{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:00Z","timestamp":1772138040551,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,10,18]],"date-time":"2020-10-18T00:00:00Z","timestamp":1602979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Australian Technology Network"},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DE200100200"],"award-info":[{"award-number":["DE200100200"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Research Council Discovery","award":["ARC DP170101306"],"award-info":[{"award-number":["ARC DP170101306"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>microRNAs (miRNAs) are important gene regulators and they are involved in many biological processes, including cancer progression. Therefore, correctly identifying miRNA\u2013mRNA interactions is a crucial task. To this end, a huge number of computational methods has been developed, but they mainly use the data at one snapshot and ignore the dynamics of a biological process. The recent development of single cell data and the booming of the exploration of cell trajectories using \u2018pseudotime\u2019 concept have inspired us to develop a pseudotime-based method to infer the miRNA\u2013mRNA relationships characterizing a biological process by taking into account the temporal aspect of the process.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a novel approach, called pseudotime causality, to find the causal relationships between miRNAs and mRNAs during a biological process. We have applied the proposed method to both single cell and bulk sequencing datasets for Epithelia to Mesenchymal Transition, a key process in cancer metastasis. The evaluation results show that our method significantly outperforms existing methods in finding miRNA\u2013mRNA interactions in both single cell and bulk data. The results suggest that utilizing the pseudotemporal information from the data helps reveal the gene regulation in a biological process much better than using the static information.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>R scripts and datasets can be found at https:\/\/github.com\/AndresMCB\/PTC.<\/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\/btaa899","type":"journal-article","created":{"date-parts":[[2020,10,6]],"date-time":"2020-10-06T07:39:37Z","timestamp":1601969977000},"page":"807-814","source":"Crossref","is-referenced-by-count":6,"title":["A pseudotemporal causality approach to identifying miRNA\u2013mRNA interactions during biological processes"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1880-3624","authenticated-orcid":false,"given":"Andres M","family":"Cifuentes-Bernal","sequence":"first","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8884-3584","authenticated-orcid":false,"given":"Vu Vh","family":"Pham","sequence":"additional","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]},{"given":"Xiaomei","family":"Li","sequence":"additional","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9732-4313","authenticated-orcid":false,"given":"Thuc Duy","family":"Le","sequence":"additional","affiliation":[{"name":"UniSA STEM, University of South Australia , Adelaide, South Australia, 5095 Mawson Lakes, Australia"}]}],"member":"286","published-online":{"date-parts":[[2020,10,18]]},"reference":[{"issue":"13 Supplement","key":"2023051705203961100_btaa899-B8192590","first-page":"1884","article-title":"Abstract","volume":"79","year":"2019","journal-title":"developmentof a novel vim-rfp reporter line for colorectal cancer emt study and drugdiscovery. 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