{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T21:03:29Z","timestamp":1768597409180,"version":"3.49.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T00:00:00Z","timestamp":1666915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20220279"],"award-info":[{"award-number":["BK20220279"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2021-I2M-1-061"],"award-info":[{"award-number":["2021-I2M-1-061"]}]},{"DOI":"10.13039\/501100005150","name":"Chinese Academy of Medical Sciences","doi-asserted-by":"publisher","award":["2022-RC416-01"],"award-info":[{"award-number":["2022-RC416-01"]}],"id":[{"id":"10.13039\/501100005150","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gusu Innovation and Entrepreneurship","award":["ZXL2022475"],"award-info":[{"award-number":["ZXL2022475"]}]},{"name":"Shenzhen Science and Technology","award":["JCYJ20210324125413036"],"award-info":[{"award-number":["JCYJ20210324125413036"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http:\/\/8.142.154.29 or http:\/\/speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The \u2018Pan\u2019 module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the \u2018Evo\u2019, \u2018Devo\u2019, and \u2018Diz\u2019 modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The \u2018C2C\u2019, \u2018G2G\u2019 and \u2018S2S\u2019 modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The \u2018sSearch\u2019,\u00a0\u2018sMarker\u2019, \u2018sUp\u2019, and \u2018sDown\u2019 modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules (\u2018HOME\u2019 and \u2018HELP\u2019) offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.<\/jats:p>","DOI":"10.1093\/nar\/gkac930","type":"journal-article","created":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T15:38:58Z","timestamp":1666971538000},"page":"D1150-D1159","source":"Crossref","is-referenced-by-count":25,"title":["SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases"],"prefix":"10.1093","volume":"51","author":[{"given":"Yangfeng","family":"Chen","sequence":"first","affiliation":[{"name":"Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou 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University , Aarhus 8000, Denmark"}]},{"given":"Ashley","family":"Chang","sequence":"additional","affiliation":[{"name":"Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}]},{"given":"Qizhen","family":"Yue","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, China"}]},{"given":"Mingyi","family":"Pu","sequence":"additional","affiliation":[{"name":"Department of Medicine, Sun Yat-sen University , Shenzhen 518106, China"}]},{"given":"Peixin","family":"Chen","sequence":"additional","affiliation":[{"name":"Cam-Su Genomic Resource Center, Medical College of Soochow University , Suzhou 215123 , China"}]},{"given":"Jiayi","family":"Shen","sequence":"additional","affiliation":[{"name":"Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University , Yantai 264003 , China"}]},{"given":"Mengrou","family":"Li","sequence":"additional","affiliation":[{"name":"Institutes of Biology and Medical Sciences (IBMS), Soochow University , Suzhou 215123, China"}]},{"given":"Tengfei","family":"Jia","sequence":"additional","affiliation":[{"name":"Institutes of Biology and Medical Sciences (IBMS), Soochow University , Suzhou 215123, China"}]},{"given":"Haoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"}]},{"given":"Li","family":"Huang","sequence":"additional","affiliation":[{"name":"The Future Laboratory, Tsinghua University , Beijing 100084, China"}]},{"given":"Guoji","family":"Guo","sequence":"additional","affiliation":[{"name":"Center for Stem Cell 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