Publication Information

{'id': 'https://openalex.org/W2133585817', 'doi': 'https://doi.org/10.1093/genetics/148.3.929', 'title': 'Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene', 'display_name': 'Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene', 'publication_year': 1998, 'publication_date': '1998-03-01', 'ids': {'openalex': 'https://openalex.org/W2133585817', 'doi': 'https://doi.org/10.1093/genetics/148.3.929', 'mag': '2133585817', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/9539414', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/1460041'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/genetics/148.3.929', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S65932378', 'display_name': 'Genetics', 'issn_l': '0016-6731', 'issn': ['0016-6731', '1943-2631'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'bronze', 'oa_url': 'https://doi.org/10.1093/genetics/148.3.929', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5088476239', 'display_name': 'Rasmus Nielsen', 'orcid': 'https://orcid.org/0000-0003-0513-6591'}, 'institutions': [{'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': ['US'], 'is_corresponding': False, 'raw_author_name': 'Rasmus Nielsen', 'raw_affiliation_strings': ['Department of Integrative Biology, University of California, Berkeley, California 94720-3140'], 'affiliations': [{'raw_affiliation_string': 'Department of Integrative Biology, University of California, Berkeley, California 94720-3140', 'institution_ids': ['https://openalex.org/I95457486']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5073515441', 'display_name': 'Ziheng Yang', 'orcid': 'https://orcid.org/0000-0003-3351-7981'}, 'institutions': [{'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']}, {'id': 'https://openalex.org/I45129253', 'display_name': 'University College London', 'ror': 'https://ror.org/02jx3x895', 'country_code': 'GB', 'type': 'education', 'lineage': ['https://openalex.org/I124357947', 'https://openalex.org/I45129253']}], 'countries': ['GB', 'US'], 'is_corresponding': False, 'raw_author_name': 'Ziheng Yang', 'raw_affiliation_strings': ['Department of Biology, University College London, London NW1 2HE, England', 'Department of Integrative Biology, University of California, Berkeley, California 94720-3140'], 'affiliations': [{'raw_affiliation_string': 'Department of Integrative Biology, University of California, Berkeley, California 94720-3140', 'institution_ids': ['https://openalex.org/I95457486']}, {'raw_affiliation_string': 'Department of Biology, University College London, London NW1 2HE, England', 'institution_ids': ['https://openalex.org/I45129253']}]}], 'institution_assertions': [], 'countries_distinct_count': 2, 'institutions_distinct_count': 2, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': {'value': 4264, 'currency': 'USD', 'value_usd': 4264, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 7.825, 'has_fulltext': False, 'cited_by_count': 1615, 'citation_normalized_percentile': {'value': 0.99997, 'is_in_top_1_percent': True, 'is_in_top_10_percent': True}, 'cited_by_percentile_year': {'min': 99, 'max': 100}, 'biblio': {'volume': '148', 'issue': '3', 'first_page': '929', 'last_page': '936'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10521', 'display_name': 'RNA and protein synthesis mechanisms', 'score': 0.9993, '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'}}, 'topics': [{'id': 'https://openalex.org/T10521', 'display_name': 'RNA and protein synthesis mechanisms', 'score': 0.9993, '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/T10015', 'display_name': 'Genomics and Phylogenetic Studies', 'score': 0.9987, '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': 0.9964, '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/nonsynonymous-substitution', 'display_name': 'Nonsynonymous substitution', 'score': 0.918089}, {'id': 'https://openalex.org/keywords/negative-selection', 'display_name': 'Negative selection', 'score': 0.590464}, {'id': 'https://openalex.org/keywords/positive-selection', 'display_name': 'Positive selection', 'score': 0.56447244}, {'id': 'https://openalex.org/keywords/neutral-mutation', 'display_name': 'Neutral mutation', 'score': 0.55237395}, {'id': 'https://openalex.org/keywords/synonymous-substitution', 'display_name': 'Synonymous substitution', 'score': 0.5434052}, {'id': 'https://openalex.org/keywords/coding-region', 'display_name': 'Coding region', 'score': 0.530585}, {'id': 'https://openalex.org/keywords/silent-mutation', 'display_name': 'Silent mutation', 'score': 0.41055617}], 'concepts': [{'id': 'https://openalex.org/C149904235', 'wikidata': 'https://www.wikidata.org/wiki/Q7049620', 'display_name': 'Nonsynonymous substitution', 'level': 4, 'score': 0.918089}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.7933645}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.6860509}, {'id': 'https://openalex.org/C81917197', 'wikidata': 'https://www.wikidata.org/wiki/Q628760', 'display_name': 'Selection (genetic algorithm)', 'level': 2, 'score': 0.5964777}, {'id': 'https://openalex.org/C7386963', 'wikidata': 'https://www.wikidata.org/wiki/Q3954859', 'display_name': 'Negative selection', 'level': 4, 'score': 0.590464}, {'id': 'https://openalex.org/C515207424', 'wikidata': 'https://www.wikidata.org/wiki/Q8066', 'display_name': 'Amino acid', 'level': 2, 'score': 0.57674193}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.57079303}, {'id': 'https://openalex.org/C2986302931', 'wikidata': 'https://www.wikidata.org/wiki/Q764759', 'display_name': 'Positive selection', 'level': 3, 'score': 0.56447244}, {'id': 'https://openalex.org/C149129301', 'wikidata': 'https://www.wikidata.org/wiki/Q3883802', 'display_name': 'Neutral mutation', 'level': 3, 'score': 0.55237395}, {'id': 'https://openalex.org/C138025448', 'wikidata': 'https://www.wikidata.org/wiki/Q7662597', 'display_name': 'Synonymous substitution', 'level': 5, 'score': 0.5434052}, {'id': 'https://openalex.org/C91779695', 'wikidata': 'https://www.wikidata.org/wiki/Q3780824', 'display_name': 'Coding region', 'level': 3, 'score': 0.530585}, {'id': 'https://openalex.org/C195491092', 'wikidata': 'https://www.wikidata.org/wiki/Q2717121', 'display_name': 'Silent mutation', 'level': 5, 'score': 0.41055617}, {'id': 'https://openalex.org/C87253356', 'wikidata': 'https://www.wikidata.org/wiki/Q1106472', 'display_name': 'Codon usage bias', 'level': 4, 'score': 0.36846298}, {'id': 'https://openalex.org/C501734568', 'wikidata': 'https://www.wikidata.org/wiki/Q42918', 'display_name': 'Mutation', 'level': 3, 'score': 0.3651301}, {'id': 'https://openalex.org/C78458016', 'wikidata': 'https://www.wikidata.org/wiki/Q840400', 'display_name': 'Evolutionary biology', 'level': 1, 'score': 0.3349694}, {'id': 'https://openalex.org/C141231307', 'wikidata': 'https://www.wikidata.org/wiki/Q7020', 'display_name': 'Genome', 'level': 3, 'score': 0.1141887}, {'id': 'https://openalex.org/C75563809', 'wikidata': 'https://www.wikidata.org/wiki/Q2656896', 'display_name': 'Missense mutation', 'level': 4, 'score': 0.089692205}, {'id': 'https://openalex.org/C154945302', 'wikidata': 'https://www.wikidata.org/wiki/Q11660', 'display_name': 'Artificial intelligence', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D019143', 'descriptor_name': 'Evolution, Molecular', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D015699', 'descriptor_name': 'HIV Envelope Protein gp120', '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': 'D008957', 'descriptor_name': 'Models, Genetic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D015233', 'descriptor_name': 'Models, Statistical', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D010446', 'descriptor_name': 'Peptide Fragments', 'qualifier_ui': 'Q000235', 'qualifier_name': 'genetics', 'is_major_topic': True}, {'descriptor_ui': 'D012641', 'descriptor_name': 'Selection, Genetic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000596', 'descriptor_name': 'Amino Acids', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D000596', 'descriptor_name': 'Amino Acids', 'qualifier_ui': 'Q000235', 'qualifier_name': 'genetics', 'is_major_topic': False}, {'descriptor_ui': 'D001665', 'descriptor_name': 'Binding Sites', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D003062', 'descriptor_name': 'Codon', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D003576', 'descriptor_name': 'Electron Transport Complex IV', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D003576', 'descriptor_name': 'Electron Transport Complex IV', 'qualifier_ui': 'Q000235', 'qualifier_name': 'genetics', 'is_major_topic': False}, {'descriptor_ui': 'D015699', 'descriptor_name': 'HIV Envelope Protein gp120', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D015497', 'descriptor_name': 'HIV-1', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D006801', 'descriptor_name': 'Humans', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016013', 'descriptor_name': 'Likelihood Functions', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016297', 'descriptor_name': 'Mutagenesis, Site-Directed', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D010446', 'descriptor_name': 'Peptide Fragments', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 3, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/genetics/148.3.929', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S65932378', 'display_name': 'Genetics', 'issn_l': '0016-6731', 'issn': ['0016-6731', '1943-2631'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1460041', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S2764455111', 'display_name': 'PubMed Central', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/9539414', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/genetics/148.3.929', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S65932378', 'display_name': 'Genetics', 'issn_l': '0016-6731', 'issn': ['0016-6731', '1943-2631'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [{'id': 'https://metadata.un.org/sdg/3', 'score': 0.77, 'display_name': 'Good health and well-being'}], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 24, 'referenced_works': ['https://openalex.org/W1576953632', 'https://openalex.org/W1827709268', 'https://openalex.org/W1844951369', 'https://openalex.org/W1907806866', 'https://openalex.org/W1920973730', 'https://openalex.org/W1957469265', 'https://openalex.org/W1993351732', 'https://openalex.org/W1997321423', 'https://openalex.org/W2007325254', 'https://openalex.org/W2017519756', 'https://openalex.org/W2029353325', 'https://openalex.org/W2042601802', 'https://openalex.org/W2050120307', 'https://openalex.org/W2056384440', 'https://openalex.org/W2063034269', 'https://openalex.org/W2081347192', 'https://openalex.org/W2093246625', 'https://openalex.org/W2104306559', 'https://openalex.org/W2104393767', 'https://openalex.org/W2124608480', 'https://openalex.org/W2124790653', 'https://openalex.org/W2141201180', 'https://openalex.org/W2150970405', 'https://openalex.org/W4240865251'], 'related_works': ['https://openalex.org/W4390258057', 'https://openalex.org/W3167015799', 'https://openalex.org/W2792500674', 'https://openalex.org/W2539510218', 'https://openalex.org/W2470001062', 'https://openalex.org/W2063135364', 'https://openalex.org/W1978561489', 'https://openalex.org/W1965233192', 'https://openalex.org/W1951333111', 'https://openalex.org/W1536760631'], 'abstract_inverted_index': {'Abstract': [0], 'Several': [1], 'codon-based': [2], 'models': [3, 77], 'for': [4, 15, 73, 108], 'the': [5, 85, 89, 98, 124, 128, 134, 143, 147], 'evolution': [6], 'of': [7, 29, 48, 84, 88, 100, 123, 130], 'protein-coding': [8], 'DNA': [9], 'sequences': [10], 'are': [11, 36, 78, 139], 'developed': [12], 'that': [13], 'account': [14], 'varying': [16], 'selection': [17, 110, 132], 'intensity': [18, 111], 'among': [19, 112], 'amino': [20, 33, 113], 'acid': [21, 34, 114], 'sites.': [22], 'The': [23, 41, 76, 103, 116], '“neutral': [24], 'model”': [25, 43], 'assumes': [26, 44], 'two': [27], 'categories': [28], 'sites': [30, 51, 72, 115, 138], 'at': [31, 52, 57, 94], 'which': [32, 53], 'replacements': [35], 'either': [37], 'neutral': [38, 117], 'or': [39], 'deleterious.': [40], '“positive-selection': [42], 'an': [45], 'additional': [46], 'category': [47], 'positively': [49], 'selected': [50, 137], 'nonsynonymous': [54], 'substitutions': [55], 'occur': [56], 'a': [58, 81], 'higher': [59], 'rate': [60], 'than': [61], 'synonymous': [62], 'ones.': [63], 'This': [64], 'model': [65, 118], 'is': [66, 119], 'also': [67], 'used': [68], 'to': [69, 80], 'identify': [70], 'target': [71], 'positive': [74, 131], 'selection.': [75], 'applied': [79], 'data': [82], 'set': [83], 'V3': [86, 144], 'region': [87, 145], 'HIV-1': [90], 'envelope': [91], 'gene,': [92], 'sequenced': [93], 'different': [95], 'years': [96], 'after': [97], 'infection': [99], 'one': [101], 'patient.': [102], 'results': [104], 'provide': [105], 'strong': [106], 'support': [107], 'variable': [109], 'rejected': [120], 'in': [121, 133, 141], 'favor': [122], 'positive-selection': [125], 'model,': [126], 'indicating': [127], 'operation': [129], 'region.': [135], 'Positively': [136], 'found': [140], 'both': [142], 'and': [146], 'flanking': [148], 'regions.': [149]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2133585817', 'counts_by_year': [{'year': 2024, 'cited_by_count': 26}, {'year': 2023, 'cited_by_count': 37}, {'year': 2022, 'cited_by_count': 35}, {'year': 2021, 'cited_by_count': 36}, {'year': 2020, 'cited_by_count': 42}, {'year': 2019, 'cited_by_count': 56}, {'year': 2018, 'cited_by_count': 54}, {'year': 2017, 'cited_by_count': 55}, {'year': 2016, 'cited_by_count': 57}, {'year': 2015, 'cited_by_count': 71}, {'year': 2014, 'cited_by_count': 95}, {'year': 2013, 'cited_by_count': 76}, {'year': 2012, 'cited_by_count': 91}], 'updated_date': '2024-12-12T11:57:49.065069', 'created_date': '2016-06-24'}