{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:05:47Z","timestamp":1790121947818,"version":"4.0.1"},"reference-count":18,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013195","name":"William M Wood Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013195","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.xpro.2026.104730","type":"journal-article","created":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T20:57:22Z","timestamp":1785531442000},"page":"104730","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol for automated optimization of feature selection and clustering parameters in single-cell RNA-seq using scAutoTune"],"prefix":"10.1016","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0221-1691","authenticated-orcid":false,"given":"Shi Hai","family":"Sun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5071-7478","authenticated-orcid":false,"given":"John S.","family":"Pezaris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2026.104730_bib1","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/s12035-025-05361-y","article-title":"Single-Cell Transcriptomic Analysis of Macaque LGN Neurons Reveals Novel Subpopulations","volume":"63","author":"Sun","year":"2026","journal-title":"Mol. Neurobiol."},{"key":"10.1016\/j.xpro.2026.104730_bib2","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2026.104730_bib3","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/s41592-019-0537-1","article-title":"Data denoising with transfer learning in single-cell transcriptomics","volume":"16","author":"Wang","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104730_bib4","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xpro.2026.104730_bib6","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.64875","article-title":"Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans","volume":"10","author":"Bakken","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.xpro.2026.104730_bib7","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.xpro.2026.104730_bib8","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.xpro.2026.104730_bib9","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2026.104730_bib10","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2026.104730_bib11","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104730_bib12","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.1467-9868.2010.00749.x","article-title":"Fast Stable Restricted Maximum Likelihood and Marginal Likelihood Estimation of Semiparametric Generalized Linear Models","volume":"73","author":"Wood","year":"2011","journal-title":"J. R. Stat. Soc., Ser. B Stat. Methodol."},{"key":"10.1016\/j.xpro.2026.104730_bib13","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1198\/016214504000000980","article-title":"Stable and Efficient Multiple Smoothing Parameter Estimation for Generalized Additive Models","volume":"99","author":"Wood","year":"2004","journal-title":"J. Am. Stat. Assoc."},{"key":"10.1016\/j.xpro.2026.104730_bib14","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1111\/1467-9868.00374","article-title":"Thin Plate Regression Splines","volume":"65","author":"Wood","year":"2003","journal-title":"J. R. Stat. Soc., Ser. B Stat. Methodol."},{"key":"10.1016\/j.xpro.2026.104730_bib15","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1080\/01621459.2016.1180986","article-title":"Smoothing Parameter and Model Selection for General Smooth Models","volume":"111","author":"Wood","year":"2016","journal-title":"J. Am. Stat. Assoc."},{"key":"10.1016\/j.xpro.2026.104730_bib16","article-title":"igraph enables fast and robust network analysis across programming languages","author":"Antonov","year":"2023","journal-title":"arXiv"},{"key":"10.1016\/j.xpro.2026.104730_bib17","first-page":"1","article-title":"The igraph software","volume":"1695","author":"Csardi","year":"2006","journal-title":"Complex Syst."},{"key":"10.1016\/j.xpro.2026.104730_bib18","series-title":"cluster: Cluster Analysis Basics and Extensions. R package version 2.1.8.1.","author":"Maechler","year":"2025"},{"key":"10.1016\/j.xpro.2026.104730_bib19","article-title":"UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction","author":"McInnes","year":"2020","journal-title":"arXiv"}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726003837?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726003837?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T23:35:47Z","timestamp":1790120147000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166726003837"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":18,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2666166726003837"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104730","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for automated optimization of feature selection and clustering parameters in single-cell RNA-seq using scAutoTune","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104730","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104730"}}