{"id":"https://openalex.org/W6930995537","doi":"https://doi.org/10.5281/zenodo.5090169","title":"Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence","display_name":"Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence","publication_year":2021,"publication_date":"2021-07-11","ids":{"openalex":"https://openalex.org/W6930995537","doi":"https://doi.org/10.5281/zenodo.5090169"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:5090169","is_oa":true,"landing_page_url":"https://zenodo.org/record/5090169","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"software"},"type":"software","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/5090169","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Bernasconi, Anna","orcid":"https://orcid.org/0000-0001-8016-5750"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Bernasconi, Anna","raw_affiliation_strings":["Department of Electronics, Information and Bioengineering - Politecnico di Milano"],"raw_orcid":"https://orcid.org/0000-0001-8016-5750","affiliations":[{"raw_affiliation_string":"Department of Electronics, Information and Bioengineering - Politecnico di Milano","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mari, Lorenzo","orcid":"https://orcid.org/0000-0003-1326-9992"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mari, Lorenzo","raw_affiliation_strings":["Department of Electronics, Information and Bioengineering - Politecnico di Milano"],"raw_orcid":"https://orcid.org/0000-0003-1326-9992","affiliations":[{"raw_affiliation_string":"Department of Electronics, Information and Bioengineering - Politecnico di Milano","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Casagrandi, Renato","orcid":"https://orcid.org/0000-0001-5177-803X"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Casagrandi, Renato","raw_affiliation_strings":["Department of Electronics, Information and Bioengineering - Politecnico di Milano"],"raw_orcid":"https://orcid.org/0000-0001-5177-803X","affiliations":[{"raw_affiliation_string":"Department of Electronics, Information and Bioengineering - Politecnico di Milano","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":null,"display_name":"Ceri, Stefano","orcid":"https://orcid.org/0000-0003-0671-2415"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ceri, Stefano","raw_affiliation_strings":["Department of Electronics, Information and Bioengineering - Politecnico di Milano"],"raw_orcid":"https://orcid.org/0000-0003-0671-2415","affiliations":[{"raw_affiliation_string":"Department of Electronics, Information and Bioengineering - Politecnico di Milano","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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":true,"primary_topic":{"id":"https://openalex.org/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.09870000183582306,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10195","display_name":"Antimicrobial Resistance in Staphylococcus","score":0.09870000183582306,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10200","display_name":"Rheumatoid Arthritis Research and Therapies","score":0.07440000027418137,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"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/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.06430000066757202,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.6791999936103821},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5271999835968018},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.38760000467300415},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.3662000000476837},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.3255000114440918},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.2969000041484833},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.2935999929904938},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.2831999957561493}],"concepts":[{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.6791999936103821},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5271999835968018},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.38760000467300415},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3741999864578247},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.3662000000476837},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33230000734329224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33149999380111694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3255999982357025},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.3255000114440918},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30489999055862427},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2976999878883362},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.2969000041484833},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.2935999929904938},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.2831999957561493},{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.26489999890327454},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2621999979019165},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.25189998745918274},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.24490000307559967},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.24130000174045563},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23029999434947968},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.22450000047683716},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2224999964237213},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.22059999406337738},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.21819999814033508},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.21780000627040863},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21240000426769257},{"id":"https://openalex.org/C2993070364","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Amino acid analysis","level":3,"score":0.2110999971628189},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.1981000006198883},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.19280000030994415},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.19020000100135803},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.18790000677108765},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.1843000054359436},{"id":"https://openalex.org/C49555168","wikidata":"https://www.wikidata.org/wiki/Q176583","display_name":"Stochastic matrix","level":3,"score":0.18140000104904175},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.18000000715255737},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.17949999868869781},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.17870000004768372},{"id":"https://openalex.org/C2988562018","wikidata":"https://www.wikidata.org/wiki/Q1063","display_name":"Biological evolution","level":2,"score":0.17790000140666962},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1770000010728836},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.17630000412464142},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.17000000178813934}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:5090169","is_oa":true,"landing_page_url":"https://zenodo.org/record/5090169","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"software"},{"id":"doi:10.5281/zenodo.5090169","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.5090169","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:5090169","is_oa":true,"landing_page_url":"https://zenodo.org/record/5090169","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"software"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1050025816","display_name":"Data-Driven Genomic Computing","funder_award_id":"693174","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Data":[0],"and":[1,31],"code":[2],"for":[3,23,72],"paper":[4,79],"\"<strong>Analysis":[5],"of":[6,25,38,47,57,77],"amino":[7,39,50],"acid":[8,40,51],"change":[9,52],"dynamics":[10],"reveals":[11],"SARS-CoV-2":[12],"variant":[13],"emergence</strong>\",":[14],"now":[15],"under":[16],"revision.":[17],"The":[18],"repository":[19],"contains:":[20],"two":[21],"files":[22],"each":[24,62],"44":[26],"locations":[27],"(including":[28],"19":[29],"countries":[30],"25":[32],"US":[33],"states)":[34],"CoV_&lt;location&gt;_mut5_obs3_absolute.csv":[35],"(a":[36,55],"matrix":[37],"changes":[41],"[rows],":[42],"collection":[43],"weeks":[44],"[columns],":[45],"counts":[46],"sequences":[48,60],"with":[49],"[cells])":[53],"CoV_&lt;location&gt;_mut5_obs3_totals.csv":[54],"vector":[56],"total":[58],"collected":[59],"per":[61],"week":[63],"[columns])":[64],"one":[65,69],"lineage":[66],"dictionary":[67],"(lins_changes75_2_5000_1000.csv)":[68],"MATLAB":[70],"script":[71],"reproducing":[73],"all":[74],"the":[75,78],"results":[76],"(variants_clustering.m)":[80]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}