{"id":"https://openalex.org/W4409727217","doi":"https://doi.org/10.1101/2025.04.16.649189","title":"Automated Bacteriophage Evolution Studies with the Aionostat","display_name":"Automated Bacteriophage Evolution Studies with the Aionostat","publication_year":2025,"publication_date":"2025-04-21","ids":{"openalex":"https://openalex.org/W4409727217","doi":"https://doi.org/10.1101/2025.04.16.649189"},"language":"en","primary_location":{"id":"doi:10.1101/2025.04.16.649189","doi":"https://doi.org/10.1101/2025.04.16.649189","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649189","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/21/2025.04.16.649189.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","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/21/2025.04.16.649189.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020010179","display_name":"Valentin Druelle","orcid":"https://orcid.org/0000-0002-2554-4982","observed_orcids":["https://orcid.org/0000-0002-2554-4982"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Valentin Druelle","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2554-4982","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043346468","display_name":"Marco Molari","orcid":"https://orcid.org/0000-0001-8838-4093","observed_orcids":["https://orcid.org/0000-0001-8838-4093"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marco Molari","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-8838-4093","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117275295","display_name":"Giacomo Castagnetti","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["CH","IT"],"is_corresponding":false,"raw_author_name":"Giacomo Castagnetti","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","University of Bologna, Bologna, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"University of Bologna, Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059961308","display_name":"Alexander Harms","orcid":"https://orcid.org/0000-0003-2106-1286","observed_orcids":["https://orcid.org/0000-0003-2106-1286"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Alexander Harms","raw_affiliation_strings":["Dep. of Health Sciences and Technology - ETHZ, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2106-1286","affiliations":[{"raw_affiliation_string":"Dep. of Health Sciences and Technology - ETHZ, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037559147","display_name":"Richard A. Neher","orcid":"https://orcid.org/0000-0003-2525-1407","observed_orcids":["https://orcid.org/0000-0003-2525-1407"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Richard A. Neher","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2525-1407","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5037559147"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1850255"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9067000150680542,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9067000150680542,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.09269999712705612,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.0,"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/phage-evolution","display_name":"phage evolution","score":0.9589999914169312},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.9039999842643738},{"id":"https://openalex.org/keywords/phage-infectivity","display_name":"phage infectivity","score":0.7770000100135803},{"id":"https://openalex.org/keywords/phage-recombination","display_name":"phage recombination","score":0.8679999709129333},{"id":"https://openalex.org/keywords/phage-therapy","display_name":"phage therapy","score":0.8989999890327454}],"concepts":[{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.7852110862731934},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4308527708053589},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4078870117664337},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3922072649002075},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27180254459381104},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.09106948971748352},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06702268123626709}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2025.04.16.649189","doi":"https://doi.org/10.1101/2025.04.16.649189","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649189","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/21/2025.04.16.649189.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","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/785822","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/785822","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"info:eu-repo/semantics/workingPaper"},{"id":"doi:10.3929/ethz-c-000785822","doi":"https://doi.org/10.3929/ethz-c-000785822","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-c-000785822","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1101/2025.04.16.649189","doi":"https://doi.org/10.1101/2025.04.16.649189","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649189","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/21/2025.04.16.649189.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","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G8690818240","display_name":null,"funder_award_id":"310030","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8742969729","display_name":"Recombination and reassortement in viral evolution","funder_award_id":"188547","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320310466","display_name":"Universit\u00e4t Basel","ror":"https://ror.org/02s6k3f65"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409727217.pdf","grobid_xml":"https://content.openalex.org/works/W4409727217.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1519734172","https://openalex.org/W1916922087","https://openalex.org/W1972412013","https://openalex.org/W1976852236","https://openalex.org/W1988885405","https://openalex.org/W2012977051","https://openalex.org/W2072002842","https://openalex.org/W2076706379","https://openalex.org/W2099539515","https://openalex.org/W2123689779","https://openalex.org/W2233603983","https://openalex.org/W2597558540","https://openalex.org/W2735062779","https://openalex.org/W2756174590","https://openalex.org/W2769427798","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2790114318","https://openalex.org/W2795964999","https://openalex.org/W2922498192","https://openalex.org/W2943895022","https://openalex.org/W2945505394","https://openalex.org/W2988797876","https://openalex.org/W2999765413","https://openalex.org/W3003557640","https://openalex.org/W3011976166","https://openalex.org/W3035092496","https://openalex.org/W3165265585","https://openalex.org/W3165329360","https://openalex.org/W3181998104","https://openalex.org/W3192943233","https://openalex.org/W3210596119","https://openalex.org/W3211357821","https://openalex.org/W4200166960","https://openalex.org/W4403946928","https://openalex.org/W4409225935","https://openalex.org/W4414910709"],"related_works":["https://openalex.org/W7017965508","https://openalex.org/W4381549638","https://openalex.org/W3076463426","https://openalex.org/W2009786768","https://openalex.org/W2606964582","https://openalex.org/W3099819518","https://openalex.org/W4323321846","https://openalex.org/W6927363923","https://openalex.org/W7153333223","https://openalex.org/W2015789053"],"abstract_inverted_index":{"Abstract":[0],"Bacteriophages,":[1],"the":[2,8,105,123,150,154,174,185,191,203],"viruses":[3],"that":[4,169,213],"infect":[5],"bacteria,":[6],"are":[7,27],"most":[9],"abundant":[10],"and":[11,26,43,82,86,167,232],"diverse":[12],"biological":[13,238],"entities":[14],"on":[15,53,61,184],"our":[16,38,76],"planet.":[17],"They":[18],"play":[19],"a":[20,54,99,125,160,179],"critical":[21],"role":[22],"in":[23,33,236],"shaping":[24],"ecosystems":[25],"increasingly":[28],"recognized":[29],"for":[30,107,111,225],"their":[31,41,80,171],"potential":[32,142],"treating":[34],"bacterial":[35],"infections.":[36],"Yet,":[37],"comprehension":[39],"of":[40,69,101,114,181,193,210],"biology":[42],"evolutionary":[44,234],"dynamics":[45],"is":[46,143],"limited,":[47],"largely":[48],"because":[49],"research":[50],"has":[51],"concentrated":[52],"select":[55],"few":[56],"well-characterized":[57],"phages":[58,152,183,195],"or":[59],"relies":[60],"broad":[62],"metagenomic":[63],"studies":[64,89,209],"with":[65,196],"limited":[66],"follow-up":[67],"analysis":[68],"individual":[70],"phages.":[71],"This":[72],"knowledge":[73],"gap":[74],"hinders":[75],"capacity":[77],"to":[78,92,132,159,190,217],"exploit":[79],"therapeutic":[81],"ecological":[83],"possibilities":[84],"\u2013":[85],"while":[87],"some":[88],"have":[90],"attempted":[91],"bridge":[93],"it,":[94],"such":[95],"efforts":[96],"typically":[97],"require":[98],"lot":[100],"manual":[102],"labor,":[103],"highlighting":[104],"need":[106],"high-throughput,":[108],"reproducible":[109,208],"methods":[110],"in-depth":[112],"study":[113],"phage":[115,211,230],"evolution.":[116],"To":[117],"address":[118],"this":[119],"gap,":[120],"we":[121,177],"introduce":[122],"Aionostat,":[124],"novel":[126],"automated":[127],"continuous":[128],"culture":[129],"device":[130],"designed":[131],"facilitate":[133],"bacteriophage":[134],"directed":[135],"evolution":[136,212],"experiments":[137],"at":[138],"scale.":[139],"The":[140],"Aionostat\u2019s":[141],"showcased":[144],"through":[145],"two":[146],"example":[147],"experiments.":[148],"In":[149,173],"first,":[151],"from":[153],"BASEL":[155],"collection":[156],"rapidly":[157],"adapted":[158],"challenging":[161],"E.":[162],"coli":[163],"strain,":[164,188],"acquiring":[165],"mutations":[166],"deletions":[168],"improved":[170],"infectivity.":[172],"second":[175],"experiment,":[176],"evolved":[178],"mixture":[180],"these":[182,201],"same":[186],"E.coli":[187],"leading":[189],"emergence":[192],"recombinant":[194],"increased":[197],"fitness.":[198],"By":[199],"automating":[200],"experiments,":[202],"Aionostat":[204],"enables":[205],"faster,":[206],"more":[207],"would":[214],"be":[215],"impractical":[216],"perform":[218],"by":[219],"hand,":[220],"thereby":[221],"opening":[222],"new":[223],"avenues":[224],"investigating":[226],"viral":[227],"dynamics,":[228],"engineering":[229],"therapies,":[231],"studying":[233],"principles":[235],"broader":[237],"contexts.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2025-04-24T00:00:00"}
