{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T15:01:30Z","timestamp":1761490890793,"version":"3.37.3"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Strategic Priority Research Program of Chinese Academy of Science","award":["XDB13000000"],"award-info":[{"award-number":["XDB13000000"]}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["11871463","61671444","61621003","91730301","11661141019"],"award-info":[{"award-number":["11871463","61671444","61621003","91730301","11661141019"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single cell RNA-seq data offers us new resource and resolution to study cell type identity and its conversion. However, data analyses are challenging in dealing with noise, sparsity and poor annotation at single cell resolution. Detecting cell-type-indicative markers is promising to help denoising, clustering and cell type annotation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a new method, scTIM, to reveal cell-type-indicative markers. scTIM is based on a multi-objective optimization framework to simultaneously maximize gene specificity by considering gene-cell relationship, maximize gene\u2019s ability to reconstruct cell\u2013cell relationship and minimize gene redundancy by considering gene\u2013gene relationship. Furthermore, consensus optimization is introduced for robust solution. Experimental results on three diverse single cell RNA-seq datasets show scTIM\u2019s advantages in identifying cell types (clustering), annotating cell types and reconstructing cell development trajectory. Applying scTIM to the large-scale mouse cell atlas data identifies critical markers for 15 tissues as \u2018mouse cell marker atlas\u2019, which allows us to investigate identities of different tissues and subtle cell types within a tissue. scTIM will serve as a useful method for single cell RNA-seq data mining.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>scTIM is freely available at https:\/\/github.com\/Frank-Orwell\/scTIM.<\/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\/btz936","type":"journal-article","created":{"date-parts":[[2019,12,13]],"date-time":"2019-12-13T12:12:09Z","timestamp":1576239129000},"page":"2474-2485","source":"Crossref","is-referenced-by-count":15,"title":["scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5727-3929","authenticated-orcid":false,"given":"Zhanying","family":"Feng","sequence":"first","affiliation":[{"name":"CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianwen","family":"Ren","sequence":"additional","affiliation":[{"name":"School of Life Sciences , Peking University, Beijing 100871, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Fang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yining","family":"Yin","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chutian","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yimin","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[{"name":"CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,17]]},"reference":[{"key":"2023013110250609900_btz936-B1","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/bty1044","article-title":"M3Drop: dropout-based feature selection for scRNASeq","volume":"35","author":"Andrews","year":"2018","journal-title":"Bioinformatics"},{"key":"2023013110250609900_btz936-B2","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1038\/nmeth.2645","article-title":"Accounting for technical noise in single-cell RNA-seq experiments","volume":"10","author":"Brennecke","year":"2013","journal-title":"Nat. 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