{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T08:03:16Z","timestamp":1775116996580,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T00:00:00Z","timestamp":1620691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"The Novo Nordisk Foundation Center for Stem Cell Biology","award":["NNF17CC0027852"],"award-info":[{"award-number":["NNF17CC0027852"]}]},{"DOI":"10.13039\/501100003554","name":"Lundbeck Foundation","doi-asserted-by":"publisher","award":["R313-2019-421"],"award-info":[{"award-number":["R313-2019-421"]}],"id":[{"id":"10.13039\/501100003554","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004836","name":"Independent Research Fund Denmark","doi-asserted-by":"publisher","award":["0135-00243B"],"award-info":[{"award-number":["0135-00243B"]}],"id":[{"id":"10.13039\/501100004836","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Trajectory inference (TI) for single cell RNA sequencing (scRNAseq) data is a powerful approach to interpret dynamic cellular processes such as cell cycle and development. Still, however, accurate inference of trajectory is challenging. Recent development of RNA velocity provides an approach to visualize cell state transition without relying on prior knowledge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To perform TI and group cells based on RNA velocity we developed VeTra. By applying cosine similarity and merging weakly connected components, VeTra identifies cell groups from the direction of cell transition. Besides, VeTra suggests key regulators from the inferred trajectory. VeTra is a useful tool for TI and subsequent analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Vetra is available at https:\/\/github.com\/wgzgithub\/VeTra.<\/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\/btab364","type":"journal-article","created":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T09:09:04Z","timestamp":1620637744000},"page":"3509-3513","source":"Crossref","is-referenced-by-count":25,"title":["VeTra: a tool for trajectory inference based on RNA velocity"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1422-2830","authenticated-orcid":false,"given":"Guangzheng","family":"Weng","sequence":"first","affiliation":[{"name":"Department of Biology, The Bioinformatics Centre, University of Copenhagen , 2200 Copenhagen N, Denmark"},{"name":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen , 2200 Copenhagen N, Denmark"},{"name":"Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen , 2200 Copenhagen N, Denmark"}]},{"given":"Junil","family":"Kim","sequence":"additional","affiliation":[{"name":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen , 2200 Copenhagen N, Denmark"},{"name":"Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen , 2200 Copenhagen N, Denmark"},{"name":"Department of Bioinformatics, School of Systems Biomedical Science, Soongsil University , 06978 Seoul, South Korea"}]},{"given":"Kyoung Jae","family":"Won","sequence":"additional","affiliation":[{"name":"Biotech Research and Innovation Centre (BRIC), University of Copenhagen , 2200 Copenhagen N, Denmark"},{"name":"Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health and Medical Sciences, University of Copenhagen , 2200 Copenhagen N, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2021,5,11]]},"reference":[{"key":"2023051609013655800_btab364-B1","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1007\/s10115-003-0128-3","article-title":"Characterizing and mining the citation graph of the computer science literature","volume":"6","author":"An","year":"2004","journal-title":"Knowledge Inf. Syst"},{"key":"2023051609013655800_btab364-B2","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.ydbio.2004.01.040","article-title":"Conditional inactivation of Pax6 in the pancreas causes early onset of diabetes","volume":"269","author":"Ashery-Padan","year":"2004","journal-title":"Dev. Biol"},{"key":"2023051609013655800_btab364-B3","doi-asserted-by":"crossref","first-page":"dev173849","DOI":"10.1242\/dev.173849","article-title":"Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis","volume":"146","author":"Bastidas-Ponce","year":"2019","journal-title":"Development"},{"key":"2023051609013655800_btab364-B4","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","article-title":"Generalizing RNA velocity to transient cell states through dynamical modeling","volume":"38","author":"Bergen","year":"2020","journal-title":"Nat. Biotechnol"},{"key":"2023051609013655800_btab364-B5","article-title":"dyngen: a multi-modal simulator for spearheading new single-cell omics analyses","author":"Cannoodt","year":"2020","journal-title":"BioRxiv"},{"key":"2023051609013655800_btab364-B6","doi-asserted-by":"crossref","first-page":"eaal3753","DOI":"10.1126\/science.aal3753","article-title":"Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla","volume":"357","author":"Furlan","year":"2017","journal-title":"Science"},{"key":"2023051609013655800_btab364-B7","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1111\/j.1463-1326.2011.01445.x","article-title":"Glucagon gene expression in the endocrine pancreas: the role of the transcription factor Pax6 in \u03b1-cell differentiation, glucagon biosynthesis and secretion","volume":"13","author":"Gosmain","year":"2011","journal-title":"Diabetes Obesity Metab"},{"key":"2023051609013655800_btab364-B8","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1073\/pnas.97.4.1607","article-title":"neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas","volume":"97","author":"Gradwohl","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023051609013655800_btab364-B9","doi-asserted-by":"crossref","first-page":"2447","DOI":"10.1242\/dev.129.10.2447","article-title":"Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors","volume":"129","author":"Gu","year":"2002","journal-title":"Development"},{"key":"2023051609013655800_btab364-B10","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nmeth.3971","article-title":"Diffusion pseudotime robustly reconstructs lineage branching","volume":"13","author":"Haghverdi","year":"2016","journal-title":"Nat. Methods"},{"key":"2023051609013655800_btab364-B11","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1080\/01621459.1989.10478797","article-title":"Principal curves","volume":"84","author":"Hastie","year":"1989","journal-title":"J. Am. Stat. Assoc"},{"key":"2023051609013655800_btab364-B12","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/nmeth.4662","article-title":"FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data","volume":"15","author":"Herman","year":"2018","journal-title":"Nat. Methods"},{"key":"2023051609013655800_btab364-B13","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/s41593-017-0056-2","article-title":"Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing","volume":"21","author":"Hochgerner","year":"2018","journal-title":"Nat. Neurosci"},{"key":"2023051609013655800_btab364-B14","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gkaa1014","article-title":"TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data","volume":"49","author":"Kim","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023051609013655800_btab364-B15","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"2023051609013655800_btab364-B16","doi-asserted-by":"crossref","first-page":"2314","DOI":"10.1093\/bioinformatics\/btx194","article-title":"SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation","volume":"33","author":"Matsumoto","year":"2017","journal-title":"Bioinformatics"},{"key":"2023051609013655800_btab364-B17","doi-asserted-by":"crossref","first-page":"9070","DOI":"10.1128\/MCB.24.20.9070-9078.2004","article-title":"nor-1 regulates hippocampal axon guidance, pyramidal cell survival, and seizure susceptibility","volume":"24","author":"P\u00f6nni\u00f6","year":"2004","journal-title":"Mol. Cell. Biol"},{"key":"2023051609013655800_btab364-B18","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.cels.2020.02.003","article-title":"Inferring causal gene regulatory networks from coupled single-cell expression dynamics using Scribe","volume":"10","author":"Qiu","year":"2020","journal-title":"Cell Syst"},{"key":"2023051609013655800_btab364-B19","doi-asserted-by":"crossref","first-page":"4572","DOI":"10.1172\/JCI57131","article-title":"Pancreatic ductal cells in development, regeneration, and neoplasia","volume":"121","author":"Reichert","year":"2011","journal-title":"J. Clin. Investig"},{"key":"2023051609013655800_btab364-B20","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023051609013655800_btab364-B21","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1242\/dev.127.16.3533","article-title":"Expression of neurogenin3 reveals an islet cell precursor population in the pancreas","volume":"127","author":"Schwitzgebel","year":"2000","journal-title":"Development"},{"key":"2023051609013655800_btab364-B22","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nbt.3569","article-title":"Wishbone identifies bifurcating developmental trajectories from single-cell data","volume":"34","author":"Setty","year":"2016","journal-title":"Nat. Biotechnol"},{"key":"2023051609013655800_btab364-B23","doi-asserted-by":"crossref","first-page":"e1008585","DOI":"10.1371\/journal.pcbi.1008585","article-title":"Preprocessing choices affect RNA velocity results for droplet scRNA-seq data","volume":"17","author":"Soneson","year":"2021","journal-title":"PLoS Comput. Biol"},{"key":"2023051609013655800_btab364-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"Street","year":"2018","journal-title":"BMC Genomics"},{"key":"2023051609013655800_btab364-B25","doi-asserted-by":"crossref","first-page":"e1008205","DOI":"10.1371\/journal.pcbi.1008205","article-title":"Tempora: cell trajectory inference using time-series single-cell RNA sequencing data","volume":"16","author":"Tran","year":"2020","journal-title":"PLoS Comput. Biol"},{"key":"2023051609013655800_btab364-B26","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023051609013655800_btab364-B27"},{"key":"2023051609013655800_btab364-B28","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13059-019-1663-x","article-title":"PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells","volume":"20","author":"Wolf","year":"2019","journal-title":"Genome Biol"},{"key":"2023051609013655800_btab364-B29","doi-asserted-by":"crossref","first-page":"19490","DOI":"10.1073\/pnas.1912459116","article-title":"Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression","volume":"116","author":"Xia","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023051609013655800_btab364-B30","article-title":"Inference of high-resolution trajectories in single cell RNA-Seq data from RNA velocity","volume-title":"bioRxiv","author":"Zhang","year":"2021"},{"key":"2023051609013655800_btab364-B31","article-title":"VeloSim: simulating single cell gene-expression and RNA velocity","author":"Zhang","year":"2021","journal-title":"bioRxiv"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab364\/38603648\/btab364.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/20\/3509\/50338190\/btab364.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/20\/3509\/50338190\/btab364.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T05:02:31Z","timestamp":1684213351000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/20\/3509\/6273660"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,5,11]]},"references-count":31,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2021,10,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab364","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.09.01.277095","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,10,15]]},"published":{"date-parts":[[2021,5,11]]}}}