{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T03:04:50Z","timestamp":1776481490869,"version":"3.51.2"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["031L0309A"],"award-info":[{"award-number":["031L0309A"]}]},{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Stiftung","doi-asserted-by":"publisher","award":["00.003.2024"],"award-info":[{"award-number":["00.003.2024"]}],"id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"DFG, German Research Foundation","award":["516188180"],"award-info":[{"award-number":["516188180"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U19AI135990"],"award-info":[{"award-number":["U19AI135990"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54AI170792"],"award-info":[{"award-number":["U54AI170792"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54CA274502"],"award-info":[{"award-number":["U54CA274502"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Differential kinase interaction networks (DKINs) are networks containing kinase\u2013substrate links that are differentially active between two conditions. Existing methods are either able to predict condition-agnostic kinase\u2013substrate links or condition-specific differential kinase activity, but do not provide differential kinase\u2013substrate links. Moreover, existing methods for predicting kinase\u2013substrate links usually rely on curated biochemical knowledge. Thus, there is a lack of data-driven DKIN inference methods that are also applicable when prior knowledge is scarce.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address this need, we present KINference. KINference combines computation of a baseline KIN representing the space of all possible kinase\u2013substrate links with filters applied to nodes and edges to identify differentially active subnetworks that are relevant in the context of a specific phosphoproteomics dataset. For the node filters, we rely on functional relevance and differential phosphorylation scores; for the edge filters, we make use of prize-collecting Steiner trees and correlations between phosphorylation sites of kinases and their target proteins. Tests on two phosphoproteomics datasets (kinase inhibition in breast cancer cells, SARS-CoV-2 infection in Calu-3 cells) show that the proposed filters produce significant results in terms of overlap with known interactions between kinases and phosphorylation sites. Furthermore, a case study on the SARS-CoV-2 infection data, suggests a potential host pathway linked to virus replication, showcasing the process of hypothesis generation utilizing DKINs computed by KINference.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>KINference is available as an R package at https:\/\/github.com\/bionetslab\/KINference and https:\/\/doi.org\/10.5281\/zenodo.15411150. Scripts to reproduce the results are available at https:\/\/github.com\/bionetslab\/KINference-Evaluation-Scripts and https:\/\/doi.org\/10.5281\/zenodo.15424599.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf349","type":"journal-article","created":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T07:51:22Z","timestamp":1750233082000},"source":"Crossref","is-referenced-by-count":2,"title":["Inference of differential kinase interaction networks with KINference"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-7829-2881","authenticated-orcid":false,"given":"Nicolai","family":"Meyerh\u00f6fer","sequence":"first","affiliation":[{"name":"Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU) , 91052 Erlangen,","place":["Germany"]},{"name":"Quantitative Biosciences Institute (QBI), University of California , San Francisco, CA 94158,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nevan J","family":"Krogan","sequence":"additional","affiliation":[{"name":"Quantitative Biosciences Institute (QBI), University of California , San Francisco, CA 94158,","place":["United States"]},{"name":"Department of Cellular and Molecular Pharmacology, University of California , San Francisco, CA 94158,","place":["United States"]},{"name":"Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes , San Francisco, CA 94158,","place":["United States"]},{"name":"Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), University of California , San Francisco, CA 94158,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin J","family":"Polacco","sequence":"additional","affiliation":[{"name":"Quantitative Biosciences Institute (QBI), University of California , San Francisco, CA 94158,","place":["United States"]},{"name":"Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes , San Francisco, CA 94158,","place":["United States"]},{"name":"Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), University of California , San Francisco, CA 94158,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8651-750X","authenticated-orcid":false,"given":"David B","family":"Blumenthal","sequence":"additional","affiliation":[{"name":"Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU) , 91052 Erlangen,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,6,20]]},"reference":[{"key":"2025071715364251800_btaf349-B1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with alphafold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2025071715364251800_btaf349-B2","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s12863-023-01173-y","article-title":"SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study","volume":"24","author":"Akbari","year":"2023","journal-title":"BMC Genom Data"},{"key":"2025071715364251800_btaf349-B3","doi-asserted-by":"crossref","first-page":"e1006678","DOI":"10.1371\/journal.pcbi.1006678","article-title":"Cophosk: a method for comprehensive kinase substrate annotation using co-phosphorylation analysis","volume":"15","author":"Ayati","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2025071715364251800_btaf349-B4","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1016\/j.cell.2020.10.004","article-title":"SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses","volume":"183","author":"Banerjee","year":"2020","journal-title":"Cell"},{"key":"2025071715364251800_btaf349-B5","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btab876","article-title":"Robust disease module mining via enumeration of diverse prize-collecting steiner trees","volume":"38","author":"Bernett","year":"2022","journal-title":"Bioinformatics"},{"key":"2025071715364251800_btaf349-B6","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1039\/C4LC00797B","article-title":"Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip","volume":"15","author":"Blazek","year":"2015","journal-title":"Lab Chip"},{"key":"2025071715364251800_btaf349-B7","doi-asserted-by":"crossref","first-page":"4597","DOI":"10.1016\/j.cell.2023.08.026","article-title":"SARS-CoV-2 variants evolve convergent strategies to remodel the host response","volume":"186","author":"Bouhaddou","year":"2023","journal-title":"Cell"},{"key":"2025071715364251800_btaf349-B8","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.molcel.2020.07.001","article-title":"Kinase interaction network expands functional and disease roles of human kinases","volume":"79","author":"Buljan","year":"2020","journal-title":"Mol Cell"},{"key":"2025071715364251800_btaf349-B9","author":"Chinmay","year":"2014"},{"key":"2025071715364251800_btaf349-B10","doi-asserted-by":"crossref","first-page":"4283","DOI":"10.1038\/s41467-022-32017-5","article-title":"Kstar: an algorithm to predict patient-specific kinase activities from phosphoproteomic data","volume":"13","author":"Crowl","year":"2022","journal-title":"Nat Commun"},{"key":"2025071715364251800_btaf349-B11","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJournal"},{"key":"2025071715364251800_btaf349-B12","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1038\/s41592-024-02201-0","article-title":"scgpt: toward building a foundation model for single-cell multi-omics using generative ai","volume":"21","author":"Cui","year":"2024","journal-title":"Nat Methods"},{"key":"2025071715364251800_btaf349-B13","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/nsmb.1842","article-title":"Post-translational modifications in signal integration","volume":"17","author":"Deribe","year":"2010","journal-title":"Nat Struct Mol Biol"},{"key":"2025071715364251800_btaf349-B14","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.jprot.2014.01.020","article-title":"Bias tradeoffs in the creation and analysis of protein\u2013protein interaction networks","volume":"100","author":"Gillis","year":"2014","journal-title":"J Proteomics"},{"key":"2025071715364251800_btaf349-B15","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1137\/S0097539793242618","article-title":"A general approximation technique for constrained forest problems","volume":"24","author":"Goemans","year":"1995","journal-title":"SIAM J Comput"},{"key":"2025071715364251800_btaf349-B16","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nmeth.2968","article-title":"KinomeXplorer: an integrated platform for kinome biology studies","volume":"11","author":"Horn","year":"2014","journal-title":"Nat Methods"},{"key":"2025071715364251800_btaf349-B17","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B18","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.cels.2020.04.005","article-title":"Prediction of signed protein kinase regulatory circuits","volume":"10","author":"Invergo","year":"2020","journal-title":"Cell Syst"},{"key":"2025071715364251800_btaf349-B19","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.cstres.2024.03.002","article-title":"The S1 spike protein of SARS-CoV-2 upregulates the ERK\/MAPK signaling pathway in DC-SIGN-expressing THP-1 cells","volume":"29","author":"Johnson","year":"2024","journal-title":"Cell Stress Chaperones"},{"key":"2025071715364251800_btaf349-B20","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41586-022-05575-3","article-title":"An atlas of substrate specificities for the human serine\/threonine kinome","volume":"613","author":"Johnson","year":"2023","journal-title":"Nature"},{"key":"2025071715364251800_btaf349-B21","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B22","first-page":"85","volume-title":"Reducibility among Combinatorial Problems","author":"Karp","year":"1972"},{"key":"2025071715364251800_btaf349-B23","doi-asserted-by":"crossref","first-page":"W207","DOI":"10.1093\/nar\/gkad347","article-title":"g: profiler\u2014interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)","volume":"51","author":"Kolberg","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B24","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s00277-022-05026-z","article-title":"BRAF inhibitor treatment of classical hairy cell leukemia allows successful vaccination against SARS-CoV-2","volume":"102","author":"Konrat","year":"2023","journal-title":"Ann Hematol"},{"key":"2025071715364251800_btaf349-B25","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"Wgcna: an r package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2025071715364251800_btaf349-B26","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab066","article-title":"On the limits of active module identification","volume":"22","author":"Lazareva","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025071715364251800_btaf349-B27","doi-asserted-by":"crossref","first-page":"e9593","DOI":"10.15252\/msb.20209593","article-title":"DOMINO: a network-based active module identification algorithm with reduced rate of false calls","volume":"17","author":"Levi","year":"2021","journal-title":"Mol Syst Biol"},{"key":"2025071715364251800_btaf349-B28","doi-asserted-by":"crossref","first-page":"E5192","DOI":"10.1073\/pnas.1603435113","article-title":"p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PL pro via E3 ubiquitin ligase RCHY1","volume":"113","author":"Ma-Lauer","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025071715364251800_btaf349-B29","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/S0968-0004(02)02179-5","article-title":"Evolution of protein kinase signaling from yeast to man","volume":"27","author":"Manning","year":"2002","journal-title":"Trends Biochem Sci"},{"key":"2025071715364251800_btaf349-B30","doi-asserted-by":"crossref","first-page":"1912","DOI":"10.1126\/science.1075762","article-title":"The protein kinase complement of the human genome","volume":"298","author":"Manning","year":"2002","journal-title":"Science"},{"key":"2025071715364251800_btaf349-B31","doi-asserted-by":"crossref","first-page":"105550","DOI":"10.1016\/j.antiviral.2023.105550","article-title":"Nucleolin mediates SARS-CoV-2 replication and viral-induced apoptosis of host cells","volume":"211","author":"Merino","year":"2023","journal-title":"Antiviral Res"},{"key":"2025071715364251800_btaf349-B32","doi-asserted-by":"crossref","first-page":"D672","DOI":"10.1093\/nar\/gkad1025","article-title":"The reactome pathway knowledgebase 2024","volume":"52","author":"Milacic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B33","doi-asserted-by":"crossref","first-page":"ra2","DOI":"10.1126\/scisignal.1159433","article-title":"Linear motif atlas for phosphorylation-dependent signaling","volume":"1","author":"Miller","year":"2008","journal-title":"Sci Signal"},{"key":"2025071715364251800_btaf349-B34","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":"2025071715364251800_btaf349-B35","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.sbi.2009.02.007","article-title":"Computational studies of protein regulation by post-translational phosphorylation","volume":"19","author":"Narayanan","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"2025071715364251800_btaf349-B36","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1080\/1744666X.2021.1945443","article-title":"Phosphatidylinositol 3-kinase signaling and immune regulation: insights into disease pathogenesis and clinical implications","volume":"17","author":"Nguyen","year":"2021","journal-title":"Expert Rev Clin Immunol"},{"key":"2025071715364251800_btaf349-B37","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/s41587-019-0344-3","article-title":"The functional landscape of the human phosphoproteome","volume":"38","author":"Ochoa","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2025071715364251800_btaf349-B38","doi-asserted-by":"crossref","first-page":"e175","DOI":"10.1002\/mco2.175","article-title":"Role of protein phosphorylation in cell signaling, disease, and the intervention therapy","volume":"3","author":"Pang","year":"2022","journal-title":"MedComm (2020)"},{"key":"2025071715364251800_btaf349-B39","doi-asserted-by":"crossref","first-page":"e2000140","DOI":"10.1002\/pmic.202000140","article-title":"Advances in quantitative high-throughput phosphoproteomics with sample multiplexing","volume":"21","author":"Paulo","year":"2021","journal-title":"Proteomics"},{"key":"2025071715364251800_btaf349-B40","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3390\/kinasesphosphatases1020009","article-title":"Protein kinase ck2 and sars-cov-2: an expected interplay story","volume":"1","author":"Quezada Meza","year":"2023","journal-title":"Kinases Phosphatases"},{"key":"2025071715364251800_btaf349-B41","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad345","article-title":"Online bias-aware disease module mining with ROBUST-Web","volume":"39","author":"Sarkar","year":"2023","journal-title":"Bioinformatics"},{"key":"2025071715364251800_btaf349-B42","doi-asserted-by":"crossref","first-page":"23928","DOI":"10.1038\/s41598-021-03309-5","article-title":"Identification of transcriptional regulatory network associated with response of host epithelial cells to sars-cov-2","volume":"11","author":"Su","year":"2021","journal-title":"Sci Rep"},{"key":"2025071715364251800_btaf349-B43","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41392-022-01296-1","article-title":"Host cell cycle checkpoint as antiviral target for sars-cov-2 revealed by integrative transcriptome and proteome analyses","volume":"8","author":"Sui","year":"2023","journal-title":"Signal Transduct Target Ther"},{"key":"2025071715364251800_btaf349-B44","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B45","doi-asserted-by":"crossref","first-page":"532","DOI":"10.3390\/ijms22020532","article-title":"Mapping the SARS-CoV-2-host protein\u2013protein interactome by affinity purification mass spectrometry and proximity-dependent biotin labeling: a rational and straightforward route to discover host-directed anti-SARS-CoV-2 therapeutics","volume":"22","author":"Terracciano","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2025071715364251800_btaf349-B46","doi-asserted-by":"crossref","first-page":"e9923","DOI":"10.15252\/msb.20209923","article-title":"Integrated intra- and intercellular signaling knowledge for multicellular omics analysis","volume":"17","author":"T\u00fcrei","year":"2021","journal-title":"Mol Syst Biol"},{"key":"2025071715364251800_btaf349-B47","doi-asserted-by":"crossref","first-page":"6747","DOI":"10.3390\/ijms23126747","article-title":"The inositol phosphate system-a coordinator of metabolic adaptability","volume":"23","author":"Tu-Sekine","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025071715364251800_btaf349-B48","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/nrm2203","article-title":"Jr. Mechanisms of specificity in protein phosphorylation","volume":"8","author":"Ubersax","year":"2007","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025071715364251800_btaf349-B49","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"UniProt Consortium","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071715364251800_btaf349-B50","doi-asserted-by":"crossref","first-page":"7719","DOI":"10.1073\/pnas.1423344112","article-title":"Empirical inference of circuitry and plasticity in a kinase signaling network","volume":"112","author":"Wilkes","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025071715364251800_btaf349-B51","doi-asserted-by":"crossref","first-page":"e109858","DOI":"10.1371\/journal.pone.0109858","article-title":"Induced expression of nucleolin phosphorylation-deficient mutant confers dominant-negative effect on cell proliferation","volume":"9","author":"Xiao","year":"2014","journal-title":"PLoS One"},{"key":"2025071715364251800_btaf349-B52","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1021\/acschembio.2c00378","article-title":"Host kinase CSNK2 is a target for inhibition of pathogenic SARS-like \u03b2-coronaviruses","volume":"17","author":"Yang","year":"2022","journal-title":"ACS Chem Biol"},{"key":"2025071715364251800_btaf349-B53","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1038\/s41586-024-07407-y","article-title":"The intrinsic substrate specificity of the human tyrosine kinome","volume":"629","author":"Yaron-Barir","year":"2024","journal-title":"Nature"},{"key":"2025071715364251800_btaf349-B54","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad046","article-title":"Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions","volume":"39","author":"Zhou","year":"2023","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf349\/63536680\/btaf349.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf349\/63536680\/btaf349.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/7\/btaf349\/63536680\/btaf349.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,17]],"date-time":"2025-07-17T19:36:55Z","timestamp":1752781015000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf349\/8169929"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,20]]},"references-count":54,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf349","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,6,20]]},"article-number":"btaf349"}}