{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T15:26:47Z","timestamp":1769873207779,"version":"3.49.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T00:00:00Z","timestamp":1766707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korea government","award":["RS-2024-00342721"],"award-info":[{"award-number":["RS-2024-00342721"]}]},{"name":"Korea government","award":["RS-2025-02263724"],"award-info":[{"award-number":["RS-2025-02263724"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Reconstructing gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is fundamental for understanding cellular dynamics at the molecular level but requires sophisticated workflows. Here, we introduce CellCraft, a web-based application designed to streamline GRN inference. CellCraft integrates multiple GRN reconstruction tools, including TENET, within a unified web application featuring an intuitive graphical user interface. Notably, CellCraft provides a visual programming interface that simplifies the design and execution of complex multistep analyses, thereby enhancing accessibility and facilitating the visualization and interpretation of computational experiments. Furthermore, its modular plugin architecture ensures extensibility, enabling the incorporation of newly developed single-cell analysis algorithms. Consequently, CellCraft provides a user-friendly and extensible application for integrative GRN analysis of scRNA-seq datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CellCraft is available on GitHub at https:\/\/github.com\/cxinsys\/cellcraft. The source code has been archived on Zenodo at 10.5281\/zenodo.17865848.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf684","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T13:03:37Z","timestamp":1766581417000},"source":"Crossref","is-referenced-by-count":0,"title":["CellCraft: an extensible visual programming application for gene regulatory network inference"],"prefix":"10.1093","volume":"42","author":[{"given":"Dongmin","family":"Shin","sequence":"first","affiliation":[{"name":"Department of Applied Art and Technology, College of Art and Technology, Chung-Ang University , Anseong 17546,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeonghwan Henry","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , Seoul 06978,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rakbin","family":"Sung","sequence":"additional","affiliation":[{"name":"Department of Applied Art and Technology, College of Art and Technology, Chung-Ang University , Anseong 17546,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1202-1808","authenticated-orcid":false,"given":"Junil","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , Seoul 06978,","place":["Republic of Korea"]},{"name":"School of Systems Biomedical Science, Soongsil University , Seoul 06978,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3004-2901","authenticated-orcid":false,"given":"Daewon","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Applied Art and Technology, College of Art and Technology, Chung-Ang University , Anseong 17546,","place":["Republic of Korea"]},{"name":"School of Art and Technology, College of Art and Technology, Chung-Ang University , Anseong 17546,","place":["Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,12,26]]},"reference":[{"key":"2026013020114591200_btaf684-B1","doi-asserted-by":"crossref","first-page":"W83","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Abueg","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026013020114591200_btaf684-B2","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat Methods"},{"key":"2026013020114591200_btaf684-B3","author":"Solem A.","year":"2009"},{"key":"2026013020114591200_btaf684-B4","volume-title":"The Architecture of Open Source Applications (Volume II)","author":"Bayer","year":"2012"},{"key":"2026013020114591200_btaf684-B5","volume-title":"Studies in Classification, Data Analysis, and Knowledge Organization","author":"Berthold"},{"key":"2026013020114591200_btaf684-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"key":"2026013020114591200_btaf684-B7","doi-asserted-by":"crossref","first-page":"7298","DOI":"10.1093\/nar\/gkac593","article-title":"Systemic approaches using single cell transcriptome reveal that c\/ebp regulates autophagy under amino acid starved condition","volume":"50","author":"Kim","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026013020114591200_btaf684-B8","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/s41540-023-00312-6","article-title":"Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data","volume":"9","author":"Kim","year":"2023","journal-title":"NPJ Syst Biol Appl"},{"key":"2026013020114591200_btaf684-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s13258-023-01473-8","article-title":"A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing","volume":"46","author":"Kim","year":"2024","journal-title":"Genes Genomics"},{"key":"2026013020114591200_btaf684-B10","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":"2026013020114591200_btaf684-B11","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":"2026013020114591200_btaf684-B12","first-page":"2","article-title":"Docker: lightweight linux containers for consistent development and deployment","volume":"2014","author":"Merkel","year":"2014","journal-title":"Linux J"},{"key":"2026013020114591200_btaf684-B13","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","article-title":"GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks","volume":"35","author":"Moerman","year":"2019","journal-title":"Bioinformatics"},{"key":"2026013020114591200_btaf684-B14","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with Snakemake","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res"},{"key":"2026013020114591200_btaf684-B15","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","article-title":"Taverna: a tool for the composition and enactment of bioinformatics workflows","volume":"20","author":"Oinn","year":"2004","journal-title":"Bioinformatics"},{"key":"2026013020114591200_btaf684-B16","author":"Plotly Technologies Inc","year":"2015"},{"key":"2026013020114591200_btaf684-B17","author":"PostgreSQL Global Development Group","year":"1996"},{"key":"2026013020114591200_btaf684-B18","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41592-019-0690-6","article-title":"Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data","volume":"17","author":"Pratapa","year":"2020","journal-title":"Nat Methods"},{"key":"2026013020114591200_btaf684-B19","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":"2026013020114591200_btaf684-B20","author":"RabbitMQ Team","year":":\/\/.."},{"key":"2026013020114591200_btaf684-B21","author":"Ram\u00edrez","year":"2018"},{"key":"2026013020114591200_btaf684-B22","first-page":"2","article-title":"Nginx: the high-performance web server and reverse proxy","volume":"2008","author":"Reese","year":"2008","journal-title":"Linux J"},{"key":"2026013020114591200_btaf684-B23","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2026013020114591200_btaf684-B24","author":"Soler","year":"2020"},{"key":"2026013020114591200_btaf684-B25","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btw729","article-title":"LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering","volume":"33","author":"Specht","year":"2017","journal-title":"Bioinformatics"},{"key":"2026013020114591200_btaf684-B26","doi-asserted-by":"crossref","first-page":"btae699","DOI":"10.1093\/bioinformatics\/btae699","article-title":"FastTENET: an accelerated tenet algorithm based on manycore computing in python","volume":"40","author":"Sung","year":"2024","journal-title":"Bioinformatics"},{"key":"2026013020114591200_btaf684-B27","doi-asserted-by":"crossref","first-page":"btaf624","DOI":"10.1093\/bioinformatics\/btaf624","article-title":"FastSCODE: An accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors","volume":"41","author":"Sung","year":"2025","journal-title":"Bioinformatics"},{"key":"2026013020114591200_btaf684-B28","author":"You","year":"2014"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf684\/66133783\/btaf684.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/1\/btaf684\/66133783\/btaf684.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/1\/btaf684\/66133783\/btaf684.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T01:11:54Z","timestamp":1769821914000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf684\/8405385"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,26]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf684","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2025,12,26]]},"article-number":"btaf684"}}