{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:22:59Z","timestamp":1778127779442,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007828","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T00:00:00Z","timestamp":1588896000000}}],"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T00:00:00Z","timestamp":1588032000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000086","name":"Directorate for Mathematical and Physical Sciences","doi-asserted-by":"publisher","award":["1651995"],"award-info":[{"award-number":["1651995"]}],"id":[{"id":"10.13039\/100000086","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000006","name":"Office of Naval Research","doi-asserted-by":"crossref","award":["N00014-17-1-2147"],"award-info":[{"award-number":["N00014-17-1-2147"]}],"id":[{"id":"10.13039\/100000006","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000006","name":"Office of Naval Research","doi-asserted-by":"crossref","award":["N00014-18-1-2765"],"award-info":[{"award-number":["N00014-18-1-2765"]}],"id":[{"id":"10.13039\/100000006","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["Simons Investigator"],"award-info":[{"award-number":["Simons Investigator"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["Graduate Research Fellowship"],"award-info":[{"award-number":["Graduate Research Fellowship"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001459","name":"Ministry of Education - Singapore","doi-asserted-by":"publisher","award":["Tier 3"],"award-info":[{"award-number":["Tier 3"]}],"id":[{"id":"10.13039\/501100001459","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007828","type":"journal-article","created":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T17:41:22Z","timestamp":1588095682000},"page":"e1007828","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":52,"title":["Predicting cell lineages using autoencoders and optimal transport"],"prefix":"10.1371","volume":"16","author":[{"given":"Karren Dai","family":"Yang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karthik","family":"Damodaran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7639-0506","authenticated-orcid":true,"given":"Saradha","family":"Venkatachalapathy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9338-9232","authenticated-orcid":true,"given":"Ali C.","family":"Soylemezoglu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3445-4567","authenticated-orcid":true,"given":"G. V.","family":"Shivashankar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7008-0216","authenticated-orcid":true,"given":"Caroline","family":"Uhler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2020,4,28]]},"reference":[{"issue":"6","key":"pcbi.1007828.ref001","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41576-018-0015-0","article-title":"Tracing cell-lineage histories","volume":"19","author":"DJ Burgess","year":"2018","journal-title":"Nature Reviews Genetics"},{"issue":"4","key":"pcbi.1007828.ref002","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/nrg.2016.159","article-title":"Building a lineage from single cells: genetic techniques for cell lineage tracking","volume":"18","author":"MB Woodworth","year":"2017","journal-title":"Nature Reviews Genetics"},{"issue":"1-2","key":"pcbi.1007828.ref003","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.cell.2012.01.002","article-title":"Lineage tracing","volume":"148","author":"K Kretzschmar","year":"2012","journal-title":"Cell"},{"issue":"4","key":"pcbi.1007828.ref004","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":"C Trapnell","year":"2014","journal-title":"Nature biotechnology"},{"issue":"10","key":"pcbi.1007828.ref005","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/nmeth.4402","article-title":"Reversed graph embedding resolves complex single-cell trajectories","volume":"14","author":"X Qiu","year":"2017","journal-title":"Nature methods"},{"issue":"7","key":"pcbi.1007828.ref006","first-page":"e54","article-title":"SLICE: determining cell differentiation and lineage based on single cell entropy","volume":"45","author":"M Guo","year":"2017","journal-title":"Nucleic acids research"},{"issue":"3","key":"pcbi.1007828.ref007","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.stem.2015.07.013","article-title":"Single-cell RNA-seq with waterfall reveals molecular cascades underlying adult neurogenesis","volume":"17","author":"J Shin","year":"2015","journal-title":"Cell stem cell"},{"issue":"13","key":"pcbi.1007828.ref008","doi-asserted-by":"crossref","first-page":"e117","DOI":"10.1093\/nar\/gkw430","article-title":"TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis","volume":"44","author":"Z Ji","year":"2016","journal-title":"Nucleic acids research"},{"issue":"52","key":"pcbi.1007828.ref009","doi-asserted-by":"crossref","first-page":"E5643","DOI":"10.1073\/pnas.1408993111","article-title":"Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape","volume":"111","author":"E Marco","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"3","key":"pcbi.1007828.ref010","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":"SC Bendall","year":"2014","journal-title":"Cell"},{"issue":"6","key":"pcbi.1007828.ref011","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":"M Setty","year":"2016","journal-title":"Nature biotechnology"},{"issue":"1","key":"pcbi.1007828.ref012","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":"FA Wolf","year":"2019","journal-title":"Genome biology"},{"issue":"10","key":"pcbi.1007828.ref013","doi-asserted-by":"crossref","first-page":"E2467","DOI":"10.1073\/pnas.1714723115","article-title":"Fundamental limits on dynamic inference from single-cell snapshots","volume":"115","author":"C Weinreb","year":"2018","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"4","key":"pcbi.1007828.ref014","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1016\/j.cell.2019.01.006","article-title":"Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming","volume":"176","author":"G Schiebinger","year":"2019","journal-title":"Cell"},{"issue":"7553","key":"pcbi.1007828.ref015","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep learning","volume":"521","author":"Y LeCun","year":"2015","journal-title":"Nature"},{"key":"pcbi.1007828.ref016","volume-title":"Deep Learning","author":"I Goodfellow","year":"2016"},{"issue":"1","key":"pcbi.1007828.ref017","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1561\/2200000006","article-title":"Learning deep architectures for AI","volume":"2","author":"Y Bengio","year":"2009","journal-title":"Foundations and Trends\u00ae in Machine Learning"},{"issue":"24","key":"pcbi.1007828.ref018","doi-asserted-by":"crossref","first-page":"5529","DOI":"10.1242\/jcs.123604","article-title":"Machine learning in cell biology\u2013teaching computers to recognize phenotypes","volume":"126","author":"C Sommer","year":"2013","journal-title":"J Cell Sci"},{"key":"pcbi.1007828.ref019","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev-bioeng-071516-044442","article-title":"Deep learning in medical image analysis","volume":"19","author":"D Shen","year":"2017","journal-title":"Annual Review of Biomedical Engineering"},{"issue":"1","key":"pcbi.1007828.ref020","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1083\/jcb.201610026","article-title":"Machine learning and computer vision approaches for phenotypic profiling","volume":"216","author":"BT Grys","year":"2017","journal-title":"J Cell Biol"},{"issue":"5786","key":"pcbi.1007828.ref021","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1126\/science.1127647","article-title":"Reducing the dimensionality of data with neural networks","volume":"313","author":"GE Hinton","year":"2006","journal-title":"Science"},{"key":"pcbi.1007828.ref022","first-page":"3","volume-title":"Advances in Neural Information Processing Systems","author":"GE Hinton","year":"1994"},{"key":"pcbi.1007828.ref023","unstructured":"Kingma DP, Welling M. Auto-encoding variational bayes. arXiv preprint arXiv:13126114. 2013;."},{"key":"pcbi.1007828.ref024","unstructured":"Monge G. M\u00e9moire sur la th\u00e9orie des d\u00e9blais et des remblais. Histoire de l\u2019Acad\u00e9mie Royale des Sciences de Paris. 1781;."},{"key":"pcbi.1007828.ref025","unstructured":"Kantorovich LV. On the translocation of masses. In: Dokl. Akad. Nauk. USSR (NS). vol. 37; 1942. p. 199\u2013201."},{"key":"pcbi.1007828.ref026","volume-title":"Optimal Transport: Old and New","author":"C Villani","year":"2008"},{"key":"pcbi.1007828.ref027","first-page":"2292","volume-title":"Advances in Neural Information Processing Systems","author":"M Cuturi","year":"2013"},{"key":"pcbi.1007828.ref028","unstructured":"Makhzani A, Shlens J, Jaitly N, Goodfellow I, Frey B. Adversarial autoencoders. arXiv preprint arXiv:151105644. 2015;."},{"key":"pcbi.1007828.ref029","unstructured":"Tolstikhin I, Bousquet O, Gelly S, Schoelkopf B. Wasserstein auto-encoders. arXiv preprint arXiv:171101558. 2017;."},{"key":"pcbi.1007828.ref030","doi-asserted-by":"crossref","unstructured":"Weinreb C, Rodriguez-Fraticelli AE, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. bioRxiv. 2018; p. 467886.","DOI":"10.1101\/467886"},{"issue":"9","key":"pcbi.1007828.ref031","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/nrc.2016.73","article-title":"The biology and function of fibroblasts in cancer","volume":"16","author":"R Kalluri","year":"2016","journal-title":"Nature Reviews Cancer"},{"issue":"1","key":"pcbi.1007828.ref032","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1172\/JCI93554","article-title":"The fibrotic tumor stroma","volume":"128","author":"M Yamauchi","year":"2018","journal-title":"Journal of Clinical Investigation"},{"key":"pcbi.1007828.ref033","first-page":"33","volume-title":"Seminars in Cell & Developmental Biology","author":"OE Franco","year":"2010"},{"key":"pcbi.1007828.ref034","unstructured":"Coelho LP. Mahotas: Open source software for scriptable computer vision. arXiv preprint arXiv:12114907. 2012;."},{"key":"pcbi.1007828.ref035","article-title":"Multivariate analysis reveals activation-primed fibroblast geometric states in engineered 3D tumor microenvironments","author":"S Venkatachalapathy","year":"2020","journal-title":"Molecular Biology of the Cell"},{"issue":"4","key":"pcbi.1007828.ref036","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.trecan.2018.02.009","article-title":"Nuclear mechanopathology and cancer diagnosis","volume":"4","author":"C Uhler","year":"2018","journal-title":"Trends in Cancer"},{"issue":"4","key":"pcbi.1007828.ref037","doi-asserted-by":"crossref","first-page":"e8046","DOI":"10.15252\/msb.20178046","article-title":"Using single-cell genomics to understand developmental processes and cell fate decisions","volume":"14","author":"JA Griffiths","year":"2018","journal-title":"Molecular Systems Biology"},{"issue":"12","key":"pcbi.1007828.ref038","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1038\/nrg3980","article-title":"Single-cell epigenomics: Techniques and emerging applications","volume":"16","author":"O Schwartzman","year":"2015","journal-title":"Nature Reviews Genetics"},{"issue":"3-4","key":"pcbi.1007828.ref039","doi-asserted-by":"crossref","first-page":"1600267","DOI":"10.1002\/pmic.201600267","article-title":"Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis","volume":"17","author":"Y Su","year":"2017","journal-title":"Proteomics"},{"issue":"12","key":"pcbi.1007828.ref040","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nrm.2017.101","article-title":"Regulation of genome organization and gene expression by nuclear mechanotransduction","volume":"18","author":"C Uhler","year":"2017","journal-title":"Nature Reviews Molecular Cell Biology"},{"issue":"52","key":"pcbi.1007828.ref041","doi-asserted-by":"crossref","first-page":"13714","DOI":"10.1073\/pnas.1708028115","article-title":"Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription","volume":"114","author":"A Belyaeva","year":"2017","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"2","key":"pcbi.1007828.ref042","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nrg2041","article-title":"Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions","volume":"8","author":"C Lanct\u00f4t","year":"2007","journal-title":"Nature Reviews Genetics"},{"issue":"6286","key":"pcbi.1007828.ref043","doi-asserted-by":"crossref","first-page":"aad6933","DOI":"10.1126\/science.aad6933","article-title":"Nongenetic functions of the genome","volume":"352","author":"M Bustin","year":"2016","journal-title":"Science"},{"key":"pcbi.1007828.ref044","first-page":"1","article-title":"Emerging views of the nucleus as a cellular mechanosensor","author":"TJ Kirby","year":"2018","journal-title":"Nature Cell Biology"},{"issue":"2","key":"pcbi.1007828.ref045","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1083\/jcb.201610042","article-title":"Mechanosensing by the nucleus: From pathways to scaling relationships","volume":"216","author":"S Cho","year":"2017","journal-title":"J Cell Biol"},{"key":"pcbi.1007828.ref046","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"},{"key":"pcbi.1007828.ref047","unstructured":"Paszke A, Gross S, Chintala S, Chanan G, Yang E, DeVito Z, et al. Automatic differentiation in pytorch. https:\/\/openreviewnet\/pdf?id=BJJsrmfCZ. 2017;."},{"key":"pcbi.1007828.ref048","unstructured":"Kingma DP, Ba J. Adam: A method for stochastic optimization. arXiv preprint arXiv:14126980. 2014;."},{"key":"pcbi.1007828.ref049","doi-asserted-by":"crossref","unstructured":"Maturana D, Scherer S. Voxnet: A 3d convolutional neural network for real-time object recognition. In: 2015 IEEE\/RSJ International Conference on Intelligent Robots and Systems (IROS); 2015. p. 922\u2013928.","DOI":"10.1109\/IROS.2015.7353481"},{"issue":"1","key":"pcbi.1007828.ref050","doi-asserted-by":"crossref","first-page":"E32","DOI":"10.1073\/pnas.1513189113","article-title":"Nuclear deformability and telomere dynamics are regulated by cell geometric constraints","volume":"113","author":"E Makhija","year":"2016","journal-title":"Proceedings of the National Academy of Sciences, USA"},{"issue":"7","key":"pcbi.1007828.ref051","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nature Methods"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007828","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T00:00:00Z","timestamp":1588896000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007828","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T17:33:30Z","timestamp":1588959210000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007828"}},"subtitle":[],"editor":[{"given":"Jian","family":"Ma","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,4,28]]},"references-count":51,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007828","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1007828","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,28]]}}}