{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:07:33Z","timestamp":1792786053428,"version":"4.5.0"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T00:00:00Z","timestamp":1792368000000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)\u2014Finance Code 001","award":["035\/2019"],"award-info":[{"award-number":["035\/2019"]}],"id":[{"id":"https:\/\/ror.org\/00x0ma614","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)\u2014Finance Code 001","award":["138\/2021"],"award-info":[{"award-number":["138\/2021"]}],"id":[{"id":"https:\/\/ror.org\/00x0ma614","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["440412\/2022-6"],"award-info":[{"award-number":["440412\/2022-6"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["408312\/2023-8"],"award-info":[{"award-number":["408312\/2023-8"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"publisher","award":["2025\/10318-5"],"award-info":[{"award-number":["2025\/10318-5"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Scalable analysis of biological sequences is essential for functional characterization, biomarker discovery, and therapeutic and vaccine development. Alignment-based pipelines often fail to capture intraspecific variation and become computationally limited on large datasets, while alignment-free methods treat each class as homogeneous, ignoring sample heterogeneity. We present CAMELLIA (Combining AlignMent-free fEature seLection cLassIficAtion), an alignment-free framework that combines feature selection with explainable machine learning for genomic sequence analysis and classification. CAMELLIA identifies subgroups within classes and ensures underrepresented subgroups are captured by the selected features, yielding a more accurate and scalable data-driven representation. Sequences are represented as graphs, from which structural patterns are extracted as features for supervised classifiers, enabling accurate class discrimination. In an HIV-1 case study, CAMELLIA accurately classified sequences into eight subtypes, reduced processing time versus MEGA (MUSCLE) and FAMSA, matched CASTOR-KRFE under identical splits, and outperformed COMET and REGA in accuracy. Beyond predictive performance, CAMELLIA recovered structural patterns beyond class labels, improving feature selection and interpretability. We further examined feature-count sensitivity, showing how selected feature numbers relate to underfitting or noise-driven overfitting. By balancing scalability, accuracy, and interpretability, CAMELLIA offers a new lens for genomic sequence classification and sets a new standard for data-driven, heterogeneity-aware analysis.<\/jats:p>","DOI":"10.1093\/nargab\/lqag124","type":"journal-article","created":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T08:33:12Z","timestamp":1792398792000},"source":"Crossref","is-referenced-by-count":0,"title":["CAMELLIA: an alignment-free pipeline integrating\n                    <i>k<\/i>\n                    -mer feature selection and supervised classification for genomic sequence subtyping"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5891-4724","authenticated-orcid":false,"given":"Tatiana Mari","family":"Saita","sequence":"first","affiliation":[{"name":"Associated Graduate Program in Bioinformatics (PPGAB), Universidade Tecnol\u00f3gica Federal do Paran\u00e1 (UTFPR) , Alberto Carazzai, 1640, Corn\u00e9lio Proc\u00f3pio, 86300-000, Paran\u00e1 ,","place":["Brasil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matheus Henrique","family":"Pimenta-Zanon","sequence":"additional","affiliation":[{"name":"Associated Graduate Program in Bioinformatics (PPGAB), Universidade Tecnol\u00f3gica Federal do Paran\u00e1 (UTFPR) , Alberto Carazzai, 1640, Corn\u00e9lio Proc\u00f3pio, 86300-000, Paran\u00e1 ,","place":["Brasil"]},{"name":"Departamento de Gen\u00e9tica Escola Superior de Agricultura \u2018Luiz de Queiroz\u2019, Universidade de S\u00e3o Paulo , P\u00e1dua Dias Av., 11, 13418-900, S\u00e3o Paulo ,","place":["Brasil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artur Trancoso Lopo","family":"de\u00a0Queiroz","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Pesquisas Cl\u00ednicas e Translacionais, Instituto Gon\u00e7alo Moniz, Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ) , Rua Waldemar Falc\u00e3o, 121, Salvador, 40296-710, Bahia ,","place":["Brasil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glaucia Maria","family":"Bressan","sequence":"additional","affiliation":[{"name":"Associated Graduate Program in Bioinformatics (PPGAB), Universidade Tecnol\u00f3gica Federal do Paran\u00e1 (UTFPR) , Alberto Carazzai, 1640, Corn\u00e9lio Proc\u00f3pio, 86300-000, Paran\u00e1 ,","place":["Brasil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8786-3313","authenticated-orcid":false,"given":"Fabricio Martins","family":"Lopes","sequence":"additional","affiliation":[{"name":"Associated Graduate Program in Bioinformatics (PPGAB), Universidade Tecnol\u00f3gica Federal do Paran\u00e1 (UTFPR) , Alberto Carazzai, 1640, Corn\u00e9lio Proc\u00f3pio, 86300-000, Paran\u00e1 ,","place":["Brasil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,19]]},"reference":[{"key":"2026101904330797300_B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Scientific data"},{"key":"2026101904330797300_B2","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1007\/978-3-319-33793-7_15","article-title":"Applications of bio-molecular databases in bioinformatics","volume-title":"Medical Imaging in Clinical Applications: Algorithmic and Computer-Based Approaches","author":"Kumari","year":"2016"},{"key":"2026101904330797300_B3","doi-asserted-by":"publisher","first-page":"D701","DOI":"10.1093\/nar\/gkad958","article-title":"COV2Var, a function annotation database of SARS-CoV-2 genetic variation","volume":"52","author":"Feng","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B4","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/s13059-019-1755-7","article-title":"Benchmarking of alignment-free sequence comparison methods","volume":"20","author":"Zielezinski","year":"2019","journal-title":"Genome Biol"},{"key":"2026101904330797300_B5","doi-asserted-by":"publisher","first-page":"RRN1198","DOI":"10.1371\/currents.RRN1198","article-title":"Multiple sequence alignment: a major challenge to large-scale phylogenetics","volume":"2","author":"Liu","year":"2011","journal-title":"PLoS Curr"},{"key":"2026101904330797300_B6","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1089\/cmb.2017.0042","article-title":"An efficient approach to explore and discriminate anomalous regions in bacterial genomes based on maximum entropy","volume":"24","author":"Barros-Carvalho","year":"2017","journal-title":"J Comput Biol"},{"key":"2026101904330797300_B7","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s12859-025-06037-z","article-title":"GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs","volume":"26","author":"Pimenta-Zanon","year":"2025","journal-title":"BMC Bioinform"},{"key":"2026101904330797300_B8","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1007\/978-3-032-09336-3_12","article-title":"BITSER: an alignment-free approach for feature extraction and classification of viral genomes","volume-title":"Brazilian Congress on Bioinformatics","author":"Fuganti","year":"2025"},{"key":"2026101904330797300_B9","doi-asserted-by":"publisher","first-page":"14295","DOI":"10.48084\/etasr.7401","article-title":"Adaptive method for feature selection in the machine learning context","volume":"14","author":"El\u00a0Touati","year":"2024","journal-title":"Eng Technol Appl Sci Res"},{"key":"2026101904330797300_B10","doi-asserted-by":"publisher","first-page":"23","DOI":"10.62347\/ZWRY8401","article-title":"Comparative analysis of dimensionality reduction techniques for EEG-based emotional state classification","volume":"13","author":"Sadegh-Zadeh","year":"2024","journal-title":"Am J Neurodegen Dis"},{"key":"2026101904330797300_B11","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-89010-0_15","article-title":"Random forest for genomic prediction","volume-title":"Multivariate Statistical Machine Learning Methods for Genomic Prediction","author":"Montesinos\u00a0L\u00f3pez","year":"2022"},{"key":"2026101904330797300_B12","doi-asserted-by":"publisher","first-page":"e0328253","DOI":"10.1371\/journal.pone.0328253","article-title":"DNA sequence classification for diabetes mellitus using NuSVC and XGBoost: a comparative","volume":"20","author":"Salloum","year":"2025","journal-title":"PLoS One"},{"key":"2026101904330797300_B13","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/scientificamerican0592-58","article-title":"Understanding the AIDS pandemic","volume":"266","author":"Anderson","year":"1992","journal-title":"Sci Am"},{"key":"2026101904330797300_B14","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1093\/nar\/18.8.2163","article-title":"Chaos game representation of gene structure","volume":"18","author":"Jeffrey","year":"1990","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B15","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1016\/j.ympev.2012.07.003","article-title":"Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping","volume":"65","author":"Kolekar","year":"2012","journal-title":"Mol Phylogenet Evol"},{"key":"2026101904330797300_B16","doi-asserted-by":"publisher","first-page":"1991","DOI":"10.1093\/bioinformatics\/btu177","article-title":"Fast alignment-free sequence comparison using spaced-word frequencies","volume":"30","author":"Leimeister","year":"2014","journal-title":"Bioinformatics"},{"key":"2026101904330797300_B17","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1089\/cmb.2018.0239","article-title":"Toward an alignment-free method for feature extraction and accurate classification of viral sequences","volume":"26","author":"Lebatteux","year":"2019","journal-title":"J Comput Biol"},{"key":"2026101904330797300_B18","doi-asserted-by":"publisher","first-page":"e144","DOI":"10.1093\/nar\/gku739","article-title":"Danielle Perez Bercoff, COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification","volume":"42","author":"Struck","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B19","doi-asserted-by":"publisher","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences","volume":"21","author":"De\u00a0Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"2026101904330797300_B20","doi-asserted-by":"publisher","first-page":"33964","DOI":"10.1038\/srep33964","article-title":"FAMSA: Fast and accurate multiple sequence alignment of huge protein families","volume":"6","author":"Deorowicz","year":"2016","journal-title":"Sci Rep"},{"key":"2026101904330797300_B21","doi-asserted-by":"publisher","first-page":"msae263","DOI":"10.1093\/molbev\/msae263","article-title":"MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing","volume":"41","author":"Kumar","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026101904330797300_B22","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B23","doi-asserted-by":"publisher","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2026101904330797300_B24","doi-asserted-by":"publisher","first-page":"3293","DOI":"10.1007\/s00705-014-2197-x","article-title":"Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification","volume":"159","author":"Bao","year":"2014","journal-title":"Arch Virol"},{"key":"2026101904330797300_B25","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1038\/nrg2323","article-title":"Rates of evolutionary change in viruses: patterns and determinants","volume":"9","author":"Duffy","year":"2008","journal-title":"Nat Rev Genet"},{"key":"2026101904330797300_B26","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1186\/1471-2105-11-538","article-title":"pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree","volume":"11","author":"Matsen","year":"2010","journal-title":"BMC Bioinform"},{"key":"2026101904330797300_B27","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1093\/bioinformatics\/btg005","article-title":"Alignment-free sequence comparison\u2014a review","volume":"19","author":"Vinga","year":"2003","journal-title":"Bioinformatics"},{"key":"2026101904330797300_B28","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s40168-017-0283-5","article-title":"VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data","volume":"5","author":"Ren","year":"2017","journal-title":"Microbiome"},{"key":"2026101904330797300_B29","doi-asserted-by":"publisher","first-page":"100147","DOI":"10.1016\/j.slast.2024.100147","article-title":"Assessment and classification of COVID-19 DNA sequence using pairwise features concatenation from multi-transformer and deep features with machine learning models","volume":"29","author":"Qayyum","year":"2024","journal-title":"SLAS Technol"},{"key":"2026101904330797300_B30","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1186\/s12864-025-11554-5","article-title":"Alignment-free viral sequence classification at scale","volume":"26","author":"van\u00a0Zyl","year":"2025","journal-title":"BMC Genomics"},{"key":"2026101904330797300_B31","doi-asserted-by":"publisher","first-page":"41642","DOI":"10.48550\/arXiv.2306.15006","article-title":"DNABERT-2: efficient foundation model and benchmark for multi-species genome","volume-title":"International Conference on Learning Representations","author":"Zhou","year":"2024"},{"key":"2026101904330797300_B32","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1038\/s41592-024-02523-z","article-title":"Nucleotide transformer: building and evaluating robust foundation models for human genomics","volume":"22","author":"Dalla-Torre","year":"2025","journal-title":"Nat Methods"},{"key":"2026101904330797300_B33","doi-asserted-by":"publisher","first-page":"43177","DOI":"10.52202\/075280-1872","article-title":"HyenaDNA: long-range genomic sequence modeling at single nucleotide resolution","volume-title":"Advances in Neural Information Processing Systems","author":"Nguyen","year":"2023"},{"key":"2026101904330797300_B34","doi-asserted-by":"publisher","first-page":"W654","DOI":"10.1093\/nar\/gkh419","article-title":"A web-based genotyping resource for viral sequences","volume":"32","author":"Rozanov","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B35","doi-asserted-by":"publisher","first-page":"W634","DOI":"10.1093\/nar\/gkp455","article-title":"A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences","volume":"37","author":"Alcantara","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B36","doi-asserted-by":"publisher","first-page":"vbae108","DOI":"10.1093\/bioadv\/vbae108","article-title":"Investigating alignment-free machine learning methods for HIV-1 subtype classification","volume":"4","author":"Wade","year":"2024","journal-title":"Bioinform Adv"},{"key":"2026101904330797300_B37","doi-asserted-by":"publisher","first-page":"109218","DOI":"10.1016\/j.compbiomed.2024.109218","article-title":"HIV-1 M group subtype classification using deep learning approach","volume":"183","author":"Peng","year":"2024","journal-title":"Comput Biol Med"},{"key":"2026101904330797300_B38","article-title":"Molecular biology of the Cell","author":"Alberts","year":"2002","edition":"4th edition"},{"key":"2026101904330797300_B39","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 nomenclature proposal","volume":"288","author":"Robertson","year":"2000","journal-title":"Science"},{"key":"2026101904330797300_B40","doi-asserted-by":"publisher","first-page":"138","DOI":"10.3390\/toxins14020138","article-title":"Infectious RNA: human immunodeficiency virus (HIV) biology, therapeutic intervention, and the quest for a vaccine","volume":"14","author":"Van\u00a0Heuvel","year":"2022","journal-title":"Toxins"},{"key":"2026101904330797300_B41","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1097\/qai.0000000000002246","article-title":"Brief Report: complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L","volume":"83","author":"Yamaguchi","year":"2019","journal-title":"J Acquired Immune Deficiency Syndromes"},{"key":"2026101904330797300_B42","doi-asserted-by":"publisher","first-page":"10752","DOI":"10.1128\/JVI.74.22.10752-10765.2000","article-title":"Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E","volume":"74","author":"Anderson","year":"2000","journal-title":"J Virol"},{"key":"2026101904330797300_B43","doi-asserted-by":"publisher","first-page":"1583","DOI":"10.1093\/infdis\/jiad327","article-title":"Geographic and Population Distributions of Human Immunodeficiency Virus (HIV)\u20131 and HIV-2 Circulating Subtypes: A Systematic Literature Review and Meta-analysis (2010\u20132021)","volume":"228","author":"Williams","year":"2023","journal-title":"J Infect Dis"},{"key":"2026101904330797300_B44","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/S1473-3099(18)30647-9","article-title":"2. Global and regional molecular epidemiology of HIV-1, 1990\u20132015: a systematic review, global survey, and trend analysis","volume":"19","author":"Hemelaar","year":"2018","journal-title":"Lancet Infectious Diseases"},{"key":"2026101904330797300_B45","article-title":"Global health sector strategies on HIV, viral hepatitis and sexually transmitted infections, 2022\u20132030: 2026 mid-term progress report","author":"World Health Organization","year":"2026"},{"key":"2026101904330797300_B46","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1080\/00018730601170527","article-title":"Characterization of complex networks: a survey of measurements","volume":"56","author":"Costa","year":"2007","journal-title":"Adv Phys"},{"key":"2026101904330797300_B47","doi-asserted-by":"publisher","first-page":"e96","DOI":"10.1093\/nar\/gky462","article-title":"BASiNET\u2014BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification","volume":"46","author":"Ito","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026101904330797300_B48","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/0893-6080(94)90109-0","article-title":"Topology representing networks","volume":"7","author":"Martinetz","year":"1994","journal-title":"Neural Netw"},{"key":"2026101904330797300_B49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/HPEC.2016.7761646","article-title":"Mathematical foundations of the GraphBLAS","volume-title":"IEEE High Performance Extreme Computing Conference (HPEC)","author":"Kepner","year":"2016"},{"key":"2026101904330797300_B50","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1201\/9781315108230","volume-title":"Feature Engineering and Selection: A Practical Approach for Predictive Models","author":"Kuhn","year":"2019"},{"key":"2026101904330797300_B51","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1186\/1471-2105-9-451","article-title":"Feature selection environment for genomic applications","volume":"9","author":"Lopes","year":"2008","journal-title":"BMC Bioinform"},{"key":"2026101904330797300_B52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ins.2014.02.096","article-title":"A feature selection technique for inference of graphs from their known topological properties: revealing scale-free gene regulatory networks","volume":"272","author":"Lopes","year":"2014","journal-title":"Inform Sci"},{"key":"2026101904330797300_B53","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1145\/502512.502546","article-title":"Random projection in dimensionality reduction: applications to image and text data","volume-title":"Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining","author":"Bingham","year":"2001"},{"key":"2026101904330797300_B54","doi-asserted-by":"publisher","first-page":"320","DOI":"10.25007\/ajnu.v12n2a1612","article-title":"eXtreme gradient boosting algorithm with machine learning: a review","volume":"12","author":"Arif\u00a0Ali","year":"2023","journal-title":"Acad J Nawroz Univ"},{"key":"2026101904330797300_B55","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.62527\/joiv.8.3-2.3451","article-title":"Comparative analysis of machine learning algorithms for cross-site scripting (XSS) attack detection","volume":"8","author":"Hamzah","year":"2024","journal-title":"Int J Inform Visualization"},{"key":"2026101904330797300_B56","doi-asserted-by":"publisher","first-page":"987","DOI":"10.32604\/iasc.2024.059429","article-title":"Overfitting in machine learning: a comparative analysis of decision trees and random forests","volume":"39","author":"Halabaku","year":"2024","journal-title":"Intelligent Automation Soft Computing"},{"key":"2026101904330797300_B57","doi-asserted-by":"publisher","first-page":"btae192","DOI":"10.1093\/bioinformatics\/btae192","article-title":"VirusPredictor: XGBoost-based software to predict virus-related sequences in human data","volume":"40","author":"Liu","year":"2024","journal-title":"Bioinformatics"},{"key":"2026101904330797300_B58","first-page":"11","article-title":"A review of evaluation metrics in machine learning algorithms","volume-title":"International Conference on Artificial Intelligence and Technologies","author":"Naidu","year":"2023"},{"key":"2026101904330797300_B59","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1007\/s00357-014-9161-z","article-title":"Ward\u2019s hierarchical agglomerative clustering method: which algorithms implement Ward\u2019s criterion?","volume":"31","author":"Murtagh","year":"2014","journal-title":"J Classif"},{"key":"2026101904330797300_B60","doi-asserted-by":"crossref","DOI":"10.32614\/R.manuals","article-title":"R: a Language and Environment for Statistical Computing","author":"R Core Team","year":"2026"},{"key":"2026101904330797300_B61","first-page":"25673","article-title":"HIV Sequence Compendium 2015","volume-title":"Theoretical Biology and Biophysics Group","author":"Foley","year":"2018"},{"key":"2026101904330797300_B62","doi-asserted-by":"publisher","first-page":"3043076","DOI":"10.2139\/ssrn.3043076","article-title":"Introducing Unit Invariant Knee (UIK) As an Objective Choice for Elbow Point in Multivariate Data Analysis Techniques","author":"Christopoulos","year":"2016"},{"key":"2026101904330797300_B63","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/1742-4690-9-92","article-title":"The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus","volume":"9","author":"van\u00a0der\u00a0Kuyl","year":"2012","journal-title":"Retrovirology"},{"key":"2026101904330797300_B64","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/nature24039","article-title":"CG dinucleotide suppression enables antiviral defence targeting non-self RNA","volume":"550","author":"Takata","year":"2017","journal-title":"Nature"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/4\/lqag124\/72085441\/lqag124.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/4\/lqag124\/72085441\/lqag124.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T08:33:15Z","timestamp":1792398795000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag124\/8937188"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":64,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,9,28]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag124","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,12]]},"published":{"date-parts":[[2026,9,28]]},"article-number":"lqag124"}}