{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T22:24:01Z","timestamp":1791498241561,"version":"4.3.4"},"posted":{"date-parts":[[2026,9,17]]},"group-title":"Systems Biology","reference-count":15,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["U01CA284193"],"award-info":[{"award-number":["U01CA284193"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>KSTAR is an algorithm with high flexibility for inferring kinase activity from any phosphoproteomic pipeline. However, in its first instantiation (v0.1) it requires Python programming and lots of memory and computational resources.<\/jats:p>\n                  <jats:p>Hence, we wished to improve speed and accessibility for broader uptake by researchers.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we provide an updated algorithm that improves speed and memory, without affecting accuracy, along with some new features for increased usability and insight. KSTAR v1.2 has also been integrated into Galaxy for programming-free activity analysis and ProteomeScout for dataset preparation and interactive plotting.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>\n                    <jats:bold>KSTAR is available at<\/jats:bold>\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/NaegleLab\/KSTAR\">https:\/\/github.com\/NaegleLab\/KSTAR<\/jats:ext-link>\n                    <jats:bold>or on Galaxy on<\/jats:bold>\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/usegalaxy.org\/\">https:\/\/usegalaxy.org\/<\/jats:ext-link>\n                    .\n                    <jats:bold>KSTAR Network resource assets are managed on Figshare at:<\/jats:bold>\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/doi.org\/10.6084\/m9.figshare.14944305\">https:\/\/doi.org\/10.6084\/m9.figshare.14944305<\/jats:ext-link>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.14.751568","type":"posted-content","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T10:25:32Z","timestamp":1789640732000},"source":"Crossref","is-referenced-by-count":1,"title":["KSTAR v1.2: A faster and more and accessible KSTAR for kinase activity inference"],"prefix":"10.64898","author":[{"given":"Sam","family":"Crowl","sequence":"first","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph-Levi","family":"Custer","sequence":"additional","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela Salazar","family":"Lopez","sequence":"additional","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Candace","family":"Lei-Dadey","sequence":"additional","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0782-0496","authenticated-orcid":false,"given":"Adrian A.","family":"Shimpi","sequence":"additional","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7146-9592","authenticated-orcid":false,"given":"Kristen M.","family":"Naegle","sequence":"additional","affiliation":[{"name":"Biomedical Engineering, University of Virginia, Charlottesville, 22903, Virginia, USA"},{"name":"Department of Genome Sciences, University of Virginia, Charlottesville, 22903, Virginia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092107500926000_2026.09.14.751568v1.1","doi-asserted-by":"crossref","unstructured":"Misty M. Attwood , Doriano Fabbro , Aleksandr V. Sokolov , Stefan Knapp , and Helgi B. Schi\u00f6th . Trends in kinase drug discovery: targets, indications and inhibitor design. Nature Reviews Drug Discovery, pages 1\u201323, August 2021.","DOI":"10.1038\/s41573-021-00252-y"},{"key":"2026092107500926000_2026.09.14.751568v1.2","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.2003573"},{"key":"2026092107500926000_2026.09.14.751568v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31217-3"},{"key":"2026092107500926000_2026.09.14.751568v1.4","unstructured":"Sam Crowl , Saqib Rizvi , Logan Campbell , Alekhya Kandoor , and K.M. Naegle . ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications. In Prep."},{"issue":"6","key":"2026092107500926000_2026.09.14.751568v1.5","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nmeth.2968","article-title":"KinomeXplorer: an integrated platform for kinome biology studies","volume":"11","year":"2014","journal-title":"Nature Methods"},{"key":"2026092107500926000_2026.09.14.751568v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-022-05575-3"},{"key":"2026092107500926000_2026.09.14.751568v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2014.08.007"},{"issue":"5","key":"2026092107500926000_2026.09.14.751568v1.8","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry\u2013based proteomics","volume":"14","year":"2017","journal-title":"Nature Methods"},{"issue":"3","key":"2026092107500926000_2026.09.14.751568v1.9","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1074\/mcp.TIR118.000943","article-title":"A Curated Resource for Phosphosite-specific Signature Analysis","volume":"18","year":"2019","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026092107500926000_2026.09.14.751568v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1154"},{"issue":"1","key":"2026092107500926000_2026.09.14.751568v1.11","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1038\/s41467-020-15346-1","article-title":"Generating high quality libraries for DIA MS with empirically corrected peptide predictions","volume":"11","year":"2020","journal-title":"Nature Communications"},{"key":"2026092107500926000_2026.09.14.751568v1.12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae410"},{"issue":"12","key":"2026092107500926000_2026.09.14.751568v1.13","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","year":"2016","journal-title":"Nature Protocols"},{"issue":"2","key":"2026092107500926000_2026.09.14.751568v1.14","doi-asserted-by":"crossref","first-page":"e1008681","DOI":"10.1371\/journal.pcbi.1008681","article-title":"KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions","volume":"17","year":"2021","journal-title":"PLOS Computational Biology"},{"key":"2026092107500926000_2026.09.14.751568v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07407-y"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.14.751568","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T14:50:23Z","timestamp":1790002223000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.14.751568"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,17]]},"references-count":15,"URL":"https:\/\/doi.org\/10.64898\/2026.09.14.751568","relation":{},"subject":[],"published":{"date-parts":[[2026,9,17]]},"subtype":"preprint"}}