Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2167455933', 'doi': 'https://doi.org/10.1101/gr.8.3.163', 'title': 'Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis', 'display_name': 'Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis', 'publication_year': 1998, 'publication_date': '1998-03-01', 'ids': {'openalex': 'https://openalex.org/W2167455933', 'doi': 'https://doi.org/10.1101/gr.8.3.163', 'mag': '2167455933', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/9521918'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1101/gr.8.3.163', 'pdf_url': 'https://genome.cshlp.org/content/8/3/163.full.pdf', 'source': {'id': 'https://openalex.org/S43092948', 'display_name': 'Genome Research', 'issn_l': '1088-9051', 'issn': ['1088-9051', '1549-5469'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315909', 'host_organization_name': 'Cold Spring Harbor Laboratory Press', 'host_organization_lineage': ['https://openalex.org/P4310315909'], 'host_organization_lineage_names': ['Cold Spring Harbor Laboratory Press'], 'type': 'journal'}, 'license': 'cc-by-nc', 'license_id': 'https://openalex.org/licenses/cc-by-nc', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'review', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'hybrid', 'oa_url': 'https://genome.cshlp.org/content/8/3/163.full.pdf', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5059066311', 'display_name': 'Jonathan A. Eisen', 'orcid': 'https://orcid.org/0000-0002-0159-2197'}, 'institutions': [{'id': 'https://openalex.org/I97018004', 'display_name': 'Stanford University', 'ror': 'https://ror.org/00f54p054', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I97018004']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Jonathan A. Eisen', 'raw_affiliation_strings': ['Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 USA'], 'affiliations': [{'raw_affiliation_string': 'Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 USA', 'institution_ids': ['https://openalex.org/I97018004']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5059066311'], 'corresponding_institution_ids': ['https://openalex.org/I97018004'], 'apc_list': None, 'apc_paid': None, 'fwci': 2.043, 'has_fulltext': True, 'fulltext_origin': 'pdf', 'cited_by_count': 632, 'citation_normalized_percentile': {'value': 0.999454, 'is_in_top_1_percent': True, 'is_in_top_10_percent': True}, 'cited_by_percentile_year': {'min': 99, 'max': 100}, 'biblio': {'volume': '8', 'issue': '3', 'first_page': '163', 'last_page': '167'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10015', 'display_name': 'Genomics and Phylogenetic Studies', 'score': 0.9991, '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/T10015', 'display_name': 'Genomics and Phylogenetic Studies', 'score': 0.9991, '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/T10887', 'display_name': 'Bioinformatics and Genomic Networks', 'score': 0.9929, '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/T10012', 'display_name': 'Genetic diversity and population structure', 'score': 0.9893, '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'}}], 'keywords': [{'id': 'https://openalex.org/keywords/sequence', 'display_name': 'Sequence (biology)', 'score': 0.6427194}, {'id': 'https://openalex.org/keywords/similarity', 'display_name': 'Similarity (geometry)', 'score': 0.6334125}, {'id': 'https://openalex.org/keywords/identification', 'display_name': 'Identification', 'score': 0.5292368}, {'id': 'https://openalex.org/keywords/functional-genomics', 'display_name': 'Functional Genomics', 'score': 0.52108634}, {'id': 'https://openalex.org/keywords/gene-prediction', 'display_name': 'Gene prediction', 'score': 0.4881061}, {'id': 'https://openalex.org/keywords/phylogenomics', 'display_name': 'Phylogenomics', 'score': 0.4634668}, {'id': 'https://openalex.org/keywords/comparative-genomics', 'display_name': 'Comparative Genomics', 'score': 0.43412203}], 'concepts': [{'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.7600981}, {'id': 'https://openalex.org/C2778112365', 'wikidata': 'https://www.wikidata.org/wiki/Q3511065', 'display_name': 'Sequence (biology)', 'level': 2, 'score': 0.6427194}, {'id': 'https://openalex.org/C103278499', 'wikidata': 'https://www.wikidata.org/wiki/Q254465', 'display_name': 'Similarity (geometry)', 'level': 3, 'score': 0.6334125}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.6247164}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.62020475}, {'id': 'https://openalex.org/C14036430', 'wikidata': 'https://www.wikidata.org/wiki/Q3736076', 'display_name': 'Function (biology)', 'level': 2, 'score': 0.5719277}, {'id': 'https://openalex.org/C116834253', 'wikidata': 'https://www.wikidata.org/wiki/Q2039217', 'display_name': 'Identification (biology)', 'level': 2, 'score': 0.5292368}, {'id': 'https://openalex.org/C161078062', 'wikidata': 'https://www.wikidata.org/wiki/Q1068690', 'display_name': 'Functional genomics', 'level': 5, 'score': 0.52108634}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.49027637}, {'id': 'https://openalex.org/C105565629', 'wikidata': 'https://www.wikidata.org/wiki/Q1248292', 'display_name': 'Gene prediction', 'level': 4, 'score': 0.4881061}, {'id': 'https://openalex.org/C61053724', 'wikidata': 'https://www.wikidata.org/wiki/Q1154615', 'display_name': 'Sequence analysis', 'level': 3, 'score': 0.4658687}, {'id': 'https://openalex.org/C70343354', 'wikidata': 'https://www.wikidata.org/wiki/Q3381973', 'display_name': 'Phylogenomics', 'level': 5, 'score': 0.4634668}, {'id': 'https://openalex.org/C45484198', 'wikidata': 'https://www.wikidata.org/wiki/Q827246', 'display_name': 'Sequence alignment', 'level': 4, 'score': 0.43590528}, {'id': 'https://openalex.org/C105176652', 'wikidata': 'https://www.wikidata.org/wiki/Q1147112', 'display_name': 'Comparative genomics', 'level': 5, 'score': 0.43412203}, {'id': 'https://openalex.org/C189206191', 'wikidata': 'https://www.wikidata.org/wiki/Q222046', 'display_name': 'Genomics', 'level': 4, 'score': 0.42129558}, {'id': 'https://openalex.org/C90132467', 'wikidata': 'https://www.wikidata.org/wiki/Q171184', 'display_name': 'Phylogenetics', 'level': 3, 'score': 0.25205958}, {'id': 'https://openalex.org/C141231307', 'wikidata': 'https://www.wikidata.org/wiki/Q7020', 'display_name': 'Genome', 'level': 3, 'score': 0.20164412}, {'id': 'https://openalex.org/C167625842', 'wikidata': 'https://www.wikidata.org/wiki/Q899763', 'display_name': 'Peptide sequence', 'level': 3, 'score': 0.18674797}, {'id': 'https://openalex.org/C154945302', 'wikidata': 'https://www.wikidata.org/wiki/Q11660', 'display_name': 'Artificial intelligence', 'level': 1, 'score': 0.14794439}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.13532156}, {'id': 'https://openalex.org/C44465124', 'wikidata': 'https://www.wikidata.org/wiki/Q713623', 'display_name': 'Clade', 'level': 4, 'score': 0.0}, {'id': 'https://openalex.org/C59822182', 'wikidata': 'https://www.wikidata.org/wiki/Q441', 'display_name': 'Botany', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C115961682', 'wikidata': 'https://www.wikidata.org/wiki/Q860623', 'display_name': 'Image (mathematics)', 'level': 2, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D019143', 'descriptor_name': 'Evolution, Molecular', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D005796', 'descriptor_name': 'Genes', 'qualifier_ui': 'Q000502', 'qualifier_name': 'physiology', 'is_major_topic': True}, {'descriptor_ui': 'D016678', 'descriptor_name': 'Genome', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D010802', 'descriptor_name': 'Phylogeny', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000818', 'descriptor_name': 'Animals', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D005796', 'descriptor_name': 'Genes', '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': 'D017422', 'descriptor_name': 'Sequence Analysis, DNA', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017422', 'descriptor_name': 'Sequence Analysis, DNA', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': False}], 'locations_count': 3, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1101/gr.8.3.163', 'pdf_url': 'https://genome.cshlp.org/content/8/3/163.full.pdf', 'source': {'id': 'https://openalex.org/S43092948', 'display_name': 'Genome Research', 'issn_l': '1088-9051', 'issn': ['1088-9051', '1549-5469'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315909', 'host_organization_name': 'Cold Spring Harbor Laboratory Press', 'host_organization_lineage': ['https://openalex.org/P4310315909'], 'host_organization_lineage_names': ['Cold Spring Harbor Laboratory Press'], 'type': 'journal'}, 'license': 'cc-by-nc', 'license_id': 'https://openalex.org/licenses/cc-by-nc', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://escholarship.org/uc/item/2g4367dw', 'pdf_url': 'https://escholarship.org/content/qt2g4367dw/qt2g4367dw.pdf?t=p1930c', 'source': {'id': 'https://openalex.org/S4306400115', 'display_name': 'eScholarship (California Digital Library)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I2801248553', 'host_organization_name': 'California Digital Library', 'host_organization_lineage': ['https://openalex.org/I2801248553'], 'host_organization_lineage_names': ['California Digital Library'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': 'submittedVersion', 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/9521918', '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/10.1101/gr.8.3.163', 'pdf_url': 'https://genome.cshlp.org/content/8/3/163.full.pdf', 'source': {'id': 'https://openalex.org/S43092948', 'display_name': 'Genome Research', 'issn_l': '1088-9051', 'issn': ['1088-9051', '1549-5469'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310315909', 'host_organization_name': 'Cold Spring Harbor Laboratory Press', 'host_organization_lineage': ['https://openalex.org/P4310315909'], 'host_organization_lineage_names': ['Cold Spring Harbor Laboratory Press'], 'type': 'journal'}, 'license': 'cc-by-nc', 'license_id': 'https://openalex.org/licenses/cc-by-nc', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 22, 'referenced_works': ['https://openalex.org/W1488711241', 'https://openalex.org/W1578832578', 'https://openalex.org/W1969620339', 'https://openalex.org/W1990453950', 'https://openalex.org/W1990586926', 'https://openalex.org/W1991669894', 'https://openalex.org/W2013410948', 'https://openalex.org/W2033775040', 'https://openalex.org/W2038407153', 'https://openalex.org/W2045098899', 'https://openalex.org/W2072769447', 'https://openalex.org/W2081614588', 'https://openalex.org/W2089773829', 'https://openalex.org/W2108836454', 'https://openalex.org/W2110132014', 'https://openalex.org/W2134153749', 'https://openalex.org/W2141171315', 'https://openalex.org/W2145340597', 'https://openalex.org/W2158714788', 'https://openalex.org/W2159266221', 'https://openalex.org/W4206702770', 'https://openalex.org/W4245513787'], 'related_works': ['https://openalex.org/W4385370162', 'https://openalex.org/W4322421693', 'https://openalex.org/W4295013818', 'https://openalex.org/W2364340602', 'https://openalex.org/W2353729507', 'https://openalex.org/W2164364816', 'https://openalex.org/W2129833142', 'https://openalex.org/W2116734196', 'https://openalex.org/W2092829297', 'https://openalex.org/W1485242531'], 'abstract_inverted_index': {'The': [0], 'ability': [1], 'to': [2, 88, 126, 143, 148, 268, 277, 286], 'accurately': [3], 'predict': [4, 287], 'gene': [5, 9, 34, 64, 258, 272, 281, 288, 295], 'function': [6, 147, 289], 'based': [7], 'on': [8, 53, 194, 206], 'sequence': [10, 60, 76, 84, 106, 125, 137, 201, 208, 282], 'is': [11, 73, 77, 86, 94, 100, 115, 139, 212, 232, 275, 283], 'an': [12, 149], 'important': [13, 26], 'tool': [14], 'in': [15, 27, 31, 102, 124, 200, 254], 'many': [16, 216], 'areas': [17], 'of': [18, 59, 65, 82, 91, 119, 136, 157, 179, 218, 251, 257, 264, 271], 'biological': [19], 'research.': [20], 'Such': [21], 'predictions': [22, 187], 'have': [23, 127, 154], 'become': [24], 'particularly': [25], 'the': [28, 54, 63, 78, 134, 177, 196, 207, 249, 255, 262, 269], 'genomics': [29], 'age': [30], 'which': [32, 70], 'numerous': [33], 'sequences': [35], 'are': [36, 122], 'generated': [37], 'with': [38, 162], 'little': [39], 'or': [40], 'no': [41, 95, 233], 'accompanying': [42], 'experimentally': [43], 'determined': [44], 'functional': [45, 49, 71, 169, 186], 'information.': [46], 'Almost': [47], 'all': [48], 'prediction': [50, 170, 256, 270], 'methods': [51, 171], 'rely': [52], 'identification,': [55], 'characterization,': [56], 'and': [57, 67, 113, 228, 290], 'quantification': [58], 'similarity': [61, 85, 90, 107, 138, 180, 209], 'between': [62], 'interest': [66], 'genes': [68, 120, 161, 197], 'for': [69, 117], 'information': [72, 253], 'available.': [74], 'Because': [75], 'prime': [79], 'determining': [80], 'factor': [81], 'function,': [83, 273], 'taken': [87], 'imply': [89], 'function.': [92, 259], 'There': [93], 'doubt': [96], 'that': [97, 121, 185, 215], 'this': [98, 245], 'assumption': [99], 'valid': [101], 'most': [103, 168], 'cases.': [104], 'However,': [105], 'does': [108], 'not': [109, 141], 'ensure': [110], 'identical': [111], 'functions,': [112], 'it': [114, 274], 'common': [116], 'groups': [118], 'similar': [123, 160, 199], 'diverse': [128], '(although': [129], 'usually': [130], 'related)': [131], 'functions.': [132, 164], 'Therefore,': [133], 'identification': [135], 'frequently': [140], 'enough': [142], 'assign': [144, 172], 'a': [145, 155, 265], 'predicted': [146], 'uncharacterized': [150], 'gene;': [151], 'one': [152], 'must': [153], 'method': [156], 'choosing': [158], 'among': [159, 181], 'different': [163], 'In': [165, 244], 'such': [166], 'cases,': [167], 'likely': [173], 'functions': [174], 'by': [175, 192], 'quantifying': [176], 'levels': [178], 'genes.': [182], 'I': [183, 247], 'suggest': [184], 'can': [188, 221], 'be': [189], 'greatly': [190], 'improved': [191], 'focusing': [193], 'how': [195, 280], 'became': [198], '(i.e.,': [202], 'evolution)': [203], 'rather': [204], 'than': [205], 'itself.': [210], 'It': [211], 'well': [213], 'established': [214], 'aspects': [217], 'comparative': [219, 229], 'biology': [220, 231], 'benefit': [222], 'from': [223], 'evolutionary': [224, 252], 'studies': [225], '(Felsenstein': [226], '1985),': [227], 'molecular': [230], 'exception': [234], '(e.g.,': [235], 'Altschul': [236], 'et': [237, 241], 'al.': [238, 242], '1989;': [239], 'Goldman': [240], '1996).': [243], 'commentary,': [246], 'discuss': [248, 279], 'use': [250], 'To': [260], 'appreciate': [261], 'potential': [263], 'phylogenomic': [266], 'approach': [267], 'necessary': [276], 'first': [278], 'commonly': [284], 'used': [285], 'some': [291], 'general': [292], 'features': [293], 'about': [294], 'evolution.': [296]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2167455933', 'counts_by_year': [{'year': 2024, 'cited_by_count': 14}, {'year': 2023, 'cited_by_count': 20}, {'year': 2022, 'cited_by_count': 15}, {'year': 2021, 'cited_by_count': 13}, {'year': 2020, 'cited_by_count': 39}, {'year': 2019, 'cited_by_count': 29}, {'year': 2018, 'cited_by_count': 23}, {'year': 2017, 'cited_by_count': 23}, {'year': 2016, 'cited_by_count': 23}, {'year': 2015, 'cited_by_count': 12}, {'year': 2014, 'cited_by_count': 30}, {'year': 2013, 'cited_by_count': 31}, {'year': 2012, 'cited_by_count': 25}], 'updated_date': '2025-01-02T10:10:19.047988', 'created_date': '2016-06-24'}