{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T12:21:01Z","timestamp":1790166061161,"version":"4.1.0"},"reference-count":32,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T00:00:00Z","timestamp":1733875200000},"content-version":"am","delay-in-days":10,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T00:00:00Z","timestamp":1733875200000},"content-version":"vor","delay-in-days":10,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["75N93021C00014"],"award-info":[{"award-number":["75N93021C00014"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009168","name":"Animal and Plant Health Inspection Service","doi-asserted-by":"publisher","award":["AP19VSNVSL00C043"],"award-info":[{"award-number":["AP19VSNVSL00C043"]}],"id":[{"id":"10.13039\/100009168","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Though receptor binding specificity is well established as a contributor to host tropism and spillover potential of influenza A viruses, determining receptor binding preference of a specific virus still requires expensive and time\u2010consuming laboratory analyses. In this study, we pilot a machine learning approach for prediction of binding preference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We trained a convolutional neural network to predict the \u03b12,6\u2010linked sialic acid preference of influenza A viruses given the hemagglutinin amino acid sequence. The model was evaluated with an independent test dataset to assess the standard performance metrics, the impact of missing data in the test sequences, and the prediction performance on novel subtypes. Further, features found to be important to the generation of predictions were tested via targeted mutagenesis of H9 and H16 proteins expressed on pseudoviruses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The final model developed in this study produced predictions on a test dataset correctly 94% of the time and an area under the receiver operating characteristic curve of 0.93. The model tolerated about 10% missing test data without compromising accurate prediction performance. Predictions on novel subtypes revealed that the model can extrapolate feature relationships between subtypes when generating binding predictions. Finally, evaluation of the features important for model predictions helped identify positions that alter the sialic acid conformation preference of hemagglutinin proteins in practice.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Ultimately, our results provide support to this in silico approach to hemagglutinin receptor binding preference prediction. This work emphasizes the need for ongoing research efforts to produce tools that may aid future pandemic risk assessment.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/irv.70044","type":"journal-article","created":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T21:40:06Z","timestamp":1733953206000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Examining the Influenza A Virus Sialic Acid Binding Preference Predictions of a Sequence\u2010Based Convolutional Neural Network"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5619-2609","authenticated-orcid":false,"given":"Laura\u00a0K.","family":"Borkenhagen","sequence":"first","affiliation":[{"name":"Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University  North Grafton Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan\u00a0A.","family":"Runstadler","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University  North Grafton Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,12,11]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/embj.201387442"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11262\u2010019\u201001700\u2010z"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cwj080"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.000809"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw857"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560\u20107917.ES.2017.22.13.30494"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cww020"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112302"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp033"},{"key":"e_1_2_9_12_1","first-page":"2825","article-title":"Scikit\u2010Learn: Machine Learning in Python","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1089\/hs.2019.0055"},{"key":"e_1_2_9_14_1","unstructured":"C.Fao \u201cKeras \u201dhttps:\/\/keras.io."},{"key":"e_1_2_9_15_1","first-page":"1","article-title":"A Unified Approach to Interpreting Model Predictions","volume":"30","author":"Lundberg S. 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