{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T22:58:06Z","timestamp":1771628286821,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,14]],"date-time":"2021-05-14T00:00:00Z","timestamp":1620950400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Ministry of Education and Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Ligand\u2013receptor (LR) network analysis allows the characterization of cellular crosstalk based on single cell RNA-seq data. However, current methods typically provide a list of inferred LR interactions and do not allow the researcher to focus on specific cell types, ligands or receptors. In addition, most of these methods cannot quantify changes in crosstalk between two biological phenotypes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>CrossTalkeR is a framework for network analysis and visualization of LR interactions. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological phenotypes, i.e. disease versus homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterization of changes in cellular crosstalk in disease.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CrosstalkeR is an R package available at: Github: https:\/\/github.com\/CostaLab\/CrossTalkeR.<\/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\/btab370","type":"journal-article","created":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T14:31:46Z","timestamp":1620743506000},"page":"4263-4265","source":"Crossref","is-referenced-by-count":50,"title":["CrossTalkeR: analysis and visualization of ligand\u2013receptorne tworks"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7655-7206","authenticated-orcid":false,"given":"James S","family":"Nagai","sequence":"first","affiliation":[{"name":"Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School , Aachen 52062, Germany"}]},{"given":"Nils B","family":"Leimk\u00fchler","sequence":"additional","affiliation":[{"name":"Department of Hematology and Stem Cell Transplantation, University Hospital Essen , Essen 45147, Germany"},{"name":"Department of Hematology, Erasmus Medical Center , Rotterdam 3015 GD, The Netherlands"}]},{"given":"Michael T","family":"Schaub","sequence":"additional","affiliation":[{"name":"Department of Computer Science, RWTH Aachen University , Aachen 52062, Germany"}]},{"given":"Rebekka K","family":"Schneider","sequence":"additional","affiliation":[{"name":"Department of Hematology, Erasmus Medical Center , Rotterdam 3015 GD, The Netherlands"},{"name":"Department of Cell Biology, Institute for Biomedical Engineering, Faculty of Medicine, RWTH Aachen University , Aachen 52062, Germany"},{"name":"Oncode Institute, Erasmus Medical Center , Rotterdam 3015 GD, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2890-8697","authenticated-orcid":false,"given":"Ivan G","family":"Costa","sequence":"additional","affiliation":[{"name":"Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School , Aachen 52062, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,5,14]]},"reference":[{"key":"2023051607090866500_btab370-B1","doi-asserted-by":"crossref","first-page":"3137","DOI":"10.1083\/jcb.109.6.3137","article-title":"Membrane-anchored and soluble forms of betaglycan, a polymorphic proteoglycan that binds transforming growth factor-beta","volume":"109","author":"Andres","year":"1989","journal-title":"J. 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