{"id":"https://openalex.org/W1965850069","doi":"https://doi.org/10.1186/1471-2148-13-164","title":"Synonymous site conservation in the HIV-1 genome","display_name":"Synonymous site conservation in the HIV-1 genome","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W1965850069","doi":"https://doi.org/10.1186/1471-2148-13-164","mag":"1965850069","pmid":"https://pubmed.ncbi.nlm.nih.gov/23914950","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3750384"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2148-13-164","doi":"https://doi.org/10.1186/1471-2148-13-164","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-13-164","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-13-164","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-13-164","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024800697","display_name":"Itay Mayrose","orcid":"https://orcid.org/0000-0002-8460-1502","observed_orcids":["https://orcid.org/0000-0002-8460-1502"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Itay Mayrose","raw_affiliation_strings":["Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel-Aviv 69978, Israel. itaymay@post.tau.ac.il","Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel-Aviv 69978, Israel. itaymay@post.tau.ac.il","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067804324","display_name":"Adi Stern","orcid":"https://orcid.org/0000-0002-2919-3542","observed_orcids":["https://orcid.org/0000-0002-2919-3542"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Adi Stern","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Integrative Biology, University of California, Berkeley, USA","Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel","Department of Microbiology and Immunology, University of California, , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Integrative Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, University of California, , USA","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034605158","display_name":"Ela O Burdelova","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I2799807261","display_name":"Tel Aviv Sourasky Medical Center","ror":"https://ror.org/04nd58p63","country_code":"IL","type":"healthcare","lineage":["https://openalex.org/I2799807261"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ela O Burdelova","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel","Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Center for Digestive Tract and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192","https://openalex.org/I2799807261"]},{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062181862","display_name":"Yosef Sabo","orcid":"https://orcid.org/0000-0002-4973-8247","observed_orcids":["https://orcid.org/0000-0002-4973-8247"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Yosef Sabo","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, USA","Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068850149","display_name":"Nihay Laham-Karam","orcid":"https://orcid.org/0000-0001-8718-4612","observed_orcids":["https://orcid.org/0000-0001-8718-4612"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI","IL"],"is_corresponding":false,"raw_author_name":"Nihay Laham-Karam","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland","Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]},{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003060975","display_name":"Rachel Zamostiano","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Rachel Zamostiano","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089389573","display_name":"Eran Bacharach","orcid":"https://orcid.org/0000-0001-8341-2833","observed_orcids":["https://orcid.org/0000-0001-8341-2833"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Eran Bacharach","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070736617","display_name":"Tal Pupko","orcid":"https://orcid.org/0000-0001-9463-2575","observed_orcids":["https://orcid.org/0000-0001-9463-2575"]},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Tal Pupko","raw_affiliation_strings":["Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, 69978, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Cell Research and Immunology Tel-Aviv University Tel-Aviv  Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024800697","https://openalex.org/A5070736617","https://openalex.org/A5089389573"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.6449,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82671726,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"164","last_page":"164"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7261000275611877,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7261000275611877,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.20739999413490295,"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"}},{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.0502999983727932,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hiv-1","display_name":"HIV-1","score":0.9739999771118164},{"id":"https://openalex.org/keywords/synonymous-mutations","display_name":"synonymous mutations","score":0.8619999885559082},{"id":"https://openalex.org/keywords/purifying-selection","display_name":"purifying selection","score":0.8429999947547913},{"id":"https://openalex.org/keywords/viral-fitness","display_name":"viral fitness","score":0.5759999752044678},{"id":"https://openalex.org/keywords/viral-replication","display_name":"viral replication","score":0.7450000047683716},{"id":"https://openalex.org/keywords/rna-structure","display_name":"RNA structure","score":0.4569999873638153},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.8349999785423279},{"id":"https://openalex.org/keywords/overlapping-genes","display_name":"overlapping genes","score":0.6100000143051147},{"id":"https://openalex.org/keywords/randomization-procedures","display_name":"randomization procedures","score":0.3659999966621399}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7880278825759888},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7588104009628296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6613461971282959},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.5325730443000793},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5111177563667297},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4990253448486328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4702538251876831},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.453274130821228},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.43556341528892517},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4326511025428772},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.41661375761032104},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.3863930106163025},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.11798617243766785}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2148-13-164","doi":"https://doi.org/10.1186/1471-2148-13-164","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-13-164","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-13-164","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2741905","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3750384","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmid:23914950","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23914950","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC evolutionary biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3750384","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3750384/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evol Biol","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.796.3326","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.796.3326","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/1f/a1/1471-2148-13-164.PMC3750384.pdf","raw_type":"text"},{"id":"doi:10.7916/d84748cf","doi":"https://doi.org/10.7916/d84748cf","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d84748cf","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"mag:2344328861","doi":null,"is_oa":false,"landing_page_url":"https://link.springer.com/content/pdf/10.1186%2F1471-2148-13-164.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1471-2148-13-164","doi":"https://doi.org/10.1186/1471-2148-13-164","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2148-13-164","pdf_url":"https://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-13-164","source":{"id":"https://openalex.org/S64097828","display_name":"BMC Evolutionary Biology","issn_l":"1471-2148","issn":["1471-2148"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","ki-jl-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Evolutionary Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1965850069.pdf","grobid_xml":"https://content.openalex.org/works/W1965850069.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W132262220","https://openalex.org/W1503889771","https://openalex.org/W1582822899","https://openalex.org/W1584076968","https://openalex.org/W1593586570","https://openalex.org/W1983297759","https://openalex.org/W1992465872","https://openalex.org/W2009736453","https://openalex.org/W2010458160","https://openalex.org/W2013235753","https://openalex.org/W2014970708","https://openalex.org/W2015625581","https://openalex.org/W2018590530","https://openalex.org/W2032136448","https://openalex.org/W2045391589","https://openalex.org/W2049595315","https://openalex.org/W2051242197","https://openalex.org/W2058864686","https://openalex.org/W2060969855","https://openalex.org/W2063779182","https://openalex.org/W2069511429","https://openalex.org/W2076793571","https://openalex.org/W2086631924","https://openalex.org/W2087127695","https://openalex.org/W2087375630","https://openalex.org/W2089558440","https://openalex.org/W2092437950","https://openalex.org/W2097204162","https://openalex.org/W2098785512","https://openalex.org/W2102698854","https://openalex.org/W2103546861","https://openalex.org/W2105294364","https://openalex.org/W2118879505","https://openalex.org/W2122273986","https://openalex.org/W2123200842","https://openalex.org/W2126675814","https://openalex.org/W2128494634","https://openalex.org/W2131974188","https://openalex.org/W2132926880","https://openalex.org/W2136933345","https://openalex.org/W2142753618","https://openalex.org/W2145992798","https://openalex.org/W2147292596","https://openalex.org/W2151102421","https://openalex.org/W2160364329","https://openalex.org/W2160718838","https://openalex.org/W2164618276","https://openalex.org/W2169316289","https://openalex.org/W2171305498","https://openalex.org/W2505211040","https://openalex.org/W2575306271","https://openalex.org/W3141316455"],"related_works":["https://openalex.org/W2344328861","https://openalex.org/W7099488997","https://openalex.org/W2136933345","https://openalex.org/W2096794279","https://openalex.org/W1874771495","https://openalex.org/W7096413608","https://openalex.org/W2976090860","https://openalex.org/W7009837511","https://openalex.org/W2126675814","https://openalex.org/W2559949255"],"abstract_inverted_index":{"BACKGROUND:":[0],"Synonymous":[1],"or":[2,24],"silent":[3,18],"mutations":[4,19,313],"are":[5,44,185,217,237],"usually":[6],"thought":[7],"to":[8,57,98,116,143,191,219,265],"evolve":[9],"neutrally.":[10],"However,":[11],"accumulating":[12],"recent":[13],"evidence":[14],"has":[15],"demonstrated":[16],"that":[17,43,125,168,248,323],"may":[20,55,317],"destabilize":[21],"RNA":[22],"structures":[23],"disrupt":[25],"cis":[26],"regulatory":[27],"motifs":[28],"superimposed":[29],"on":[30,70,103,114,163,314],"coding":[31,63],"sequences.":[32],"Such":[33,53,335],"observations":[34],"suggest":[35],"the":[36,71,87,107,112,156,194,204,231,234,246,276,284,287,292,301,307,321,324,342,357],"existence":[37],"of":[38,40,95,106,127,199,215,233,275,294,309,311,344],"stretches":[39,54,126],"codon":[41],"sites":[42,176,202],"evolutionary":[45,166],"conserved":[46,200,212],"at":[47,86],"both":[48,270],"DNA-RNA":[49],"and":[50,80,90,109,145,177,258,272,286,306,354],"protein":[51,62],"levels.":[52,92],"point":[56],"functionally":[58],"important":[59],"regions":[60,147,198,220],"within":[61,133,221],"sequences":[64],"not":[65,339],"necessarily":[66],"reflecting":[67],"functional":[68,84,228],"constraints":[69,113],"amino-acid":[72],"sequence.":[73],"The":[74,298],"HIV-1":[75,115,157,345],"genome":[76,108],"is":[77,161],"highly":[78,120],"compact,":[79],"often":[81],"harbors":[82],"overlapping":[83,222],"elements":[85],"protein,":[88],"RNA,":[89],"DNA":[91],"This":[93],"superimposition":[94],"functions":[96,232],"leads":[97],"complex":[99],"selective":[100,304],"forces":[101,305],"acting":[102],"all":[104],"levels":[105],"proteome.":[110],"Considering":[111],"maintain":[117],"such":[118],"a":[119,139,188,336],"compact":[121],"genome,":[122],"we":[123,209,244],"hypothesized":[124],"synonymous":[128,153,172,201,252,295],"conservation":[129],"would":[130],"be":[131,318],"common":[132],"its":[134],"genome.":[135,158,205],"RESULTS:":[136],"We":[137],"used":[138],"combined":[140,186],"computational-experimental":[141],"approach":[142],"detect":[144],"characterize":[146],"exhibiting":[148],"strong":[149],"purifying":[150,303],"selection":[151],"against":[152],"substitutions":[154],"along":[155,203],"Our":[159],"methodology":[160],"based":[162],"advanced":[164],"probabilistic":[165],"models":[167,184],"explicitly":[169],"account":[170,340],"for":[171,255,341],"rate":[173,178,253],"variation":[174],"among":[175,180],"dependencies":[179],"adjacent":[181],"sites.":[182],"These":[183],"with":[187,226,356],"randomization":[189],"procedure":[190,208],"automatically":[192],"identify":[193],"most":[195,250],"statistically":[196],"significant":[197],"Using":[206],"this":[207],"identified":[210],"21":[211],"regions.":[213],"Twelve":[214],"these":[216,241,312],"mapped":[218],"genes,":[223],"seven":[224],"correlate":[225],"known":[227],"elements,":[229],"while":[230],"remaining":[235],"four":[236,242],"yet":[238],"unknown.":[239],"Among":[240],"regions,":[243],"chose":[245],"one":[247],"deviates":[249],"from":[251],"homogeneity":[254],"in-depth":[256],"computational":[257],"experimental":[259],"characterization.":[260],"In":[261],"our":[262],"assays":[263,331],"aiming":[264],"quantify":[266],"viral":[267,315],"fitness":[268],"in":[269,328,332,347],"early":[271],"late":[273],"stages":[274],"replication":[277,316],"cycle,":[278],"no":[279],"differences":[280],"were":[281],"observed":[282],"between":[283,300],"mutated":[285],"wild":[288],"type":[289],"virus":[290],"following":[291],"introduction":[293],"mutations.":[296],"CONCLUSIONS:":[297],"contradiction":[299],"inferred":[302],"lack":[308],"effect":[310],"explained":[319],"by":[320],"fact":[322],"phenotype":[325],"was":[326],"measured":[327],"single-cycle":[329],"infection":[330,352],"cell":[333],"culture.":[334],"system":[337],"does":[338],"complexity":[343],"infections":[346],"vivo,":[348],"which":[349],"involves":[350],"multiple":[351],"cycles":[353],"interaction":[355],"host":[358],"immune":[359],"system.":[360]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}