{"ID": "doi:10.1101/2023.11.03.565575", "lab": {"title": "4DN DCIC, HMS", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "http://biorxiv.org/lookup/doi/10.1101/2023.11.03.565575", "award": {"description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "center_title": "DCIC - Park", "@id": "/awards/2U01CA200059-06/", "project": "4DN", "@type": ["Award", "Item"], "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "name": "2U01CA200059-06", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Pseudotime analysis for time-series single-cell sequencing and imaging data", "status": "replaced", "aliases": ["william-noble-lab:li_pseudotime_doi_10.1101_2023.11.03.565575_biorxiv"], "authors": ["Li G", "Kim H-J", "Pendyala S", "Zhang R", "Disteche CM", "Vert J-P", "Deng X", "Fowler DM", "Noble WS"], "journal": "bioRxiv", "version": "2", "abstract": "Many single-cell RNA-sequencing studies have collected time-series data to investigate transcriptional changes concerning various notions of biological time, such as cell differentiation, embryonic development, and response to stimulus. Accordingly, several unsupervised and supervised computational methods have been developed to construct single-cell pseudotime embeddings for extracting the temporal order of transcriptional cell states from these time-series scRNA-seq datasets. However, existing methods, such as psupertime, suffer from low predictive accuracy, and this problem becomes even worse when we try to generalize to other data types such as scATAC-seq or microscopy images. To address this problem, we propose Sceptic, a support vector machine model for supervised pseudotime analysis. Whereas psupertime employs a single joint regression model, Sceptic simultaneously trains multiple classifiers with separate score functions for each time point and also allows for non-linear kernel functions. Sceptic first generates a probability vector for each cell and then aims to predict chronological age via conditional expectation. We demonstrate that Sceptic achieves significantly improved prediction power (accuracy improved by 1.4 - 38.9%) for six publicly available scRNA-seq data sets over state-of-the-art methods, and that Sceptic also works well for single-nucleus image data. Moreover, we observe that the pseudotimes assigned by Sceptic show stronger correlations with nuclear morphology than the observed times, suggesting that these pseudotimes accurately capture the heterogeneity of nuclei derived from a single time point and thus provide more informative time labels than the observed times. Finally, we show that Sceptic accurately captures sex-specific differentiation timing from both scATAC-seq and scRNA-seq data.", "categories": ["integrative analysis", "technology development"], "date_created": "2024-01-17T16:00:43.627453+00:00", "published_by": "4DN", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-07-24T17:50:23.950490+00:00"}, "date_published": "2024-01-26", "public_release": "2024-01-17", "schema_version": "2", "static_content": [{"content": {"@id": "/static-sections/7d5f1f1a-a6ba-4ab3-9d69-8f30ab857d7c/", "content": "This biorxiv set was replaced by [PMID:40676652](https://data.4dnucleome.org/2399432c-2019-424d-ba69-91e1254609ab/).", "status": "released", "@type": ["StaticSection", "UserContent", "Item"], "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true, "convert_ext_links": true}, "content_as_html": "<div class=\"markdown-container\"><p>This biorxiv set was replaced by <a href=\"https://data.4dnucleome.org/2399432c-2019-424d-ba69-91e1254609ab/\" rel=\"noopener noreferrer\" target=\"_blank\">PMID:40676652</a>.</p></div>", "display_title": "Note: Replaced Biorxiv", "filetype": "md", "title": "Note: Replaced Biorxiv", "lab": {"@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "name": "static-header.replaced_item_005bc9e2-c5f5-4c43-a1e9-cc12dc7b5361", "uuid": "7d5f1f1a-a6ba-4ab3-9d69-8f30ab857d7c", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - 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