{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T08:06:18Z","timestamp":1759565178698,"version":"3.41.2"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["62072154","81921001"],"award-info":[{"award-number":["62072154","81921001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on the gene function and evolution, and thus on phenotypes and diseases. In order to identify the key nucleotides of one specific gene, it is quite crucial to quantitatively measure the importance of each base on the gene. However, there are still no sequence-based methods of doing that. Here, we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of each single base based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases through single nucleotide variations. Moreover, the BIC score in The Cancer Genome Atlas somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base importance of human mRNAs and lncRNAs.<\/jats:p>","DOI":"10.1093\/bib\/bbad321","type":"journal-article","created":{"date-parts":[[2023,9,5]],"date-time":"2023-09-05T10:28:48Z","timestamp":1693909728000},"source":"Crossref","is-referenced-by-count":1,"title":["Defining the single base importance of human mRNAs and lncRNAs"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6757-9422","authenticated-orcid":false,"given":"Rui","family":"Fan","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"},{"name":"School of Basic Medical Sciences , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangwen","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"},{"name":"School of Basic Medical Sciences , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianwei","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Computational Medicine , School of Artificial Intelligence, , Tianjin, 300401 , China"},{"name":"Hebei University of Technology , School of Artificial Intelligence, , Tianjin, 300401 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghua","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"},{"name":"School of Basic Medical Sciences , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"},{"name":"School of Sports Medicine, Wuhan Institute of Physical Education , No.461 Luoyu Rd. Wuchang District, Wuhan 430079, Hubei Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6223-5225","authenticated-orcid":false,"given":"Chunmei","family":"Cui","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , China"},{"name":"School of Basic Medical Sciences , Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, State Key Lab of Vascular Homeostasis and Remodeling, , Peking University, 38 Xueyuan Rd, Beijing, 100191 , 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