{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T15:33:14Z","timestamp":1774366394432,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T00:00:00Z","timestamp":1710460800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004099","name":"Ligue Nationale Contre le Cancer","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004099","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Several methods have been developed in the past years to infer cell\u2013cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we (i) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, (ii) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, (iii) optimized ICELLNET framework for single-cell RNA sequencing data analyses, (iv) provided new visualizations of cell\u2013cell communication results to facilitate prioritization and biological interpretation. This update will broaden the use of ICELLNET by the scientific community in different biological fields.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ICELLNET package is implemented in R. Source code, documentation and tutorials are available on GitHub (https:\/\/github.com\/soumelis-lab\/ICELLNET).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae089","type":"journal-article","created":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T23:54:30Z","timestamp":1710546870000},"source":"Crossref","is-referenced-by-count":11,"title":["ICELLNET v2: a versatile method for cell\u2013cell communication analysis from human transcriptomic data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1629-8983","authenticated-orcid":false,"given":"Lucile","family":"Massenet-Regad","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9, INSERM U976 HIPI, Paris, F-75010, France"},{"name":"Universit\u00e9 Paris-Saclay , Saint Aubin, F-91190, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1849-9834","authenticated-orcid":false,"given":"Vassili","family":"Soumelis","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9, INSERM U976 HIPI, Paris, F-75010, France"},{"name":"Department of Immunology-Histocompatibility, Saint-Louis Hospital, AP-HP.Nord, Universit\u00e9 Paris Cit\u00e9 , Paris 75010, France"},{"name":"Owkin France , Paris 75010, France"}]}],"member":"286","published-online":{"date-parts":[[2024,3,15]]},"reference":[{"key":"2024032107582614600_btae089-B1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell-cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat Rev Genet"},{"key":"2024032107582614600_btae089-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1124\/pr.113.007724","article-title":"International union of pharmacology. LXXXIX. Update on the extended family of chemokine receptors and introducing a new nomenclature for atypical chemokine receptors","volume":"66","author":"Bachelerie","year":"2014","journal-title":"Pharmacol Rev"},{"key":"2024032107582614600_btae089-B3","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/s41592-019-0667-5","article-title":"NicheNet: modeling intercellular communication by linking ligands to target genes","volume":"17","author":"Browaeys","year":"2020","journal-title":"Nat Methods"},{"key":"2024032107582614600_btae089-B4","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1111\/bph.12364","article-title":"WNT\/frizzled signalling: receptor-ligand selectivity with focus on FZD-G protein signalling and its physiological relevance: IUPHAR review 3","volume":"171","author":"Dijksterhuis","year":"2014","journal-title":"Br J Pharmacol"},{"key":"2024032107582614600_btae089-B5","doi-asserted-by":"crossref","first-page":"3224","DOI":"10.1038\/s41467-022-30755-0","article-title":"Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data","volume":"13","author":"Dimitrov","year":"2022","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B6","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat Protoc"},{"key":"2024032107582614600_btae089-B7","doi-asserted-by":"crossref","first-page":"5962","DOI":"10.1038\/ncomms6962","article-title":"Endothelial destabilization by angiopoietin-2 via integrin \u03b21 activation","volume":"6","author":"Hakanpaa","year":"2015","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B8","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1038\/s41467-022-29516-w","article-title":"PD-L1 and ICOSL discriminate human secretory and helper dendritic cells in cancer, allergy and autoimmunity","volume":"13","author":"Hoffmann","year":"2022","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B9","doi-asserted-by":"crossref","first-page":"5011","DOI":"10.1038\/s41467-020-18873-z","article-title":"Predicting cell-to-cell communication networks using NATMI","volume":"11","author":"Hou","year":"2020","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B10","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B11","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/s13059-022-02783-y","article-title":"Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information","volume":"23","author":"Liu","year":"2022","journal-title":"Genome Biol"},{"key":"2024032107582614600_btae089-B12","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1101\/gr.278001.123","article-title":"ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods","volume":"33","author":"Luo","year":"2023","journal-title":"Genome Res"},{"key":"2024032107582614600_btae089-B13","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/j.mcn.2010.11.005","article-title":"Semaphorin 4C and 4G are ligands of Plexin-B2 required in cerebellar development","volume":"46","author":"Maier","year":"2011","journal-title":"Mol Cell Neurosci"},{"key":"2024032107582614600_btae089-B14","doi-asserted-by":"crossref","first-page":"108367","DOI":"10.1016\/j.isci.2023.108367","article-title":"Large-scale analysis of cell-cell communication reveals angiogenin-dependent tumor progression in clear cell renal cell carcinoma","volume":"26","author":"Massenet-Regad","year":"2023","journal-title":"iScience"},{"key":"2024032107582614600_btae089-B15","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1038\/s41467-021-21244-x","article-title":"Dissection of intercellular communication using the transcriptome-based framework ICELLNET","volume":"12","author":"No\u00ebl","year":"2021","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B16","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1146\/annurev-biochem-040320-103615","article-title":"The wnt pathway: from signaling mechanisms to synthetic modulators","volume":"91","author":"Rim","year":"2022","journal-title":"Annu Rev Biochem"},{"key":"2024032107582614600_btae089-B17","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/s41556-021-00681-2","article-title":"Single-cell RNA sequencing of blood antigen-presenting cells in severe COVID-19 reveals multi-process defects in antiviral immunity","volume":"23","author":"Saichi","year":"2021","journal-title":"Nat Cell Biol"},{"key":"2024032107582614600_btae089-B18","doi-asserted-by":"crossref","first-page":"6513","DOI":"10.1038\/s41467-022-34081-3","article-title":"BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking clusterin expression in cancer associated fibroblasts with HSF1 signaling","volume":"13","author":"Shaashua","year":"2022","journal-title":"Nat Commun"},{"key":"2024032107582614600_btae089-B19","doi-asserted-by":"crossref","first-page":"4832","DOI":"10.1096\/fj.201700144R","article-title":"Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families","volume":"31","author":"Voloshanenko","year":"2017","journal-title":"FASEB J"},{"key":"2024032107582614600_btae089-B20","doi-asserted-by":"crossref","first-page":"22445","DOI":"10.1074\/jbc.M410367200","article-title":"Effects of protein and gene transfer of the angiopoietin-1 fibrinogen-like receptor-binding domain on endothelial and vessel organization","volume":"280","author":"Weber","year":"2005","journal-title":"J Biol Chem"},{"key":"2024032107582614600_btae089-B21","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1016\/j.cell.2020.07.025","article-title":"A human IgSF Cell-Surface interactome reveals a complex network of Protein-Protein interactions","volume":"182","author":"Wojtowicz","year":"2020","journal-title":"Cell"},{"key":"2024032107582614600_btae089-B22","doi-asserted-by":"crossref","first-page":"105420","DOI":"10.1016\/j.antiviral.2022.105420","article-title":"Interferon \u03b1 facilitates anti-HBV cellular immune response in a B cell-dependent manner","volume":"207","author":"Zhong","year":"2022","journal-title":"Antiviral Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae089\/56991626\/btae089.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae089\/57038869\/btae089.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae089\/57038869\/btae089.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,21]],"date-time":"2024-03-21T08:53:56Z","timestamp":1711011236000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae089\/7630161"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,3,1]]},"references-count":22,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae089","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,3,1]]},"article-number":"btae089"}}