Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2951608279', 'doi': 'https://doi.org/10.1093/bioinformatics/btx221', 'title': 'Domain prediction with probabilistic directional context', 'display_name': 'Domain prediction with probabilistic directional context', 'publication_year': 2017, 'publication_date': '2017-04-11', 'ids': {'openalex': 'https://openalex.org/W2951608279', 'doi': 'https://doi.org/10.1093/bioinformatics/btx221', 'mag': '2951608279', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/28407137', 'pmcid': 'https://www.ncbi.nlm.nih.gov/pmc/articles/5870623'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btx221', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/16/2471/25163528/btx221.pdf', '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': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', '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': 'hybrid', 'oa_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/16/2471/25163528/btx221.pdf', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5078947409', 'display_name': 'Alejandro Ochoa', 'orcid': 'https://orcid.org/0000-0003-4928-3403'}, 'institutions': [{'id': 'https://openalex.org/I20089843', 'display_name': 'Princeton University', 'ror': 'https://ror.org/00hx57361', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I20089843']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Alejandro Ochoa', 'raw_affiliation_strings': ['Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA', 'Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA'], 'affiliations': [{'raw_affiliation_string': 'Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA', 'institution_ids': ['https://openalex.org/I20089843']}, {'raw_affiliation_string': 'Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA', 'institution_ids': ['https://openalex.org/I20089843']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5085615320', 'display_name': 'Mona Singh', 'orcid': 'https://orcid.org/0000-0001-8271-6026'}, 'institutions': [{'id': 'https://openalex.org/I20089843', 'display_name': 'Princeton University', 'ror': 'https://ror.org/00hx57361', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I20089843']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Mona Singh', 'raw_affiliation_strings': ['Department of Computer Science, Princeton University, Princeton, NJ, USA', 'Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA'], 'affiliations': [{'raw_affiliation_string': 'Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA', 'institution_ids': ['https://openalex.org/I20089843']}, {'raw_affiliation_string': 'Department of Computer Science, Princeton University, Princeton, NJ, USA', 'institution_ids': ['https://openalex.org/I20089843']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5085615320'], 'corresponding_institution_ids': ['https://openalex.org/I20089843'], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'fwci': 0.306, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 6, 'citation_normalized_percentile': {'value': 0.554574, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 81, 'max': 82}, 'biblio': {'volume': '33', 'issue': '16', 'first_page': '2471', 'last_page': '2478'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T12254', 'display_name': 'Machine Learning in Bioinformatics', 'score': 0.9914, '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/T12254', 'display_name': 'Machine Learning in Bioinformatics', 'score': 0.9914, '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/T11550', 'display_name': 'Text and Document Classification Technologies', 'score': 0.9563, 'subfield': {'id': 'https://openalex.org/subfields/1702', 'display_name': 'Artificial Intelligence'}, 'field': {'id': 'https://openalex.org/fields/17', 'display_name': 'Computer Science'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10521', 'display_name': 'RNA and protein synthesis mechanisms', 'score': 0.932, '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': [], 'concepts': [{'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.76890707}, {'id': 'https://openalex.org/C36503486', 'wikidata': 'https://www.wikidata.org/wiki/Q11235244', 'display_name': 'Domain (mathematical analysis)', 'level': 2, 'score': 0.737079}, {'id': 'https://openalex.org/C2779343474', 'wikidata': 'https://www.wikidata.org/wiki/Q3109175', 'display_name': 'Context (archaeology)', 'level': 2, 'score': 0.65416455}, {'id': 'https://openalex.org/C49937458', 'wikidata': 'https://www.wikidata.org/wiki/Q2599292', 'display_name': 'Probabilistic logic', 'level': 2, 'score': 0.64393365}, {'id': 'https://openalex.org/C154945302', 'wikidata': 'https://www.wikidata.org/wiki/Q11660', 'display_name': 'Artificial intelligence', 'level': 1, 'score': 0.42858136}, {'id': 'https://openalex.org/C119857082', 'wikidata': 'https://www.wikidata.org/wiki/Q2539', 'display_name': 'Machine learning', 'level': 1, 'score': 0.33506033}, {'id': 'https://openalex.org/C124101348', 'wikidata': 'https://www.wikidata.org/wiki/Q172491', 'display_name': 'Data mining', 'level': 1, 'score': 0.3299205}, {'id': 'https://openalex.org/C33923547', 'wikidata': 'https://www.wikidata.org/wiki/Q395', 'display_name': 'Mathematics', 'level': 0, 'score': 0.12602189}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.06979656}, {'id': 'https://openalex.org/C134306372', 'wikidata': 'https://www.wikidata.org/wiki/Q7754', 'display_name': 'Mathematical analysis', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C151730666', 'wikidata': 'https://www.wikidata.org/wiki/Q7205', 'display_name': 'Paleontology', 'level': 1, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D008958', 'descriptor_name': 'Models, Molecular', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000072417', 'descriptor_name': 'Protein Domains', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D020539', 'descriptor_name': 'Sequence Analysis, Protein', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D012984', 'descriptor_name': 'Software', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D000465', 'descriptor_name': 'Algorithms', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', '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': 'D015233', 'descriptor_name': 'Models, Statistical', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D020539', 'descriptor_name': 'Sequence Analysis, Protein', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 5, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btx221', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/16/2471/25163528/btx221.pdf', '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': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://europepmc.org/articles/pmc5870623', 'pdf_url': 'https://europepmc.org/articles/pmc5870623?pdf=render', 'source': {'id': 'https://openalex.org/S4306400806', 'display_name': 'Europe PMC (PubMed Central)', 'issn_l': None, 'issn': None, 'is_oa': True, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1303153112', 'host_organization_name': 'European Bioinformatics Institute', 'host_organization_lineage': ['https://openalex.org/I1303153112'], 'host_organization_lineage_names': ['European Bioinformatics Institute'], 'type': 'repository'}, 'license': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870623', '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': True, 'landing_page_url': 'https://doi.org/10.1101/094284', 'pdf_url': 'https://www.biorxiv.org/content/biorxiv/early/2016/12/14/094284.full.pdf', 'source': None, 'license': 'cc-by-nd', 'license_id': 'https://openalex.org/licenses/cc-by-nd', 'version': 'submittedVersion', 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/28407137', '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/bioinformatics/btx221', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/33/16/2471/25163528/btx221.pdf', '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': 'cc-by', 'license_id': 'https://openalex.org/licenses/cc-by', 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [{'funder': 'https://openalex.org/F4320306076', 'funder_display_name': 'National Science Foundation', 'award_id': 'DGE 0646086'}, {'funder': 'https://openalex.org/F4320306076', 'funder_display_name': 'National Science Foundation', 'award_id': 'A.O., ABI 1062371'}, {'funder': 'https://openalex.org/F4320332161', 'funder_display_name': 'National Institutes of Health', 'award_id': 'R01-GM076275'}, {'funder': 'https://openalex.org/F4320332161', 'funder_display_name': 'National Institutes of Health', 'award_id': 'R21-AI085415'}], 'datasets': [], 'versions': [], 'referenced_works_count': 20, 'referenced_works': ['https://openalex.org/W1567885833', 'https://openalex.org/W1628541219', 'https://openalex.org/W1977027195', 'https://openalex.org/W1996112765', 'https://openalex.org/W2010830967', 'https://openalex.org/W2011983053', 'https://openalex.org/W2040184829', 'https://openalex.org/W2112792893', 'https://openalex.org/W2116398954', 'https://openalex.org/W2121085676', 'https://openalex.org/W2121801438', 'https://openalex.org/W2125596158', 'https://openalex.org/W2125905177', 'https://openalex.org/W2127338593', 'https://openalex.org/W2141885858', 'https://openalex.org/W2179402585', 'https://openalex.org/W2490955734', 'https://openalex.org/W4210623056', 'https://openalex.org/W4233334497', 'https://openalex.org/W4320301318'], 'related_works': ['https://openalex.org/W4287727129', 'https://openalex.org/W3041172967', 'https://openalex.org/W2960358116', 'https://openalex.org/W2943623134', 'https://openalex.org/W2938171715', 'https://openalex.org/W2749065928', 'https://openalex.org/W2494523064', 'https://openalex.org/W2368237856', 'https://openalex.org/W2215759665', 'https://openalex.org/W2030292806'], 'abstract_inverted_index': {'Protein': [0], 'domain': [1, 15, 32, 58, 66, 71, 81, 154, 166], 'prediction': [2, 67], 'is': [3, 75, 182], 'one': [4], 'of': [5, 21, 41, 122, 153, 165], 'the': [6, 46, 76, 120, 163], 'most': [7, 40], 'powerful': [8], 'approaches': [9, 25, 43], 'for': [10, 65, 93], 'sequence-based': [11], 'function': [12], 'prediction.': [13], 'Although': [14], 'instances': [16], 'are': [17, 187], 'typically': [18], 'predicted': [19], 'independently': [20], 'each': [22], 'other,': [23], 'newer': [24], 'have': [26, 44, 54], 'demonstrated': [27], 'improved': [28], 'performance': [29], 'by': [30, 168], 'rewarding': [31], 'pairs': [33, 82], 'that': [34, 68, 98, 114, 140, 159], 'frequently': [35], 'co-occur': [36, 52], 'within': [37, 83, 119], 'sequences.': [38], 'However,': [39], 'these': [42], 'ignored': [45], 'order': [47, 89], 'in': [48, 146], 'which': [49], 'domains': [50], 'preferentially': [51], 'and': [53, 113, 138, 157], 'also': [55], 'not': [56], 'modeled': [57], 'co-occurrence': [59], 'probabilistically.We': [60], 'introduce': [61], 'a': [62, 84, 102], 'probabilistic': [63], 'approach': [64, 100, 106, 172], 'models': [69], "'directional'": [70], 'context.': [72], 'Our': [73], 'method': [74], 'first': [77], 'to': [78, 107], 'score': [79, 109], 'all': [80, 110, 179], 'sequence': [85], 'while': [86], 'taking': [87], 'their': [88], 'into': [90], 'account,': [91], 'even': [92], 'non-sequential': [94], 'domains.': [95], 'We': [96, 126], 'show': [97], 'our': [99, 128, 171], 'extends': [101], 'previous': [103], 'Markov': [104, 123], 'model-based': [105], 'additionally': [108], 'pairwise': [111], 'terms,': [112], 'it': [115, 141], 'can': [116, 142], 'be': [117, 143], 'interpreted': [118], 'context': [121, 155, 161], 'random': [124], 'fields.': [125], 'formulate': [127], 'underlying': [129], 'combinatorial': [130], 'optimization': [131], 'problem': [132], 'as': [133], 'an': [134], 'integer': [135], 'linear': [136], 'program,': [137], 'demonstrate': [139, 158], 'solved': [144], 'quickly': [145], 'practice.': [147], 'Finally,': [148], 'we': [149], 'perform': [150], 'extensive': [151], 'evaluation': [152], 'methods': [156], 'incorporating': [160], 'increases': [162], 'number': [164], 'predictions': [167], '∼15%,': [169], 'with': [170], 'dPUC2': [173], '(Domain': [174], 'Prediction': [175], 'Using': [176], 'Context)': [177], 'outperforming': [178], 'competing': [180], 'approaches.dPUC2': [181], 'available': [183, 188], 'at': [184, 189], 'http://github.com/alexviiia/[email protected]': [185], 'data': [186], 'Bioinformatics': [190], 'online.': [191]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2951608279', 'counts_by_year': [{'year': 2024, 'cited_by_count': 1}, {'year': 2021, 'cited_by_count': 2}, {'year': 2019, 'cited_by_count': 2}, {'year': 2018, 'cited_by_count': 1}], 'updated_date': '2025-01-08T18:52:02.755173', 'created_date': '2019-06-27'}