{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:53:55Z","timestamp":1790610835484,"version":"4.1.0"},"reference-count":51,"publisher":"American Association for the Advancement of Science (AAAS)","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T00:00:00Z","timestamp":1750118400000},"content-version":"vor","delay-in-days":167,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006690","name":"Politecnico di Milano","doi-asserted-by":"publisher","award":["CUP D53D23017400001"],"award-info":[{"award-number":["CUP D53D23017400001"]}],"id":[{"id":"10.13039\/501100006690","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100031478","name":"NextGenerationEU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100031478","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["PRIN PNRR 2022"],"award-info":[{"award-number":["PRIN PNRR 2022"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["P2022CNN2J"],"award-info":[{"award-number":["P2022CNN2J"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012352","name":"Universit\u00e0 degli Studi di Milano","doi-asserted-by":"publisher","award":["CUP G53D23006690001"],"award-info":[{"award-number":["CUP G53D23006690001"]}],"id":[{"id":"10.13039\/100012352","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["csbj.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Comput Struct Biotechnol J"],"published-print":{"date-parts":[[2025,1,1]]},"DOI":"10.1016\/j.csbj.2025.06.030","type":"journal-article","created":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T11:48:57Z","timestamp":1750852137000},"page":"2757-2771","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"title":["A codon usage-based approach for the stratification of Influenza A across recent spillovers"],"prefix":"10.34133","volume":"27","author":[{"given":"Tommaso","family":"Alfonsi","sequence":"first","affiliation":[{"name":"Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Chiara","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Universit\u00e0 degli Studi di Milano, Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Bernasconi","sequence":"additional","affiliation":[{"name":"Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","published-online":{"date-parts":[[2025,6,27]]},"reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2010.05.009"},{"key":"e_1_3_6_3_2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/msb.2009.71","article-title":"Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences","volume":"5","author":"Bahir I.","year":"2009","unstructured":"Bahir I., Fromer M., Prat Y. and Linial M.: Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol Syst Biol 2009; 5: 311.","journal-title":"Mol Syst Biol"},{"key":"e_1_3_6_4_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0168-1702(02)00309-X","article-title":"The extent of codon usage bias in human rna viruses and its evolutionary origin","volume":"92","author":"Jenkins G.M.","year":"2003","unstructured":"Jenkins G.M. and Holmes E.C.: The extent of codon usage bias in human rna viruses and its evolutionary origin. Virus Res 2003; 92: 1.","journal-title":"Virus Res"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000079"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12250-010-3123-3"},{"key":"e_1_3_6_7_2","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.biosystems.2005.03.002","article-title":"Analysis of synonymous codon usage in h5n1 virus and other influenza A viruses","volume":"81","author":"Zhou T.","year":"2005","unstructured":"Zhou T., Gu W., Ma J., Sun X. and Lu Z.: Analysis of synonymous codon usage in h5n1 virus and other influenza A viruses. Biosystems 2005; 81: 77.","journal-title":"Biosystems"},{"key":"e_1_3_6_8_2","first-page":"1","article-title":"Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus","volume":"10","author":"Wong E.H.","year":"2010","unstructured":"Wong E.H., Smith D.K., Rabadan R., Peiris M. and Poon L.L.: Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol Biol 2010; 10: 1.","journal-title":"BMC Evol Biol"},{"key":"e_1_3_6_9_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2334-13-386","article-title":"Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains","volume":"13","author":"Iwasaki Y.","year":"2013","unstructured":"Iwasaki Y., Abe T., Wada Y., Wada K. and Ikemura T.: Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains. BMC Infect Dis 2013; 13: 1.","journal-title":"BMC Infect Dis"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aap9072"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/349139"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vez038"},{"key":"e_1_3_6_13_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21197129"},{"key":"e_1_3_6_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz276"},{"key":"e_1_3_6_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2010.05.031"},{"key":"e_1_3_6_16_2","doi-asserted-by":"publisher","DOI":"10.1111\/irv.12736"},{"key":"e_1_3_6_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tmaid.2023.102638"},{"key":"e_1_3_6_18_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adq0900"},{"key":"e_1_3_6_19_2","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494"},{"key":"e_1_3_6_20_2","unstructured":"Alfonsi T. Chiara M. and Bernasconi A.: Supplementary material for \u201cA codon bias data approach for the stratification of Influenza A virus clades\u201d. 2024. https:\/\/doi.org\/10.5281\/zenodo.14561947. last accessed: June 1st 2025."},{"key":"e_1_3_6_21_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1176225"},{"key":"e_1_3_6_22_2","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.16777","article-title":"Origins of the 2009 H1N1 influenza pandemic in swine in Mexico","volume":"5","author":"Mena I.","year":"2016","unstructured":"Mena I., Nelson M.I., Quezada-Monroy F., Dutta J., Cortes-Fern\u00e1ndez R., Lara-Puente J.H. et al: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife 2016; 5.","journal-title":"eLife"},{"key":"e_1_3_6_23_2","article-title":"Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus","author":"Ding X.","year":"2024","unstructured":"Ding X., Liu J., Jiang T. and Wu A.: Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus. Virol Sin 2024; .","journal-title":"Virol Sin"},{"key":"e_1_3_6_24_2","first-page":"1","article-title":"A dendrite method for cluster analysis","volume":"3","author":"Cali\u0144ski T.","year":"1974","unstructured":"Cali\u0144ski T. and Harabasz J.: A dendrite method for cluster analysis. Commun Stat, Theory Methods 1974; 3: 1.","journal-title":"Commun Stat, Theory Methods"},{"key":"e_1_3_6_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/0377-0427(87)90125-7"},{"key":"e_1_3_6_26_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11908-018-0642-9","article-title":"Zoonotic influenza and human health\u2014part 1: virology and epidemiology of zoonotic influenzas","volume":"20","author":"Goneau L.","year":"2018","unstructured":"Goneau L., Mehta K., Wong J., L'Huillier A. and Gubbay J.: Zoonotic influenza and human health\u2014part 1: virology and epidemiology of zoonotic influenzas. Curr Infect Dis Rep 2018; 20: 1.","journal-title":"Curr Infect Dis Rep"},{"key":"e_1_3_6_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.08.006"},{"key":"e_1_3_6_28_2","first-page":"10","article-title":"Emergence and adaptation of a novel highly pathogenic h7n9 influenza virus in birds and humans from a 2013 human-infecting low-pathogenic ancestor","volume":"92","author":"Qi W.","year":"2018","unstructured":"Qi W., Jia W., Liu D., Li J., Bi Y., Xie S. et al: Emergence and adaptation of a novel highly pathogenic h7n9 influenza virus in birds and humans from a 2013 human-infecting low-pathogenic ancestor. J Virol 2018; 92: 10.","journal-title":"J Virol"},{"key":"e_1_3_6_29_2","unstructured":"Food and Agricultural Organization of the United States and World Organization for Animal Health : Influenza A cleavage sites OFFLU - network of expertise on animal influenza. 2022. https:\/\/www.offlu.org\/wp-content\/uploads\/2022\/01\/Influenza-A-Cleavage-Sites-Final-04-01-2022.pdf. last accessed: June 1st 2025."},{"key":"e_1_3_6_30_2","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1002\/j.1460-2075.1992.tb05305.x","article-title":"Influenza virus hemagglutinin with multibasic cleavage site is activated by furin, a subtilisin-like endoprotease","volume":"11","author":"Stieneke-Gr\u00f6ber A.","year":"1992","unstructured":"Stieneke-Gr\u00f6ber A., Vey M., Angliker H., Shaw E., Thomas G., Roberts C. et al: Influenza virus hemagglutinin with multibasic cleavage site is activated by furin, a subtilisin-like endoprotease. EMBO J 1992; 11: 2407.","journal-title":"EMBO J"},{"key":"e_1_3_6_31_2","volume-title":"Human infection with avian influenza A(H5) viruses","author":"World Health Organization","year":"2024","unstructured":"World Health Organization : Human infection with avian influenza A(H5) viruses. : 2024."},{"key":"e_1_3_6_32_2","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1093\/cid\/ciz328","article-title":"Viral factors associated with the high mortality related to human infections with clade 2.1 influenza A\/H5N1 virus in Indonesia","volume":"70","author":"Pawestri H.A.","year":"2020","unstructured":"Pawestri H.A., Eggink D., Isfandari S., Thanh T.T., Rogier van Doorn H., Setiawaty V. et al: Viral factors associated with the high mortality related to human infections with clade 2.1 influenza A\/H5N1 virus in Indonesia. Clin Infect Dis 2020; 70: 1139.","journal-title":"Clin Infect Dis"},{"key":"e_1_3_6_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(08)60627-3"},{"key":"e_1_3_6_34_2","article-title":"Expansion of the early warning system for avian influenza in the eu to evaluate the risk of spillover from wild birds to poultry","volume":"21","author":"Faverjon C.","year":"2024","unstructured":"Faverjon C., Fanelli A. and Cameron A.: Expansion of the early warning system for avian influenza in the eu to evaluate the risk of spillover from wild birds to poultry. EFSA Support Publ 2024; 21: 9114E.","journal-title":"EFSA Support Publ"},{"key":"e_1_3_6_35_2","doi-asserted-by":"publisher","DOI":"10.4142\/jvs.2017.18.S1.269"},{"key":"e_1_3_6_36_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086921"},{"key":"e_1_3_6_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06631-2"},{"key":"e_1_3_6_38_2","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature14348","article-title":"Dissemination, divergence and establishment of H7N9 influenza viruses in China","volume":"522","author":"Lam T.T.-Y.","year":"2015","unstructured":"Lam T.T.-Y., Zhou B., Wang J., Chai Y., Shen Y., Chen X. et al: Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature 2015; 522: 102.","journal-title":"Nature"},{"key":"e_1_3_6_39_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2410.171063"},{"key":"e_1_3_6_40_2","doi-asserted-by":"crossref","first-page":"741","DOI":"10.3201\/eid2105.141756","article-title":"Detecting spread of avian influenza A(H7N9) virus beyond China","volume":"21","author":"Millman A.J.","year":"2015","unstructured":"Millman A.J., Havers F., Iuliano A.D., Davis C.T., Sar B., Sovann L. et al: Detecting spread of avian influenza A(H7N9) virus beyond China. Emerg Infect Dis 2015; 21: 741.","journal-title":"Emerg Infect Dis"},{"key":"e_1_3_6_41_2","volume-title":"Influenza A (H5N1) infection in mammals: suspect case definition and diagnostic testing criteria","author":"Department for Environment Food & Rural Affairs, Animal & Plant Health Agency","year":"2022","unstructured":"Department for Environment Food & Rural Affairs, Animal & Plant Health Agency : Influenza A (H5N1) infection in mammals: suspect case definition and diagnostic testing criteria. : Department for Environment 2022. https:\/\/www.gov.uk\/government\/publications\/listed-diseases-in-animals-case-definitions-testing-and-reporting\/influenza-a-h5n1-infection-in-mammals-suspect-case-definition-and-diagnostic-testing-criteria. last accessed: June 1st, 2025."},{"key":"e_1_3_6_42_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2021.1872355"},{"key":"e_1_3_6_43_2","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-55192-z","article-title":"Functional anatomy of zinc finger antiviral protein complexes","volume":"15","author":"Bohn J.A.","year":"2024","unstructured":"Bohn J.A., Meagher J.L., Takata M.A., Gon\u00e7alves-Carneiro D., Yeoh Z.C., Ohi M.D. et al: Functional anatomy of zinc finger antiviral protein complexes. Nat Commun 2024; 15: 10834.","journal-title":"Nat Commun"},{"key":"e_1_3_6_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.11.116"},{"key":"e_1_3_6_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-00496-z"},{"key":"e_1_3_6_46_2","doi-asserted-by":"publisher","DOI":"10.1101\/2025.05.24.655955"},{"key":"e_1_3_6_47_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02099948"},{"key":"e_1_3_6_48_2","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1207\/s15327906mbr0102_10","article-title":"The scree test for the number of factors","volume":"1","author":"Cattell R.B.","year":"1966","unstructured":"Cattell R.B.: The scree test for the number of factors. Multivar Behav Res 1966; 1: 245.","journal-title":"Multivar Behav Res"},{"key":"e_1_3_6_49_2","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1963.10500845"},{"key":"e_1_3_6_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"e_1_3_6_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp259"},{"key":"e_1_3_6_52_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004"}],"container-title":["Computational and Structural Biotechnology Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2001037025002466?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2001037025002466?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/spj.science.org\/doi\/pdf\/10.1016\/j.csbj.2025.06.030","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T12:34:19Z","timestamp":1775219659000},"score":1,"resource":{"primary":{"URL":"https:\/\/spj.science.org\/doi\/10.1016\/j.csbj.2025.06.030"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,1]]},"references-count":51,"alternative-id":["10.1016\/j.csbj.2025.06.030"],"URL":"https:\/\/doi.org\/10.1016\/j.csbj.2025.06.030","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-5737660\/v1","asserted-by":"object"}]},"ISSN":["2001-0370"],"issn-type":[{"value":"2001-0370","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A codon usage-based approach for the stratification of Influenza A across recent spillovers","name":"articletitle","label":"Article Title"},{"value":"Computational and Structural Biotechnology Journal","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.csbj.2025.06.030","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.","name":"copyright","label":"Copyright"}]}}