Publication Information

{'id': 'https://openalex.org/W2896281462', 'doi': 'https://doi.org/10.1093/bioinformatics/bty846', 'title': 'A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection', 'display_name': 'A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection', 'publication_year': 2018, 'publication_date': '2018-10-04', 'ids': {'openalex': 'https://openalex.org/W2896281462', 'doi': 'https://doi.org/10.1093/bioinformatics/bty846', 'mag': '2896281462', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/30295749'}, 'language': 'en', 'primary_location': {'is_oa': False, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/bty846', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, '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': None, 'is_accepted': False, 'is_published': False}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': False, 'oa_status': 'closed', 'oa_url': None, 'any_repository_has_fulltext': False}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5078826382', 'display_name': 'Neli Fonseca', 'orcid': 'https://orcid.org/0000-0001-6466-8083'}, 'institutions': [{'id': 'https://openalex.org/I110200422', 'display_name': 'Universidade Federal de Minas Gerais', 'ror': 'https://ror.org/0176yjw32', 'country_code': 'BR', 'type': 'education', 'lineage': ['https://openalex.org/I110200422']}], 'countries': ['BR'], 'is_corresponding': False, 'raw_author_name': 'Néli José da Fonseca', 'raw_affiliation_strings': ['Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil'], 'affiliations': [{'raw_affiliation_string': 'Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil', 'institution_ids': ['https://openalex.org/I110200422']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5057489258', 'display_name': 'Marcelo Querino Lima Afonso', 'orcid': 'https://orcid.org/0000-0002-9966-8187'}, 'institutions': [{'id': 'https://openalex.org/I110200422', 'display_name': 'Universidade Federal de Minas Gerais', 'ror': 'https://ror.org/0176yjw32', 'country_code': 'BR', 'type': 'education', 'lineage': ['https://openalex.org/I110200422']}], 'countries': ['BR'], 'is_corresponding': False, 'raw_author_name': 'Marcelo Querino Lima Afonso', 'raw_affiliation_strings': ['Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil'], 'affiliations': [{'raw_affiliation_string': 'Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil', 'institution_ids': ['https://openalex.org/I110200422']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5053480014', 'display_name': 'Lucas Carrijo de Oliveira', 'orcid': 'https://orcid.org/0000-0003-1855-0871'}, 'institutions': [{'id': 'https://openalex.org/I110200422', 'display_name': 'Universidade Federal de Minas Gerais', 'ror': 'https://ror.org/0176yjw32', 'country_code': 'BR', 'type': 'education', 'lineage': ['https://openalex.org/I110200422']}], 'countries': ['BR'], 'is_corresponding': False, 'raw_author_name': 'Lucas Carrijo de Oliveira', 'raw_affiliation_strings': ['Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil'], 'affiliations': [{'raw_affiliation_string': 'Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil', 'institution_ids': ['https://openalex.org/I110200422']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5006296542', 'display_name': 'Lucas Bleicher', 'orcid': 'https://orcid.org/0000-0001-7121-4952'}, 'institutions': [{'id': 'https://openalex.org/I110200422', 'display_name': 'Universidade Federal de Minas Gerais', 'ror': 'https://ror.org/0176yjw32', 'country_code': 'BR', 'type': 'education', 'lineage': ['https://openalex.org/I110200422']}], 'countries': ['BR'], 'is_corresponding': True, 'raw_author_name': 'Lucas Bleicher', 'raw_affiliation_strings': ['Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil'], 'affiliations': [{'raw_affiliation_string': 'Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil', 'institution_ids': ['https://openalex.org/I110200422']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5006296542'], 'corresponding_institution_ids': ['https://openalex.org/I110200422'], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 0.35, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 5, 'citation_normalized_percentile': {'value': 0.514283, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 79, 'max': 80}, 'biblio': {'volume': '35', 'issue': '9', 'first_page': '1478', 'last_page': '1485'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10887', 'display_name': 'Bioinformatics and Genomic Networks', 'score': 0.9903, '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/T10887', 'display_name': 'Bioinformatics and Genomic Networks', 'score': 0.9903, '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': 0.9845, '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/T12254', 'display_name': 'Machine Learning in Bioinformatics', 'score': 0.9528, '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/protein-superfamily', 'display_name': 'Protein superfamily', 'score': 0.6106884}, {'id': 'https://openalex.org/keywords/multiple-sequence-alignment', 'display_name': 'Multiple sequence alignment', 'score': 0.5036928}], 'concepts': [{'id': 'https://openalex.org/C75553542', 'wikidata': 'https://www.wikidata.org/wiki/Q178161', 'display_name': 'A priori and a posteriori', 'level': 2, 'score': 0.6479962}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.63298166}, {'id': 'https://openalex.org/C178180057', 'wikidata': 'https://www.wikidata.org/wiki/Q7251477', 'display_name': 'Protein superfamily', 'level': 3, 'score': 0.6106884}, {'id': 'https://openalex.org/C174348530', 'wikidata': 'https://www.wikidata.org/wiki/Q188635', 'display_name': 'Bridging (networking)', 'level': 2, 'score': 0.56802857}, {'id': 'https://openalex.org/C2777904410', 'wikidata': 'https://www.wikidata.org/wiki/Q7397', 'display_name': 'Software', 'level': 2, 'score': 0.56315905}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.5388581}, {'id': 'https://openalex.org/C88031987', 'wikidata': 'https://www.wikidata.org/wiki/Q1377767', 'display_name': 'Multiple sequence alignment', 'level': 5, 'score': 0.5036928}, {'id': 'https://openalex.org/C132525143', 'wikidata': 'https://www.wikidata.org/wiki/Q141488', 'display_name': 'Graph', 'level': 2, 'score': 0.47558057}, {'id': 'https://openalex.org/C45484198', 'wikidata': 'https://www.wikidata.org/wiki/Q827246', 'display_name': 'Sequence alignment', 'level': 4, 'score': 0.4479001}, {'id': 'https://openalex.org/C124101348', 'wikidata': 'https://www.wikidata.org/wiki/Q172491', 'display_name': 'Data mining', 'level': 1, 'score': 0.44553542}, {'id': 'https://openalex.org/C88230418', 'wikidata': 'https://www.wikidata.org/wiki/Q131476', 'display_name': 'Graph theory', 'level': 2, 'score': 0.41347045}, {'id': 'https://openalex.org/C80444323', 'wikidata': 'https://www.wikidata.org/wiki/Q2878974', 'display_name': 'Theoretical computer science', 'level': 1, 'score': 0.38254797}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.31015056}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.19551292}, {'id': 'https://openalex.org/C33923547', 'wikidata': 'https://www.wikidata.org/wiki/Q395', 'display_name': 'Mathematics', 'level': 0, 'score': 0.1889025}, {'id': 'https://openalex.org/C167625842', 'wikidata': 'https://www.wikidata.org/wiki/Q899763', 'display_name': 'Peptide sequence', 'level': 3, 'score': 0.16616312}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.16303599}, {'id': 'https://openalex.org/C114614502', 'wikidata': 'https://www.wikidata.org/wiki/Q76592', 'display_name': 'Combinatorics', 'level': 1, 'score': 0.1071313}, {'id': 'https://openalex.org/C31258907', 'wikidata': 'https://www.wikidata.org/wiki/Q1301371', 'display_name': 'Computer network', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C138885662', 'wikidata': 'https://www.wikidata.org/wiki/Q5891', 'display_name': 'Philosophy', 'level': 0, 'score': 0.0}, {'id': 'https://openalex.org/C111472728', 'wikidata': 'https://www.wikidata.org/wiki/Q9471', 'display_name': 'Epistemology', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C199360897', 'wikidata': 'https://www.wikidata.org/wiki/Q9143', 'display_name': 'Programming language', 'level': 1, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D000465', 'descriptor_name': 'Algorithms', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D012984', 'descriptor_name': 'Software', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D011506', 'descriptor_name': 'Proteins', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 2, 'locations': [{'is_oa': False, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/bty846', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S52395412', 'display_name': 'Bioinformatics', 'issn_l': '1367-4803', 'issn': ['1367-4803', '1367-4811'], 'is_oa': True, 'is_in_doaj': True, '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': None, 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/30295749', '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': None, 'sustainable_development_goals': [], 'grants': [{'funder': 'https://openalex.org/F4320321091', 'funder_display_name': 'Coordenação de Aperfeiçoamento de Pessoal de Nível Superior', 'award_id': '051-2013'}, {'funder': 'https://openalex.org/F4320322025', 'funder_display_name': 'Conselho Nacional de Desenvolvimento Científico e Tecnológico', 'award_id': '457851/2014-7'}, {'funder': 'https://openalex.org/F4320322980', 'funder_display_name': 'Fundação de Amparo à Pesquisa do Estado de Minas Gerais', 'award_id': None}], 'datasets': [], 'versions': [], 'referenced_works_count': 75, 'referenced_works': ['https://openalex.org/W1530641120', 'https://openalex.org/W1534406401', 'https://openalex.org/W1546022138', 'https://openalex.org/W1546341583', 'https://openalex.org/W1551152196', 'https://openalex.org/W155239904', 'https://openalex.org/W1566807187', 'https://openalex.org/W1599904921', 'https://openalex.org/W1691583558', 'https://openalex.org/W1836431516', 'https://openalex.org/W1897051525', 'https://openalex.org/W1914294109', 'https://openalex.org/W1965469766', 'https://openalex.org/W1965582988', 'https://openalex.org/W1968217253', 'https://openalex.org/W1970913835', 'https://openalex.org/W1971174646', 'https://openalex.org/W1971421925', 'https://openalex.org/W1975670646', 'https://openalex.org/W1981956283', 'https://openalex.org/W1991209494', 'https://openalex.org/W1993039539', 'https://openalex.org/W2020106188', 'https://openalex.org/W2023000972', 'https://openalex.org/W2026833480', 'https://openalex.org/W2031194966', 'https://openalex.org/W2033339460', 'https://openalex.org/W2038793346', 'https://openalex.org/W2043040588', 'https://openalex.org/W2044728500', 'https://openalex.org/W2049631297', 'https://openalex.org/W2051185826', 'https://openalex.org/W2052816778', 'https://openalex.org/W2062533676', 'https://openalex.org/W2067584879', 'https://openalex.org/W2082396928', 'https://openalex.org/W2085099772', 'https://openalex.org/W2087459024', 'https://openalex.org/W2089335658', 'https://openalex.org/W2092006899', 'https://openalex.org/W2092735663', 'https://openalex.org/W2094967199', 'https://openalex.org/W2097278341', 'https://openalex.org/W2097892623', 'https://openalex.org/W2100009368', 'https://openalex.org/W2102904949', 'https://openalex.org/W2110042475', 'https://openalex.org/W2111010158', 'https://openalex.org/W2112090702', 'https://openalex.org/W2115398984', 'https://openalex.org/W2123402141', 'https://openalex.org/W2128732528', 'https://openalex.org/W2134874967', 'https://openalex.org/W2139468798', 'https://openalex.org/W2140563512', 'https://openalex.org/W2157861841', 'https://openalex.org/W2159056360', 'https://openalex.org/W2164831247', 'https://openalex.org/W2167321512', 'https://openalex.org/W2185024408', 'https://openalex.org/W2194756172', 'https://openalex.org/W2224056471', 'https://openalex.org/W2225104588', 'https://openalex.org/W2346012195', 'https://openalex.org/W2512714520', 'https://openalex.org/W2592074636', 'https://openalex.org/W2611184689', 'https://openalex.org/W2726188591', 'https://openalex.org/W2745805188', 'https://openalex.org/W2949122710', 'https://openalex.org/W3024374631', 'https://openalex.org/W3101409477', 'https://openalex.org/W3126033509', 'https://openalex.org/W4237342718', 'https://openalex.org/W78253720'], 'related_works': ['https://openalex.org/W4200486190', 'https://openalex.org/W2574250337', 'https://openalex.org/W2275032899', 'https://openalex.org/W2155320525', 'https://openalex.org/W2029358573', 'https://openalex.org/W2028741573', 'https://openalex.org/W2015399150', 'https://openalex.org/W2009133913', 'https://openalex.org/W1992358035', 'https://openalex.org/W1983792126'], 'abstract_inverted_index': {'Computational': [0], 'studies': [1], 'of': [2, 12, 38, 46, 111, 140, 180], 'molecular': [3], 'evolution': [4], 'are': [5, 23, 29, 66, 80, 94, 183, 188], 'usually': [6], 'performed': [7], 'from': [8, 19, 43, 104], 'a': [9, 20, 39, 44, 108], 'multiple': [10], 'alignment': [11, 41], 'homologous': [13], 'sequences,': [14], 'on': [15, 68, 185], 'which': [16, 162], 'sequences': [17, 48], 'resulting': [18], 'common': [21], 'ancestor': [22], 'aligned': [24], 'so': [25], 'that': [26, 79], 'equivalent': [27], 'residues': [28, 78], 'placed': [30], 'in': [31, 83, 88, 131, 149, 161, 177], 'the': [32, 75, 112, 121, 132, 178], 'same': [33], 'position.': [34], 'Residues': [35], 'frequency': [36], 'patterns': [37], 'full': [40], 'or': [42, 62, 106], 'subset': [45], 'its': [47], 'can': [49], 'be': [50, 115], 'highly': [51], 'useful': [52], 'for': [53, 77, 96], 'suggesting': [54], 'positions': [55], 'under': [56], 'selection.': [57], 'Most': [58], 'methods': [59, 93], 'mapping': [60], 'co-evolving': [61], 'specificity': [63, 81, 164], 'determinant': [64, 165], 'sites': [65], 'focused': [67], 'positions,': [69], 'however,': [70], 'they': [71], 'do': [72], 'not': [73], 'consider': [74], 'case': [76], 'determinants': [82], 'one': [84], 'subclass,': [85], 'but': [86], 'variable': [87], 'others.': [89], 'In': [90], 'addition,': [91], 'many': [92], 'impractical': [95], 'very': [97], 'large': [98], 'alignments,': [99], 'such': [100], 'as': [101], 'those': [102], 'obtained': [103], 'Pfam,': [105], 'require': [107], 'priori': [109], 'information': [110], 'subclasses': [113], 'to': [114, 127, 137, 155], 'analyzed.In': [116], 'this': [117, 181], 'paper': [118], 'we': [119], 'apply': [120], 'complex': [122], 'networks': [123], 'theory,': [124], 'widely': [125], 'used': [126, 176], 'analyze': [128], 'co-affiliation': [129], 'systems': [130], 'social': [133], 'and': [134, 152, 167, 174], 'ecological': [135], 'contexts,': [136], 'map': [138], 'groups': [139], 'functional': [141, 168], 'related': [142], 'residues.': [143], 'This': [144], 'methodology': [145], 'was': [146], 'initially': [147], 'evaluated': [148], 'simulated': [150], 'environments': [151], 'then': [153], 'applied': [154], 'four': [156], 'different': [157], 'protein': [158], 'families': [159], 'datasets,': [160], 'several': [163], 'sets': [166], 'motifs': [169], 'were': [170], 'successfully': [171], 'detected.The': [172], 'algorithms': [173], 'datasets': [175], 'development': [179], 'project': [182], 'available': [184, 189], 'http://www.biocomp.icb.ufmg.br/biocomp/software-and-databases/networkstats/.Supplementary': [186], 'data': [187], 'at': [190], 'Bioinformatics': [191], 'online.': [192]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2896281462', 'counts_by_year': [{'year': 2022, 'cited_by_count': 1}, {'year': 2021, 'cited_by_count': 2}, {'year': 2020, 'cited_by_count': 2}], 'updated_date': '2025-01-08T20:07:09.401288', 'created_date': '2018-10-26'}