{"id":"https://openalex.org/W2903674301","doi":"https://doi.org/10.1093/bioinformatics/bty887","title":"SENSE: Siamese neural network for sequence embedding and alignment-free comparison","display_name":"SENSE: Siamese neural network for sequence embedding and alignment-free comparison","publication_year":2018,"publication_date":"2018-10-18","ids":{"openalex":"https://openalex.org/W2903674301","doi":"https://doi.org/10.1093/bioinformatics/bty887","mag":"2903674301","pmid":"https://pubmed.ncbi.nlm.nih.gov/30346493"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty887","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty887","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963080","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100763398","display_name":"Wei Zheng","orcid":"https://orcid.org/0000-0002-4581-5647"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Zheng","raw_affiliation_strings":["Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029859331","display_name":"Le Yang","orcid":"https://orcid.org/0000-0002-9750-5691"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Le Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019676251","display_name":"Robert J. Genco","orcid":"https://orcid.org/0000-0001-7604-506X"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J Genco","raw_affiliation_strings":["Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY, USA","Department of Oral Biology, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Oral Biology, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016111941","display_name":"Jean Wactawski\u2010Wende","orcid":"https://orcid.org/0000-0003-3096-9595"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean Wactawski-Wende","raw_affiliation_strings":["Department of Epidemiology and Environmental Health, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Environmental Health, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042060228","display_name":"Michael Buck","orcid":"https://orcid.org/0000-0001-5320-3678"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Buck","raw_affiliation_strings":["Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039662308","display_name":"Yijun Sun","orcid":"https://orcid.org/0000-0003-0610-6132"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yijun Sun","raw_affiliation_strings":["Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA","Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5039662308"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.951,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.87126805,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"35","issue":"11","first_page":"1820","last_page":"1828"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.998199999332428,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9979000091552734,"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/computer-science","display_name":"Computer science","score":0.6960773468017578},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6872121095657349},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6860975027084351},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6033150553703308},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5644846558570862},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.5542699694633484},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5532309412956238},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5519329309463501},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.5203865766525269},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5071108341217041},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48415428400039673},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4447666108608246},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4068983495235443},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35004615783691406},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3481311798095703},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33341482281684875}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6960773468017578},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6872121095657349},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6860975027084351},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6033150553703308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5644846558570862},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.5542699694633484},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5532309412956238},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5519329309463501},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.5203865766525269},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5071108341217041},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48415428400039673},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4447666108608246},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4068983495235443},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35004615783691406},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3481311798095703},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33341482281684875},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty887","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty887","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30346493","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30346493","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7963080","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963080","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7963080","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963080","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1665214252","https://openalex.org/W1967843471","https://openalex.org/W1971239653","https://openalex.org/W1975775747","https://openalex.org/W1986189475","https://openalex.org/W2001141328","https://openalex.org/W2064675550","https://openalex.org/W2068445909","https://openalex.org/W2073548709","https://openalex.org/W2074231493","https://openalex.org/W2086320398","https://openalex.org/W2094890728","https://openalex.org/W2095071222","https://openalex.org/W2097979671","https://openalex.org/W2120771433","https://openalex.org/W2130325614","https://openalex.org/W2140211206","https://openalex.org/W2140638310","https://openalex.org/W2147800946","https://openalex.org/W2150774511","https://openalex.org/W2152885278","https://openalex.org/W2159954944","https://openalex.org/W2171901261","https://openalex.org/W2249033064","https://openalex.org/W2252215182","https://openalex.org/W2294059674","https://openalex.org/W2321588627","https://openalex.org/W2346626577","https://openalex.org/W2559997609","https://openalex.org/W2572005288","https://openalex.org/W2604272474","https://openalex.org/W2610066872","https://openalex.org/W2761430568","https://openalex.org/W2884258548","https://openalex.org/W2919115771","https://openalex.org/W2964121744","https://openalex.org/W2999905431","https://openalex.org/W4365806527","https://openalex.org/W6631190155","https://openalex.org/W6637242042","https://openalex.org/W6639352576","https://openalex.org/W6674672532","https://openalex.org/W6677328822","https://openalex.org/W6679208599","https://openalex.org/W6684191040","https://openalex.org/W6691176567","https://openalex.org/W6696761078","https://openalex.org/W6731837907","https://openalex.org/W6753675497"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2194132979","https://openalex.org/W2141411672","https://openalex.org/W2111937814","https://openalex.org/W2730968108","https://openalex.org/W2759306076","https://openalex.org/W187239587","https://openalex.org/W2129361631","https://openalex.org/W2079145549","https://openalex.org/W2903170547"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":4}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
