{"id":"https://openalex.org/W7208750871","doi":"https://doi.org/10.64898/2026.09.01.748481","title":"NGS-RFA/FRA: A High Throughput Experimental and Computational Pipeline for Selective Mutational Scanning in Parallel","display_name":"NGS-RFA/FRA: A High Throughput Experimental and Computational Pipeline for Selective Mutational Scanning in Parallel","publication_year":2026,"publication_date":"2026-09-04","ids":{"openalex":"https://openalex.org/W7208750871","doi":"https://doi.org/10.64898/2026.09.01.748481"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.01.748481","doi":"https://doi.org/10.64898/2026.09.01.748481","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.01.748481","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.01.748481.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.01.748481.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050918199","display_name":"Sina T\u00fcreli","orcid":"https://orcid.org/0000-0001-7342-9295","observed_orcids":["https://orcid.org/0000-0001-7342-9295"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sina Tureli","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138754130","display_name":"Theo M. Bestebroer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Theo Bestebroer","raw_affiliation_strings":["Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052623851","display_name":"Sarah James","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah James","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5150031717","display_name":"Rachel Scheuer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rachel Scheuer","raw_affiliation_strings":["Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076714230","display_name":"Randall Dahn","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randall Dahn","raw_affiliation_strings":["Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077731040","display_name":"Shufang Fan","orcid":"https://orcid.org/0000-0002-1606-6229","observed_orcids":["https://orcid.org/0000-0002-1606-6229"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shufang Fan","raw_affiliation_strings":["Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5146754358","display_name":"Sam Turner","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sam Turner","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159850699","display_name":"Sam Wilks","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sam Wilks","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050022453","display_name":"Antonia Netzl","orcid":"https://orcid.org/0000-0001-8034-2382","observed_orcids":["https://orcid.org/0000-0001-8034-2382"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Antonia Netzl","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":"https://orcid.org/0000-0001-8034-2382","affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038145495","display_name":"Ana Moster\u00edn","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. Mosterin Hopping","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037157567","display_name":"Terry C. Jones","orcid":"https://orcid.org/0000-0003-1120-9531","observed_orcids":["https://orcid.org/0000-0003-1120-9531"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]},{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Terry C. Jones","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","Institute of Virology, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin and Berlin Institute of Health, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Institute of Virology, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin and Berlin Institute of Health, Berlin, Germany","institution_ids":["https://openalex.org/I39343248","https://openalex.org/I4210139777","https://openalex.org/I75951250","https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064426145","display_name":"Gabriele Neumann","orcid":"https://orcid.org/0000-0001-7054-1775","observed_orcids":["https://orcid.org/0000-0001-7054-1775"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriele Neumann","raw_affiliation_strings":["Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076363097","display_name":"Yoshihiro Kawaoka","orcid":"https://orcid.org/0000-0001-5061-8296","observed_orcids":["https://orcid.org/0000-0001-5061-8296"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yoshihiro Kawaoka","raw_affiliation_strings":["Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033922663","display_name":"Ron A. M. Fouchier","orcid":"https://orcid.org/0000-0001-8095-2869","observed_orcids":["https://orcid.org/0000-0001-8095-2869"]},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Ron Fouchier","raw_affiliation_strings":["Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055462574","display_name":"Mathilde Richard","orcid":"https://orcid.org/0000-0003-0240-9312","observed_orcids":["https://orcid.org/0000-0003-0240-9312"]},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mathilde Richard","raw_affiliation_strings":["Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, the Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056141410","display_name":"Derek J. Smith","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Derek J. Smith","raw_affiliation_strings":["Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Pathogen Evolution, Department of Zoology, University of Cambridge; Cambridge, CB25 3EJ, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5056141410"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.0026000000070780516,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/influenza-virus","display_name":"influenza virus","score":0.7649999856948853},{"id":"https://openalex.org/keywords/hemagglutinin","display_name":"hemagglutinin","score":0.9860000014305115},{"id":"https://openalex.org/keywords/antigen-escape","display_name":"antigen escape","score":0.7149999737739563},{"id":"https://openalex.org/keywords/virus-rescue","display_name":"virus rescue","score":0.5720000267028809},{"id":"https://openalex.org/keywords/replicative-fitness","display_name":"replicative fitness","score":0.8370000123977661},{"id":"https://openalex.org/keywords/neutralization","display_name":"neutralization","score":0.6899999976158142},{"id":"https://openalex.org/keywords/hemagglutination-inhibition","display_name":"hemagglutination inhibition","score":0.9190000295639038},{"id":"https://openalex.org/keywords/plaque-progression","display_name":"plaque progression","score":0.7889999747276306},{"id":"https://openalex.org/keywords/statistical-models","display_name":"statistical models","score":0.593999981880188},{"id":"https://openalex.org/keywords/high-throughput-screening","display_name":"high-throughput screening","score":0.6069999933242798},{"id":"https://openalex.org/keywords/vaccine-surveillance","display_name":"vaccine surveillance","score":0.5920000076293945}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.590399980545044},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5102999806404114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4975000023841858},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4943000078201294},{"id":"https://openalex.org/C2778692840","wikidata":"https://www.wikidata.org/wiki/Q9136673","display_name":"Hemagglutinin (influenza)","level":3,"score":0.48989999294281006},{"id":"https://openalex.org/C44210515","wikidata":"https://www.wikidata.org/wiki/Q16968978","display_name":"Bespoke","level":2,"score":0.48159998655319214},{"id":"https://openalex.org/C2777546802","wikidata":"https://www.wikidata.org/wiki/Q834390","display_name":"Influenza A virus","level":3,"score":0.4577000141143799},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3946000039577484},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.3935999870300293},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.3919000029563904},{"id":"https://openalex.org/C2780227090","wikidata":"https://www.wikidata.org/wiki/Q2636892","display_name":"Alanine scanning","level":5,"score":0.38929998874664307},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.38510000705718994},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3621000051498413},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.3506999909877777},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.3456999957561493},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.33820000290870667},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3334999978542328},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.31369999051094055},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.30970001220703125},{"id":"https://openalex.org/C9418097","wikidata":"https://www.wikidata.org/wiki/Q440681","display_name":"Directed evolution","level":4,"score":0.3068999946117401},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.29350000619888306},{"id":"https://openalex.org/C182072434","wikidata":"https://www.wikidata.org/wiki/Q3985103","display_name":"Hemagglutination assay","level":4,"score":0.28540000319480896},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.2709999978542328},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.2630000114440918},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26080000400543213},{"id":"https://openalex.org/C2910387474","wikidata":"https://www.wikidata.org/wiki/Q331710","display_name":"Genetic Fitness","level":3,"score":0.2563999891281128},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.2531999945640564}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.01.748481","doi":"https://doi.org/10.64898/2026.09.01.748481","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.01.748481","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.01.748481.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.01.748481","doi":"https://doi.org/10.64898/2026.09.01.748481","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.01.748481","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.01.748481.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.6240000128746033,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7208750871.pdf","grobid_xml":"https://content.openalex.org/works/W7208750871.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2060588922","https://openalex.org/W2203714058","https://openalex.org/W2622319469","https://openalex.org/W2920804790","https://openalex.org/W2940733686","https://openalex.org/W4319334382","https://openalex.org/W4387392387","https://openalex.org/W7153484046"],"related_works":["https://openalex.org/W2044594296","https://openalex.org/W2889138378","https://openalex.org/W2059276597","https://openalex.org/W4404294209","https://openalex.org/W2341501142","https://openalex.org/W2289690665","https://openalex.org/W2803249963","https://openalex.org/W2611946748","https://openalex.org/W7213398897","https://openalex.org/W1977522491"],"abstract_inverted_index":{"SUMMARY":[0],"Influenza":[1],"viruses":[2,40],"evade":[3],"vaccine":[4],"and":[5,41,46,112,120,153,162,197],"infection":[6],"mediated":[7],"immunity":[8],"by":[9],"accumulating":[10],"mutations":[11],"in":[12],"their":[13,43],"hemagglutinin":[14],"(HA)":[15],"protein.":[16],"Predicting":[17],"this":[18,54,82,204],"evolution":[19],"might":[20],"be":[21],"possible":[22],"via":[23],"selective":[24],"mutational":[25],"scanning":[26],"(SMS)":[27],"\u2013":[28],"the":[29,136,173,176,207],"generation":[30],"of":[31,35,65,87,114,140,200],"many":[32],"specific":[33],"mutants":[34],"interest":[36],"from":[37,187],"currently":[38],"circulating":[39],"characterizing":[42],"escape":[44],"potential":[45,208],"fitness":[47,111,164],"with":[48,184],"high":[49],"accuracy":[50],"(M\u00f6gling":[51],"2016).":[52],"However,":[53],"task":[55],"is":[56],"challenging,":[57],"even":[58],"when":[59],"focusing":[60],"on":[61,138],"a":[62,76,88,92,118,122,189],"reduced":[63],"set":[64],"key":[66],"HA":[67],"positions":[68],"(Koel":[69],"et":[70],"al.":[71],"2013).":[72],"Here":[73],"we":[74],"describe":[75],"high-throughput":[77],"SMS":[78],"method":[79,174],"to":[80,108,126,142,148,158,179,191,209],"address":[81],"challenge.":[83],"Our":[84],"approach":[85,205],"consists":[86],"three-stage":[89],"pipeline:":[90],"(1)":[91],"parallel":[93],"optimized":[94],"virus":[95,103,202],"rescue":[96],"process":[97],"that":[98],"generates":[99],"balanced":[100],"target":[101],"mutant":[102],"libraries":[104,139],"(2)":[105],"an":[106],"assay":[107],"assess":[109,159],"replicative":[110,163],"neutralisation":[113],"these":[115,132],"variants":[116,144],"as":[117,166,168],"mixture,":[119],"(3)":[121],"bespoke":[123],"statistical":[124],"model":[125],"quantify":[127],"statistically":[128],"significant":[129],"differences":[130],"between":[131],"observables.":[133],"We":[134],"tested":[135],"pipeline":[137],"up":[141],"134":[143],"finding":[145],"excellent":[146],"correlation":[147],"classical":[149,185],"hemagglutination":[150],"inhibition":[151],"(HI)":[152],"plaque":[154],"growth":[155],"assays":[156],"used":[157],"antigenic":[160],"phenotype":[161],"respectively,":[165],"well":[167],"remarkable":[169],"repeatability":[170],"overall.":[171],"Notably,":[172],"reduces":[175],"timeline":[177],"required":[178],"carry":[180],"out":[181],"such":[182],"assessments":[183],"methods":[186],"about":[188],"year":[190],"several":[192],"weeks.":[193],"By":[194],"enabling":[195],"rapid":[196],"efficient":[198],"characterization":[199],"influenza":[201],"variants,":[203],"has":[206],"greatly":[210],"enhance":[211],"surveillance":[212],"efforts,":[213],"transforming":[214],"reactive":[215],"monitoring":[216],"into":[217],"proactive":[218],"forecasting.":[219]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-05T00:00:00"}