{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T09:02:47Z","timestamp":1778144567865,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T00:00:00Z","timestamp":1665100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["xzy012022087"],"award-info":[{"award-number":["xzy012022087"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61602367"],"award-info":[{"award-number":["61602367"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The emerging single-cell Hi-C technology provides opportunities to study dynamics of chromosomal organization. How to construct a pseudotime path using single-cell Hi-C contact matrices to order cells along developmental trajectory is a challenging topic, since these matrices produced by the technology are inherently high dimensional and sparse, they suffer from noises and biases, and the topology of trajectory underlying them may be diverse.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present scHiCPTR, an unsupervised graph-based pipeline to infer pseudotime from single-cell Hi-C contact matrices. It provides a workflow consisting of imputation and embedding, graph construction, dual graph refinement, pseudotime calculation and result visualization. Beyond the few existing methods, scHiCPTR ties to optimize graph structure by two parallel procedures of graph pruning, which help reduce the spurious cell links resulted from noises and determine a global developmental directionality. Besides, it has an ability to handle developmental trajectories with multiple topologies, including linear, bifurcated and circular ones, and is competitive with methods developed for single-cell RNA-seq data. The comparative results tell that our scHiCPTR can achieve higher performance in pseudotime inference, and the inferred developmental trajectory exhibit a reasonable biological significance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>scHiCPTR is freely available at https:\/\/github.com\/lhqxinghun\/scHiCPTR.<\/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\/btac670","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T14:25:57Z","timestamp":1665152757000},"page":"5151-5159","source":"Crossref","is-referenced-by-count":8,"title":["scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5061-4762","authenticated-orcid":false,"given":"Hongqiang","family":"Lyu","sequence":"first","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Shaanxi 710049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erhu","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Shaanxi 710049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhifang","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Shaanxi 710049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yao","family":"Li","sequence":"additional","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Shaanxi 710049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Shaanxi 710049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoran","family":"Yin","sequence":"additional","affiliation":[{"name":"Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University , Shaanxi 710004, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,7]]},"reference":[{"key":"2022113016200656100_btac670-B1","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.cell.2014.04.005","article-title":"Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development","volume":"157","author":"Bendall","year":"2014","journal-title":"Cell"},{"key":"2022113016200656100_btac670-B2","doi-asserted-by":"crossref","first-page":"P10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"J. 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