{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T07:53:22Z","timestamp":1772265202290,"version":"3.50.1"},"posted":{"date-parts":[[2019,8,23]]},"group-title":"PeerJ Preprints","reference-count":0,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T00:00:00Z","timestamp":1566518400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>The recent upswing of microfluidics and combinatorial indexing strategies, further enhanced by very low sequencing costs, have turned single cell sequencing into an empowering technology; analyzing thousands\u2014or even millions\u2014of cells per experimental run is becoming a routine assignment in laboratories worldwide. As a consequence, we are witnessing a data revolution in single cell biology. Although some issues are similar in spirit to those experienced in bulk sequencing, many of the emerging data science problems are unique to single cell analysis; together, they give rise to the new realm of 'Single-Cell Data Science'.<\/jats:p>\n                <jats:p>Here, we outline twelve challenges that will be central in bringing this new field forward. For each challenge, the current state of the art in terms of prior work is reviewed, and open problems are formulated, with an emphasis on the research goals that motivate them.<\/jats:p>\n                <jats:p>This compendium is meant to serve as a guideline for established researchers, newcomers and students alike, highlighting interesting and rewarding problems in 'Single-Cell Data Science' for the coming years.<\/jats:p>","DOI":"10.7287\/peerj.preprints.27885v3","type":"posted-content","created":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T10:26:41Z","timestamp":1566556001000},"source":"Crossref","is-referenced-by-count":2,"title":["12 Grand Challenges in Single-Cell Data Science"],"prefix":"10.7287","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9138-4112","authenticated-orcid":true,"given":"David","family":"Laehnemann","sequence":"first","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany"},{"name":"Department of Paediatric Oncology, Haematology and Immunology, Medical Faculty, Heinrich Heine University, University Hospital, D\u00fcsseldorf, Germany"},{"name":"Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9818-9320","authenticated-orcid":true,"given":"Johannes","family":"K\u00f6ster","sequence":"additional","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany"},{"name":"Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America"}]},{"given":"Ewa","family":"Szczurek","sequence":"additional","affiliation":[{"name":"Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics University of Warsaw, Warsaw, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2218-6833","authenticated-orcid":true,"given":"Davis J","family":"McCarthy","sequence":"additional","affiliation":[{"name":"Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Australia"},{"name":"Melbourne Integrative Genomics, School of BioSciences \/ School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7858-0231","authenticated-orcid":true,"given":"Stephanie C","family":"Hicks","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3048-5518","authenticated-orcid":true,"given":"Mark D","family":"Robinson","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland"}]},{"given":"Catalina A","family":"Vallejos","sequence":"additional","affiliation":[{"name":"MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom"},{"name":"The Alan Turing Institute, British Library, London, United Kingdom"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"}]},{"given":"Kieran R","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of British Columbia, Vancouver, Canada"},{"name":"Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada"},{"name":"Data Science Institute, University of British Columbia, Vancouver, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8601-2149","authenticated-orcid":true,"given":"Ahmed","family":"Mahfouz","sequence":"additional","affiliation":[{"name":"Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands"},{"name":"Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands"}]},{"given":"Luca","family":"Pinello","sequence":"additional","affiliation":[{"name":"Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Charlestown, United States of America"},{"name":"Department of Pathology, Harvard Medical School, Boston, United States of America"},{"name":"Broad Institute of Harvard and MIT, Cambridge, Massachusets, United States of America"}]},{"given":"Pavel","family":"Skums","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, United States of America"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0353-0691","authenticated-orcid":true,"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany"}]},{"given":"Camille","family":"Stephan-Otto Attolini","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain"}]},{"given":"Samuel","family":"Aparicio","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada"},{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada"}]},{"given":"Jasmijn","family":"Baaijens","sequence":"additional","affiliation":[{"name":"Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"}]},{"given":"Marleen","family":"Balvert","sequence":"additional","affiliation":[{"name":"Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"},{"name":"Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands"}]},{"given":"Buys","family":"de Barbanson","sequence":"additional","affiliation":[{"name":"Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands"},{"name":"Oncode Institute, Utrecht, The Netherlands"},{"name":"Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands"}]},{"given":"Antonio","family":"Cappuccio","sequence":"additional","affiliation":[{"name":"Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands"}]},{"given":"Giacomo","family":"Corleone","sequence":"additional","affiliation":[{"name":"Department of Surgery and Cancer, The Imperial 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C","family":"Marioni","sequence":"additional","affiliation":[{"name":"Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom"},{"name":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9376-1030","authenticated-orcid":true,"given":"Tobias","family":"Marschall","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Saarland University, Saarbr\u00fccken, Germany"},{"name":"Max Planck Institute for Informatics, Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3976-9701","authenticated-orcid":true,"given":"Felix","family":"M\u00f6lder","sequence":"additional","affiliation":[{"name":"Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany"},{"name":"Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany"}]},{"given":"Amir","family":"Niknejad","sequence":"additional","affiliation":[{"name":"Computation molecular design, Zuse Institute Berlin, Berlin, Germany"},{"name":"Mathematics department, Mount Saint Vincent, New York, United States of America"}]},{"given":"\u0141ukasz","family":"R\u0105czkowski","sequence":"additional","affiliation":[{"name":"Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics University of Warsaw, Warsaw, Poland"}]},{"given":"Marcel","family":"Reinders","sequence":"additional","affiliation":[{"name":"Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands"},{"name":"Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0828-3477","authenticated-orcid":true,"given":"Jeroen","family":"de Ridder","sequence":"additional","affiliation":[{"name":"Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands"},{"name":"Oncode Institute, Utrecht, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8539-2784","authenticated-orcid":true,"given":"Antoine-Emmanuel","family":"Saliba","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, W\u00fcrzburg, Germany"}]},{"given":"Antonios","family":"Somarakis","sequence":"additional","affiliation":[{"name":"Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands"}]},{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[{"name":"Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 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Sechenov First Moscow State Medical University, Moscow, Russia"}]},{"given":"Alice C","family":"McHardy","sequence":"additional","affiliation":[{"name":"Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany"}]},{"given":"Benjamin J","family":"Raphael","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Princeton University, Princeton, United States of America"}]},{"given":"Sohrab P","family":"Shah","sequence":"additional","affiliation":[{"name":"Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, United States of America"}]},{"given":"Alexander","family":"Sch\u00f6nhuth","sequence":"additional","affiliation":[{"name":"Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"},{"name":"Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands"}]}],"member":"4443","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/peerj.com\/preprints\/27885v3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/27885v3.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/27885v3.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/27885v3.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,23]],"date-time":"2019-12-23T21:10:16Z","timestamp":1577135416000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/preprints\/27885v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,23]]},"references-count":0,"aliases":["10.7287\/peerj.preprints.27885"],"URL":"https:\/\/doi.org\/10.7287\/peerj.preprints.27885v3","relation":{"replaces":[{"id-type":"doi","id":"10.7287\/peerj.preprints.27885v2","asserted-by":"object"}]},"subject":[],"published":{"date-parts":[[2019,8,23]]},"subtype":"preprint"}}