{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T10:15:00Z","timestamp":1783678500523,"version":"3.55.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,8,18]],"date-time":"2023-08-18T00:00:00Z","timestamp":1692316800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"The Funds for Shenzhen Basic Research Institutions","award":["JCKY2020-44"],"award-info":[{"award-number":["JCKY2020-44"]}]},{"name":"Outbound Postdoctoral Research Funding in Shenzhen"},{"name":"Outbound Postdoctoral Research Funding in Dapeng New District"},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1200900"],"award-info":[{"award-number":["2021YFF1200900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFA0909300"],"award-info":[{"award-number":["2021YFA0909300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170646"],"award-info":[{"award-number":["32170646"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81872330"],"award-info":[{"award-number":["81872330"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Science and Technology Program","award":["KQTD20180411143432337"],"award-info":[{"award-number":["KQTD20180411143432337"]}]},{"name":"Shenzhen Innovation Committee of Science and Technology","award":["ZDSYS20200811144002008"],"award-info":[{"award-number":["ZDSYS20200811144002008"]}]},{"name":"Center for Computational Science and Engineering in SUSTech"}],"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>Alignment-based RNA-seq quantification methods typically involve a time-consuming alignment process prior to estimating transcript abundances. In contrast, alignment-free RNA-seq quantification methods bypass this step, resulting in significant speed improvements. Existing alignment-free methods rely on the Expectation\u2013Maximization (EM) algorithm for estimating transcript abundances. However, EM algorithms only guarantee locally optimal solutions, leaving room for further accuracy improvement by finding a globally optimal solution. In this study, we present TQSLE, the first alignment-free RNA-seq quantification method that provides a globally optimal solution for transcript abundances estimation. TQSLE adopts a two-step approach: first, it constructs a k-mer frequency matrix A for the reference transcriptome and a k-mer frequency vector b for the RNA-seq reads; then, it directly estimates transcript abundances by solving the linear equation ATAx\u2009=\u2009ATb. We evaluated the performance of TQSLE using simulated and real RNA-seq data sets and observed that, despite comparable speed to other alignment-free methods, TQSLE outperforms them in terms of accuracy. TQSLE is freely available at https:\/\/github.com\/yhg926\/TQSLE.<\/jats:p>","DOI":"10.1093\/bib\/bbad298","type":"journal-article","created":{"date-parts":[[2023,8,19]],"date-time":"2023-08-19T00:05:08Z","timestamp":1692403508000},"source":"Crossref","is-referenced-by-count":2,"title":["A fast and globally optimal solution for RNA-seq quantification"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9676-7438","authenticated-orcid":false,"given":"Huiguang","family":"Yi","sequence":"first","affiliation":[{"name":"Shenzhen Branch , Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, , 97 Buxin Rd, Shenzhen, 518000, Guangdong , China"},{"name":"Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, , 97 Buxin Rd, Shenzhen, 518000, Guangdong , 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