Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2139449083', 'doi': 'https://doi.org/10.1093/bioinformatics/btp580', 'title': 'CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score', 'display_name': 'CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score', 'publication_year': 2009, 'publication_date': '2009-10-06', 'ids': {'openalex': 'https://openalex.org/W2139449083', 'doi': 'https://doi.org/10.1093/bioinformatics/btp580', 'mag': '2139449083', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/19808876'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btp580', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/25/24/3236/48997901/bioinformatics_25_24_3236.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': 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://academic.oup.com/bioinformatics/article-pdf/25/24/3236/48997901/bioinformatics_25_24_3236.pdf', 'any_repository_has_fulltext': False}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5025857432', 'display_name': 'Michiaki Hamada', 'orcid': 'https://orcid.org/0000-0001-9466-1034'}, 'institutions': [{'id': 'https://openalex.org/I4210104082', 'display_name': 'Japan Biological Informatics Consortium', 'ror': 'https://ror.org/01astg473', 'country_code': 'JP', 'type': 'nonprofit', 'lineage': ['https://openalex.org/I4210104082']}, {'id': 'https://openalex.org/I74801974', 'display_name': 'The University of Tokyo', 'ror': 'https://ror.org/057zh3y96', 'country_code': 'JP', 'type': 'education', 'lineage': ['https://openalex.org/I74801974']}, {'id': 'https://openalex.org/I73613424', 'display_name': 'National Institute of Advanced Industrial Science and Technology', 'ror': 'https://ror.org/01703db54', 'country_code': 'JP', 'type': 'government', 'lineage': ['https://openalex.org/I73613424']}], 'countries': ['JP'], 'is_corresponding': False, 'raw_author_name': 'Michiaki Hamada', 'raw_affiliation_strings': ['1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan'], 'affiliations': [{'raw_affiliation_string': '1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan', 'institution_ids': ['https://openalex.org/I4210104082', 'https://openalex.org/I74801974', 'https://openalex.org/I73613424']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5076175043', 'display_name': 'Kengo Sato', 'orcid': 'https://orcid.org/0000-0001-6744-7390'}, 'institutions': [{'id': 'https://openalex.org/I4210104082', 'display_name': 'Japan Biological Informatics Consortium', 'ror': 'https://ror.org/01astg473', 'country_code': 'JP', 'type': 'nonprofit', 'lineage': ['https://openalex.org/I4210104082']}, {'id': 'https://openalex.org/I74801974', 'display_name': 'The University of Tokyo', 'ror': 'https://ror.org/057zh3y96', 'country_code': 'JP', 'type': 'education', 'lineage': ['https://openalex.org/I74801974']}, {'id': 'https://openalex.org/I73613424', 'display_name': 'National Institute of Advanced Industrial Science and Technology', 'ror': 'https://ror.org/01703db54', 'country_code': 'JP', 'type': 'government', 'lineage': ['https://openalex.org/I73613424']}], 'countries': ['JP'], 'is_corresponding': False, 'raw_author_name': 'Kengo Sato', 'raw_affiliation_strings': ['1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan'], 'affiliations': [{'raw_affiliation_string': '1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan', 'institution_ids': ['https://openalex.org/I4210104082', 'https://openalex.org/I74801974', 'https://openalex.org/I73613424']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5024402799', 'display_name': 'Hisanori Kiryu', 'orcid': 'https://orcid.org/0000-0003-3554-5353'}, 'institutions': [{'id': 'https://openalex.org/I4210104082', 'display_name': 'Japan Biological Informatics Consortium', 'ror': 'https://ror.org/01astg473', 'country_code': 'JP', 'type': 'nonprofit', 'lineage': ['https://openalex.org/I4210104082']}, {'id': 'https://openalex.org/I74801974', 'display_name': 'The University of Tokyo', 'ror': 'https://ror.org/057zh3y96', 'country_code': 'JP', 'type': 'education', 'lineage': ['https://openalex.org/I74801974']}, {'id': 'https://openalex.org/I73613424', 'display_name': 'National Institute of Advanced Industrial Science and Technology', 'ror': 'https://ror.org/01703db54', 'country_code': 'JP', 'type': 'government', 'lineage': ['https://openalex.org/I73613424']}], 'countries': ['JP'], 'is_corresponding': False, 'raw_author_name': 'Hisanori Kiryu', 'raw_affiliation_strings': ['1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan'], 'affiliations': [{'raw_affiliation_string': '1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan', 'institution_ids': ['https://openalex.org/I4210104082', 'https://openalex.org/I74801974', 'https://openalex.org/I73613424']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5015688097', 'display_name': 'Toutai Mituyama', 'orcid': 'https://orcid.org/0000-0002-1110-6375'}, 'institutions': [{'id': 'https://openalex.org/I4210104082', 'display_name': 'Japan Biological Informatics Consortium', 'ror': 'https://ror.org/01astg473', 'country_code': 'JP', 'type': 'nonprofit', 'lineage': ['https://openalex.org/I4210104082']}, {'id': 'https://openalex.org/I74801974', 'display_name': 'The University of Tokyo', 'ror': 'https://ror.org/057zh3y96', 'country_code': 'JP', 'type': 'education', 'lineage': ['https://openalex.org/I74801974']}, {'id': 'https://openalex.org/I73613424', 'display_name': 'National Institute of Advanced Industrial Science and Technology', 'ror': 'https://ror.org/01703db54', 'country_code': 'JP', 'type': 'government', 'lineage': ['https://openalex.org/I73613424']}], 'countries': ['JP'], 'is_corresponding': False, 'raw_author_name': 'Toutai Mituyama', 'raw_affiliation_strings': ['1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan'], 'affiliations': [{'raw_affiliation_string': '1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan', 'institution_ids': ['https://openalex.org/I4210104082', 'https://openalex.org/I74801974', 'https://openalex.org/I73613424']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5082068847', 'display_name': 'Kiyoshi Asai', 'orcid': 'https://orcid.org/0000-0003-0909-4982'}, 'institutions': [{'id': 'https://openalex.org/I4210104082', 'display_name': 'Japan Biological Informatics Consortium', 'ror': 'https://ror.org/01astg473', 'country_code': 'JP', 'type': 'nonprofit', 'lineage': ['https://openalex.org/I4210104082']}, {'id': 'https://openalex.org/I74801974', 'display_name': 'The University of Tokyo', 'ror': 'https://ror.org/057zh3y96', 'country_code': 'JP', 'type': 'education', 'lineage': ['https://openalex.org/I74801974']}, {'id': 'https://openalex.org/I73613424', 'display_name': 'National Institute of Advanced Industrial Science and Technology', 'ror': 'https://ror.org/01703db54', 'country_code': 'JP', 'type': 'government', 'lineage': ['https://openalex.org/I73613424']}], 'countries': ['JP'], 'is_corresponding': False, 'raw_author_name': 'Kiyoshi Asai', 'raw_affiliation_strings': ['1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan'], 'affiliations': [{'raw_affiliation_string': '1 Mizuho Information & Research Institute, Inc, 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2–41–6, Aomi, Koto-ku, Tokyo 135–0064, 3Japan Biological Informatics Consortium, 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan', 'institution_ids': ['https://openalex.org/I4210104082', 'https://openalex.org/I74801974', 'https://openalex.org/I73613424']}]}], 'countries_distinct_count': 1, 'institutions_distinct_count': 3, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': {'value': 3618, 'currency': 'USD', 'value_usd': 3618, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 2.225, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 49, 'citation_normalized_percentile': {'value': 0.872304, 'is_in_top_1_percent': False, 'is_in_top_10_percent': False}, 'cited_by_percentile_year': {'min': 94, 'max': 95}, 'biblio': {'volume': '25', 'issue': '24', 'first_page': '3236', 'last_page': '3243'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10521', 'display_name': 'Ribosome Structure and Translation Mechanisms', 'score': 1.0, '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': 'Ribosome Structure and Translation Mechanisms', 'score': 1.0, '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/T11482', 'display_name': 'RNA Methylation and Modification in Gene Expression', 'score': 0.9997, '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': 'RNA Sequencing Data Analysis', 'score': 0.9997, '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/benchmark', 'display_name': 'Benchmark (surveying)', 'score': 0.6560273}, {'id': 'https://openalex.org/keywords/sequence-alignment', 'display_name': 'sequence alignment', 'score': 0.601019}, {'id': 'https://openalex.org/keywords/secondary-structure-prediction', 'display_name': 'Secondary Structure Prediction', 'score': 0.507008}], 'concepts': [{'id': 'https://openalex.org/C184898388', 'wikidata': 'https://www.wikidata.org/wiki/Q1435712', 'display_name': 'Pairwise comparison', 'level': 2, 'score': 0.80931914}, {'id': 'https://openalex.org/C185429906', 'wikidata': 'https://www.wikidata.org/wiki/Q1130160', 'display_name': 'Estimator', 'level': 2, 'score': 0.75788575}, {'id': 'https://openalex.org/C185798385', 'wikidata': 'https://www.wikidata.org/wiki/Q1161707', 'display_name': 'Benchmark (surveying)', 'level': 2, 'score': 0.6560273}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.6421575}, {'id': 'https://openalex.org/C2776436953', 'wikidata': 'https://www.wikidata.org/wiki/Q5163215', 'display_name': 'Consistency (knowledge bases)', 'level': 2, 'score': 0.57823795}, {'id': 'https://openalex.org/C2777904410', 'wikidata': 'https://www.wikidata.org/wiki/Q7397', 'display_name': 'Software', 'level': 2, 'score': 0.52446604}, {'id': 'https://openalex.org/C49937458', 'wikidata': 'https://www.wikidata.org/wiki/Q2599292', 'display_name': 'Probabilistic logic', 'level': 2, 'score': 0.49089605}, {'id': 'https://openalex.org/C204241405', 'wikidata': 'https://www.wikidata.org/wiki/Q461499', 'display_name': 'Transformation (genetics)', 'level': 3, 'score': 0.43818104}, {'id': 'https://openalex.org/C11413529', 'wikidata': 'https://www.wikidata.org/wiki/Q8366', 'display_name': 'Algorithm', 'level': 1, 'score': 0.4181193}, {'id': 'https://openalex.org/C124101348', 'wikidata': 'https://www.wikidata.org/wiki/Q172491', 'display_name': 'Data mining', 'level': 1, 'score': 0.33779293}, {'id': 'https://openalex.org/C80444323', 'wikidata': 'https://www.wikidata.org/wiki/Q2878974', 'display_name': 'Theoretical computer science', 'level': 1, 'score': 0.32517222}, {'id': 'https://openalex.org/C33923547', 'wikidata': 'https://www.wikidata.org/wiki/Q395', 'display_name': 'Mathematics', 'level': 0, 'score': 0.2331782}, {'id': 'https://openalex.org/C154945302', 'wikidata': 'https://www.wikidata.org/wiki/Q11660', 'display_name': 'Artificial intelligence', 'level': 1, 'score': 0.20520243}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.17607495}, {'id': 'https://openalex.org/C105795698', 'wikidata': 'https://www.wikidata.org/wiki/Q12483', 'display_name': 'Statistics', 'level': 1, 'score': 0.16961583}, {'id': 'https://openalex.org/C13280743', 'wikidata': 'https://www.wikidata.org/wiki/Q131089', 'display_name': 'Geodesy', '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}, {'id': 'https://openalex.org/C205649164', 'wikidata': 'https://www.wikidata.org/wiki/Q1071', 'display_name': 'Geography', 'level': 0, 'score': 0.0}, {'id': 'https://openalex.org/C55493867', 'wikidata': 'https://www.wikidata.org/wiki/Q7094', 'display_name': 'Biochemistry', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D019295', 'descriptor_name': 'Computational Biology', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D012313', 'descriptor_name': 'RNA', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D016415', 'descriptor_name': 'Sequence Alignment', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D017423', 'descriptor_name': 'Sequence Analysis, RNA', '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': 'D001483', 'descriptor_name': 'Base Sequence', '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': 'D030541', 'descriptor_name': 'Databases, Genetic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D012313', 'descriptor_name': 'RNA', 'qualifier_ui': 'Q000378', 'qualifier_name': 'metabolism', 'is_major_topic': False}, {'descriptor_ui': 'D012313', 'descriptor_name': 'RNA', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D022661', 'descriptor_name': 'RNA, Untranslated', 'qualifier_ui': 'Q000378', 'qualifier_name': 'metabolism', 'is_major_topic': False}, {'descriptor_ui': 'D022661', 'descriptor_name': 'RNA, Untranslated', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': False}, {'descriptor_ui': 'D022661', 'descriptor_name': 'RNA, Untranslated', '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}, {'descriptor_ui': 'D017423', 'descriptor_name': 'Sequence Analysis, RNA', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 2, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/bioinformatics/btp580', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/25/24/3236/48997901/bioinformatics_25_24_3236.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': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/19808876', '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/btp580', 'pdf_url': 'https://academic.oup.com/bioinformatics/article-pdf/25/24/3236/48997901/bioinformatics_25_24_3236.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': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 51, 'referenced_works': ['https://openalex.org/W1489075871', 'https://openalex.org/W1522740115', 'https://openalex.org/W1861164398', 'https://openalex.org/W1866859902', 'https://openalex.org/W1909512798', 'https://openalex.org/W1981584745', 'https://openalex.org/W1984675364', 'https://openalex.org/W1988512789', 'https://openalex.org/W1993324010', 'https://openalex.org/W1994958179', 'https://openalex.org/W1997631042', 'https://openalex.org/W2001876475', 'https://openalex.org/W2003062976', 'https://openalex.org/W2011289056', 'https://openalex.org/W2018216725', 'https://openalex.org/W2038079502', 'https://openalex.org/W2049283139', 'https://openalex.org/W2069792162', 'https://openalex.org/W2071749306', 'https://openalex.org/W2074231493', 'https://openalex.org/W2087064593', 'https://openalex.org/W2095145214', 'https://openalex.org/W2099383450', 'https://openalex.org/W2101497682', 'https://openalex.org/W2101535367', 'https://openalex.org/W2102017611', 'https://openalex.org/W2103899452', 'https://openalex.org/W2110845345', 'https://openalex.org/W2111272410', 'https://openalex.org/W2115215562', 'https://openalex.org/W2118829610', 'https://openalex.org/W2121691652', 'https://openalex.org/W2122035121', 'https://openalex.org/W2127688908', 'https://openalex.org/W2128109027', 'https://openalex.org/W2131054067', 'https://openalex.org/W2140302584', 'https://openalex.org/W2140872496', 'https://openalex.org/W2141411594', 'https://openalex.org/W2141411672', 'https://openalex.org/W2141670298', 'https://openalex.org/W2142038007', 'https://openalex.org/W2142116796', 'https://openalex.org/W2142768277', 'https://openalex.org/W2151994495', 'https://openalex.org/W2163798335', 'https://openalex.org/W2166486463', 'https://openalex.org/W2170945060', 'https://openalex.org/W2610493105', 'https://openalex.org/W3214380909', 'https://openalex.org/W4245668478'], 'related_works': ['https://openalex.org/W4315563560', 'https://openalex.org/W2949152769', 'https://openalex.org/W2553559590', 'https://openalex.org/W2487162673', 'https://openalex.org/W2378211422', 'https://openalex.org/W2171766007', 'https://openalex.org/W2143990275', 'https://openalex.org/W2117163556', 'https://openalex.org/W2029032313', 'https://openalex.org/W108653788'], 'abstract_inverted_index': {'The': [0, 130], 'importance': [1], 'of': [2, 7, 31, 48, 57, 71, 81, 89, 117, 128, 136, 194, 201, 211], 'accurate': [3], 'and': [4, 120, 123, 139, 153, 190], 'fast': [5], 'predictions': [6, 32], 'multiple': [8, 46, 199], 'alignments': [9, 47, 90, 140, 157, 170, 200], 'for': [10, 36, 45, 68, 198], 'RNA': [11, 72], 'sequences': [12, 119], 'has': [13], 'increased': [14], 'due': [15], 'to': [16], 'recent': [17], 'findings': [18], 'about': [19], 'functional': [20], 'non-coding': [21], 'RNAs.': [22], 'Recent': [23], 'studies': [24], 'suggest': [25], 'that': [26, 141, 182], 'maximizing': [27, 53], 'the': [28, 54, 62, 76, 94, 100, 115, 150, 155, 164, 172, 183, 192, 212], 'expected': [29, 55, 64, 77], 'accuracy': [30, 56, 65], 'will': [33], 'be': [34], 'useful': [35], 'many': [37, 195], 'problems': [38], 'in': [39, 144, 214], 'bioinformatics.We': [40], 'designed': [41], 'a': [42, 82, 86, 187], 'novel': [43], 'estimator': [44, 67, 106, 132], 'structured': [49, 202], 'RNAs,': [50], 'based': [51], 'on': [52, 169, 220], 'predictions.': [58], 'First,': [59], 'we': [60, 103, 162], 'define': [61], 'maximum': [63], '(MEA)': [66], 'pairwise': [69, 156], 'alignment': [70, 84], 'sequences.': [73, 160], 'This': [74], 'maximizes': [75], 'sum-of-pairs': [78], 'score': [79], '(SPS)': [80], 'predicted': [83], 'under': [85], 'probability': [87], 'distribution': [88], 'given': [91], 'by': [92, 98], 'marginalizing': [93], 'Sankoff': [95], 'model.': [96], 'Then,': [97], 'approximating': [99], 'MEA': [101], 'estimator,': [102], 'obtain': [104], 'an': [105, 209], 'whose': [107], 'time': [108], 'complexity': [109], 'is': [110, 114, 208, 217], 'O(L(3)+c(2)dL(2))': [111], 'where': [112], 'L': [113], 'length': [116], 'input': [118, 159], 'both': [121], 'c': [122], 'd': [124], 'are': [125, 142, 225], 'constants': [126], 'independent': [127], 'L.': [129], 'proposed': [131, 173, 184], 'can': [133], 'handle': [134], 'uncertainty': [135], 'secondary': [137, 151], 'structures': [138, 152], 'obstacles': [143], 'Bioinformatics': [145, 228], 'because': [146], 'it': [147], 'considers': [148], 'all': [149, 154], 'as': [158], 'Moreover,': [161], 'integrate': [163], 'probabilistic': [165], 'consistency': [166], 'transformation': [167], '(PCT)': [168], 'into': [171], 'estimator.': [174], 'Computational': [175], 'experiments': [176], 'using': [177], 'six': [178], 'benchmark': [179], 'datasets': [180], 'indicate': [181], 'method': [185], 'achieved': [186], 'favorable': [188], 'SPS': [189], 'was': [191], 'fastest': [193], 'state-of-the-art': [196], 'tools': [197], 'RNAs.The': [203], 'software': [204], 'called': [205], 'CentroidAlign,': [206], 'which': [207], 'implementation': [210], 'algorithm': [213], 'this': [215], 'article,': [216], 'freely': [218], 'available': [219, 226], 'our': [221], 'website:': [222], 'http://www.ncrna.org/software/centroidalign/[email protected]': [223], 'data': [224], 'at': [227], 'online.': [229]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2139449083', 'counts_by_year': [{'year': 2023, 'cited_by_count': 2}, {'year': 2022, 'cited_by_count': 3}, {'year': 2021, 'cited_by_count': 1}, {'year': 2020, 'cited_by_count': 3}, {'year': 2019, 'cited_by_count': 4}, {'year': 2018, 'cited_by_count': 2}, {'year': 2017, 'cited_by_count': 1}, {'year': 2016, 'cited_by_count': 7}, {'year': 2015, 'cited_by_count': 2}, {'year': 2014, 'cited_by_count': 2}, {'year': 2013, 'cited_by_count': 5}, {'year': 2012, 'cited_by_count': 7}], 'updated_date': '2024-08-15T10:24:11.362559', 'created_date': '2016-06-24'}