwan","sequence":"additional","affiliation":[{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"Sch\u00e4r","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriela","family":"Senti","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Clinical Trials Center , R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"},{"name":", R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Franziska","family":"Singer","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sujana","family":"Sivapatham","sequence":"additional","affiliation":[{"name":"University of Zurich, Department of Quantitative Biomedicine , Winterthurerstrasse 190, 8057 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Berend","family":"Snijder","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bettina","family":"Sobottka","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vipin T","family":"Sreedharan","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Stark","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel J","family":"Stekhoven","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre PA","family":"Theocharides","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Department of Medical Oncology and Hematology , R\u00e4mistrasse 100, 8091 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tinu M","family":"Thomas","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Tolnay","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vinko","family":"Tosevski","sequence":"additional","affiliation":[{"name":"Roche Pharmaceutical Research and Early Development, Roche Innovation Center Zurich , Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"},{"name":", Wagistrasse 10, 8952 Schlieren , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nora C","family":"Toussaint","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mustafa A","family":"Tuncel","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biosystems Science and Engineering , Mattenstrasse 26, 4058 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina","family":"Tusup","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Department of Dermatology , Gloriastrasse 31, 8091 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Audrey Van","family":"Drogen","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcus","family":"Vetter","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Brustzentrum & Tumorzentrum , Petersgraben 4, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatjana","family":"Vlajnic","sequence":"additional","affiliation":[{"name":"University Hospital Basel, Institute of Medical Genetics and Pathology , Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"},{"name":", Sch\u00f6nbeinstrasse 40, 4031 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Weber","sequence":"additional","affiliation":[{"name":"University Hospital Zurich, Clinical Trials Center , R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"},{"name":", R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter P","family":"Weber","sequence":"additional","affiliation":[{"name":"University Hospital Basel and University of Basel, Department of Surgery , Brustzentrum, Spitalstrasse 21, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebekka","family":"Wegmann","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Weller","sequence":"additional","affiliation":[{"name":"University Hospital and University of Zurich, Department of Neurology , Frauenklinikstrasse 26, 8091 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian","family":"Wendt","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norbert","family":"Wey","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Wicki","sequence":"additional","affiliation":[{"name":"Cantonal Hospital Baselland, Medical University Clinic , Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"},{"name":", Rheinstrasse 26, 4410 Liestal , \u00a0 Switzerland"},{"name":"University Hospital Basel and University of Basel, Department of Biomedicine , Hebelstrasse 20, 4031 Basel , Switzerland"},{"name":"University Hospital Basel, Centre for Neuroendocrine & Endocrine Tumours , Spitalstrasse 21\/Petersgraben 4, 4031 Basel , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernd","family":"Wollscheid","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuqing","family":"Yu","sequence":"additional","affiliation":[{"name":"ETH Zurich, NEXUS Personalized Health Technologies , John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":", John-von-Neumann-Weg 9, 8093 Zurich , \u00a0 Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johanna","family":"Ziegler","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Health Sciences and Technology , Otto-Stern-Weg 3, 8093 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Zimmermann","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universit\u00e4tstrasse 6 , 8092 Zurich , Switzerland"},{"name":"Swiss Institute of Bioinformatics, Zurich , Switzerland"},{"name":"University Hospital Zurich, Biomedical Informatics , Schmelzbergstrasse 26, 8006 Zurich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Zoche","sequence":"additional","affiliation":[{"name":"ETH Zurich, Department of Biology , Wolfgang-Pauli-Strasse 27, 8093 Zurich , Switzerland"},{"name":"F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"},{"name":", Grenzacherstrasse 124, 4070 Basel , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregor","family":"Zuend","sequence":"additional","affiliation":[{"name":"University Hospital Zurich , R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"},{"name":", R\u00e4mistrasse 100, 8091 Zurich , \u00a0 Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine , 8057 Z\u00fcrich, Switzerland"},{"name":"Department of Quantitative Biomedicine, University of Z\u00fcrich , 8057 Z\u00fcrich, Switzerland"},{"name":"Department of Biology, ETH Z\u00fcrich , 8093 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kjong-Van","family":"Lehmann","sequence":"additional","affiliation":[{"name":"Department of Computer Science , ETH Z\u00fcrich, 8092 Z\u00fcrich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Quartier Sorge B\u00e2timent Amphip\u00f4le , 1015 Lausanne, Switzerland"},{"name":"Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine , 8057 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,29]]},"reference":[{"key":"2023062409313499300_btaa843-B1","author":"Abadi","year":"2015"},{"key":"2023062409313499300_btaa843-B2","volume-title":"Network Flows: Theory, Algorithms, and Applications","author":"Ahuja","year":"1993"},{"key":"2023062409313499300_btaa843-B3","unstructured":"Amodio\n              M.\n             and \nKrishnaswamyS. \u00a02018. MAGAN: aligning biological manifolds. In Proceedings of the 35th International Conference on Machine Learning, PMLR, Vol. 80. pp. 215\u2013223. July\u00a010th-15th\u00a0Stockholm,Sweden. http:\/\/proceedings.mlr.press\/v80\/amodio18a.html."},{"key":"2023062409313499300_btaa843-B4","doi-asserted-by":"crossref","first-page":"6813","DOI":"10.1021\/ac901049w","article-title":"Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry","volume":"81","author":"Bandura","year":"2009","journal-title":"Anal. Chem"},{"key":"2023062409313499300_btaa843-B5","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro","year":"2015","journal-title":"Nature"},{"key":"2023062409313499300_btaa843-B6","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s13059-019-1645-z","article-title":"clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers","volume":"20","author":"Campbell","year":"2019","journal-title":"Genome Biol"},{"key":"2023062409313499300_btaa843-B7","doi-asserted-by":"crossref","first-page":"i48","DOI":"10.1093\/bioinformatics\/btaa443","article-title":"Unsupervised topological alignment for single-cell multi-omics integration","volume":"36","author":"Cao","year":"2020","journal-title":"Bioinformatics"},{"key":"2023062409313499300_btaa843-B8","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.cell.2017.04.016","article-title":"An immune atlas of clear cell renal cell carcinoma","volume":"169","author":"Chevrier","year":"2017","journal-title":"Cell"},{"key":"2023062409313499300_btaa843-B9","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1016\/j.cels.2018.02.010","article-title":"Compensation of signal spillover in suspension and imaging mass cytometry","volume":"6","author":"Chevrier","year":"2018","journal-title":"Cell Syst"},{"key":"2023062409313499300_btaa843-B10","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0166-218X(99)00172-9","article-title":"Algorithms and codes for dense assignment problems: the state of the art","volume":"100","author":"Dell'Amico","year":"2000","journal-title":"Discret. Appl. Math"},{"key":"2023062409313499300_btaa843-B11","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.2869","article-title":"Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry","volume":"11","author":"Giesen","year":"2014","journal-title":"Nat. Methods"},{"key":"2023062409313499300_btaa843-B12","first-page":"6626","article-title":"GANs trained by a two time-scale update rule converge to a local nash equilibrium. In:","author":"Heusel","year":"2017"},{"key":"2023062409313499300_btaa843-B13","doi-asserted-by":"crossref","DOI":"10.1101\/2020.02.13.20017921","article-title":"The tumor profiler study: integrated, multi-omic, functional tumor profiling for clinical decision support","volume-title":"medRxiv","author":"Irmisch","year":"2020"},{"key":"2023062409313499300_btaa843-B14","article-title":"Adam: a method for stochastic optimization","author":"Kingma","year":"2014","journal-title":"arXiv."},{"key":"2023062409313499300_btaa843-B15","article-title":"Auto-encoding variational Bayes","author":"Kingma","year":"2013","journal-title":"arXiv"},{"key":"2023062409313499300_btaa843-B16","first-page":"67","article-title":"Efficient implementations of minimum-cost flow algorithms","volume":"4","author":"Kir\u00e1ly","year":"2012","journal-title":"Acta Univ. Sapientiae Inf"},{"key":"2023062409313499300_btaa843-B17","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1287\/mnsc.14.3.205","article-title":"A primal method for minimal cost flows with applications to the assignment and transportation problems","volume":"14","author":"Klein","year":"1967","journal-title":"Manag. Sci"},{"key":"2023062409313499300_btaa843-B18","first-page":"329","volume-title":"Advances in Neural Information Processing Systems","author":"Lawrence","year":"2004"},{"key":"2023062409313499300_btaa843-B19","article-title":"Jointly embedding multiple single-cell omics measurements","author":"Liu","year":"2019","journal-title":"bioRxiv"},{"key":"2023062409313499300_btaa843-B20","article-title":"Challenging common assumptions in the unsupervised learning of disentangled representations","author":"Locatello","year":"2018"},{"key":"2023062409313499300_btaa843-B21","article-title":"Disentangling factors of variation using few labels","volume-title":". In: Eights International Conference on Learning Representations","author":"Locatello","year":"2019"},{"key":"2023062409313499300_btaa843-B22","author":"Lucic","year":"2017"},{"key":"2023062409313499300_btaa843-B23","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"Maaten","year":"2008","journal-title":"J. Mach. Learn. Res"},{"key":"2023062409313499300_btaa843-B24","author":"Makhzani","year":"2015"},{"key":"2023062409313499300_btaa843-B25","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/s41592-020-0766-3","article-title":"Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes","volume":"17","author":"McCarthy","year":"2020","journal-title":"Nat. Methods"},{"key":"2023062409313499300_btaa843-B26","article-title":"Spectral normalization for generative adversarial networks","author":"Miyato","year":"2018"},{"key":"2023062409313499300_btaa843-B27","doi-asserted-by":"crossref","first-page":"e124928","DOI":"10.1172\/jci.insight.124928","article-title":"Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry","volume":"3","author":"Oetjen","year":"2018","journal-title":"JCI Insight"},{"key":"2023062409313499300_btaa843-B28","doi-asserted-by":"crossref","first-page":"3517","DOI":"10.1093\/bioinformatics\/btz078","article-title":"PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes","volume":"35","author":"Papadopoulos","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062409313499300_btaa843-B29","doi-asserted-by":"crossref","first-page":"e48051","DOI":"10.7554\/eLife.48051","article-title":"Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry","volume":"8","author":"Ramaglia","year":"2019","journal-title":"eLife"},{"key":"2023062409313499300_btaa843-B30","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/550451a","article-title":"The human cell atlas: from vision to reality","volume":"550","author":"Rozenblatt-Rosen","year":"2017","journal-title":"Nat. News"},{"key":"2023062409313499300_btaa843-B31","first-page":"2234","volume-title":"Advances in Neural Information Processing Systems","author":"Salimans","year":"2016"},{"key":"2023062409313499300_btaa843-B32","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nmeth.4380","article-title":"Simultaneous epitope and transcriptome measurement in single cells","volume":"14","author":"Stoeckius","year":"2017","journal-title":"Nat. Methods"},{"key":"2023062409313499300_btaa843-B33","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2023062409313499300_btaa843-B34","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nmeth.1315","article-title":"mRNA-Seq whole-transcriptome analysis of a single cell","volume":"6","author":"Tang","year":"2009","journal-title":"Nat. Methods"},{"key":"2023062409313499300_btaa843-B35","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science"},{"key":"2023062409313499300_btaa843-B36","article-title":"Wasserstein auto-encoders","volume-title":"Sixth International Conference on Learning Representations","author":"Tolstikhin","year":"2017"},{"key":"2023062409313499300_btaa843-B37","doi-asserted-by":"crossref","first-page":"2392","DOI":"10.1109\/TIT.2009.2016060","article-title":"Divergence estimation for multidimensional densities via k-nearest-neighbor distances","volume":"55","author":"Wang","year":"2009","journal-title":"IEEE Trans. Inf. Theory"},{"key":"2023062409313499300_btaa843-B38","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/s13059-019-1764-6","article-title":"Bermuda: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes","volume":"20","author":"Wang","year":"2019","journal-title":"Genome Biol"},{"key":"2023062409313499300_btaa843-B39","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/s13059-017-1269-0","article-title":"Matcher: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics","volume":"18","author":"Welch","year":"2017","journal-title":"Genome Biol"},{"key":"2023062409313499300_btaa843-B40","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1016\/j.cell.2019.05.006","article-title":"Single-cell multi-omic integration compares and contrasts features of brain cell identity","volume":"177","author":"Welch","year":"2019","journal-title":"Cell"},{"key":"2023062409313499300_btaa843-B41","article-title":"Multi-domain translation by learning uncoupled autoencoders","author":"Yang,","year":"2019"},{"key":"2023062409313499300_btaa843-B42","author":"Yang","year":"2019"},{"key":"2023062409313499300_btaa843-B43","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41592-019-0691-5","article-title":"Single-cell multimodal omics: the power of many","volume":"17","author":"Zhu","year":"2020","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/Supplement_2\/i919\/50693443\/btaa843.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/Supplement_2\/i919\/50693443\/btaa843.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T19:52:05Z","timestamp":1687636325000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/Supplement_2\/i919\/6055906"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12]]},"references-count":43,"journal-issue":{"issue":"Supplement_2","published-print":{"date-parts":[[2020,12,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa843","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.11.146845","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,12]]},"published":{"date-parts":[[2020,12]]}}}