{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T02:13:51Z","timestamp":1781662431586,"version":"3.54.5"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,9,30]],"date-time":"2022-09-30T00:00:00Z","timestamp":1664496000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"China's National Key R&D Program","award":["2020YFA0712403"],"award-info":[{"award-number":["2020YFA0712403"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"name":"Research Fund, Vanke School of Public Health, Tsinghua University"},{"name":"UK-China Collaboration Fund"},{"name":"China\u2019s National Key R&D Program","award":["2018YFE0102100"],"award-info":[{"award-number":["2018YFE0102100"]}]},{"name":"Collaborative Innovation Major Project of Zhengzhou","award":["20XTZX08017"],"award-info":[{"award-number":["20XTZX08017"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81702966"],"award-info":[{"award-number":["81702966"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell\u2013cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell\u2013cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell\u2013cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell\u2013cell interactions at the cell type level, which hinders the development of computational approaches to identify cell\u2013cell interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We develop a publicly accessible database, CITEdb (Cell\u2013cell InTEraction database, https:\/\/citedb.cn\/), which not only facilitates interactive exploration of cell\u2013cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell\u2013cell interactions from different tools. CITEdb contains 728 pairs of cell\u2013cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand\u2013receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell\u2013cell interactions. Users can search for cell\u2013cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell\u2013cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell\u2013cell interactions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CITEdb is freely available at https:\/\/citedb.cn\/ and the R package implementing benchmark is available at https:\/\/github.com\/shanny01\/benchmark.<\/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\/btac654","type":"journal-article","created":{"date-parts":[[2022,9,29]],"date-time":"2022-09-29T20:48:14Z","timestamp":1664484494000},"page":"5144-5148","source":"Crossref","is-referenced-by-count":16,"title":["CITEdb: a manually curated database of cell\u2013cell interactions in human"],"prefix":"10.1093","volume":"38","author":[{"given":"Nayang","family":"Shan","sequence":"first","affiliation":[{"name":"School of Statistics, Capital University of Economics and Business , Beijing 100070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Industrial Engineering, Center for Statistical Science, Tsinghua University , Beijing 100084, China"},{"name":"MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Guo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd , Nanjing 210042, China"},{"name":"Nanjing Simcere Medical Laboratory Science Co., Ltd , Nanjing 210042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyu","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Industrial Engineering, Center for Statistical Science, Tsinghua University , Beijing 100084, China"},{"name":"MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jitong","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Michigan , Ann Arbor, MI 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linlin","family":"Yan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd , Nanjing 210042, China"},{"name":"Nanjing Simcere Medical Laboratory Science Co., Ltd , Nanjing 210042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiudong","family":"Gao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd , Nanjing 210042, China"},{"name":"Nanjing Simcere Medical Laboratory Science Co., Ltd , Nanjing 210042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Ren","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd , Nanjing 210042, China"},{"name":"Nanjing Simcere Medical Laboratory Science Co., Ltd , Nanjing 210042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4531-3970","authenticated-orcid":false,"given":"Xingming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Fudan University , Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4283-8501","authenticated-orcid":false,"given":"Lin","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Industrial Engineering, Center for Statistical Science, Tsinghua University , Beijing 100084, China"},{"name":"MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,30]]},"reference":[{"key":"2023111009240086400_btac654-B1","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.coisb.2021.03.007","article-title":"The landscape of cell\u2013cell communication through single-cell transcriptomics","volume":"26","author":"Almet","year":"2021","journal-title":"Curr. 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