{"id":"https://openalex.org/W2004356294","doi":"https://doi.org/10.1109/embc.2013.6609568","title":"Nucleotide sequence alignment using sparse coding and belief propagation","display_name":"Nucleotide sequence alignment using sparse coding and belief propagation","publication_year":2013,"publication_date":"2013-07-01","ids":{"openalex":"https://openalex.org/W2004356294","doi":"https://doi.org/10.1109/embc.2013.6609568","mag":"2004356294","pmid":"https://pubmed.ncbi.nlm.nih.gov/24109755","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3909563"},"language":"en","primary_location":{"id":"doi:10.1109/embc.2013.6609568","doi":"https://doi.org/10.1109/embc.2013.6609568","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6609568","pdf_url":null,"source":{"id":"https://openalex.org/S4363608786","display_name":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","issn_l":"2375-7477","issn":["2375-7477"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["doyens","jufo-1","ki-jl-1","medline","russia-white-list-3"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3909563","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000875289","display_name":"Aminmohammad Roozgard","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4392738079","display_name":"University of Oklahoma - Tulsa","ror":"https://ror.org/04g1a0w27","country_code":"US","type":"education","lineage":["https://openalex.org/I4392738079","https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aminmohammad Roozgard","raw_affiliation_strings":["School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","institution_ids":["https://openalex.org/I4392738079"]},{"raw_affiliation_string":"[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]","institution_ids":["https://openalex.org/I4392738079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071161476","display_name":"Nafise Barzigar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4392738079","display_name":"University of Oklahoma - Tulsa","ror":"https://ror.org/04g1a0w27","country_code":"US","type":"education","lineage":["https://openalex.org/I4392738079","https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nafise Barzigar","raw_affiliation_strings":["School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","institution_ids":["https://openalex.org/I4392738079"]},{"raw_affiliation_string":"[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]","institution_ids":["https://openalex.org/I4392738079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100375557","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0001-6420-983X","observed_orcids":["https://orcid.org/0000-0001-6420-983X","https://orcid.org/0009-0001-5036-5927","https://orcid.org/0009-0009-2665-7936","https://orcid.org/0000-0002-5708-9574"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["Division of Biomedical Informatics, University of California, San Diego, CA, USA","Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055458864","display_name":"Xiaoqian Jiang","orcid":"https://orcid.org/0000-0001-9933-2205","observed_orcids":["https://orcid.org/0000-0001-9933-2205","https://orcid.org/0009-0000-0712-2164","https://orcid.org/0009-0007-8281-4479"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoqian Jiang","raw_affiliation_strings":["Division of Biomedical Informatics, University of California, San Diego, CA, USA","Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084415954","display_name":"Lucila Ohno-machado A","orcid":"https://orcid.org/0000-0002-8005-7327","observed_orcids":["https://orcid.org/0000-0002-8005-7327"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucila Ohno-Machado","raw_affiliation_strings":["Division of Biomedical Informatics, University of California, San Diego, CA, USA","Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Div. of Biomed. Inf., Univ. of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017174019","display_name":"Samuel S. M. Cheng","orcid":"https://orcid.org/0000-0002-5439-1137","observed_orcids":["https://orcid.org/0000-0002-5439-1137"]},"institutions":[{"id":"https://openalex.org/I4392738079","display_name":"University of Oklahoma - Tulsa","ror":"https://ror.org/04g1a0w27","country_code":"US","type":"education","lineage":["https://openalex.org/I4392738079","https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel Cheng","raw_affiliation_strings":["School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Oklahoma University, Tulsa, OK, USA","institution_ids":["https://openalex.org/I4392738079"]},{"raw_affiliation_string":"[Sch. of Electr. & Comput. Eng., Oklahoma Univ., Tulsa, OK, USA]","institution_ids":["https://openalex.org/I4392738079"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.934,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.87760532,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"26","issue":null,"first_page":"588","last_page":"591"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8217999935150146,"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":0.8217999935150146,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.10909999907016754,"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/T11269","display_name":"Algorithms and Data Compression","score":0.06589999794960022,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-sequence-alignment","display_name":"DNA sequence alignment","score":0.9980000257492065},{"id":"https://openalex.org/keywords/sparse-coding","display_name":"sparse coding","score":0.9919999837875366},{"id":"https://openalex.org/keywords/belief-propagation","display_name":"belief propagation","score":1.0},{"id":"https://openalex.org/keywords/dna-sequence-comparison","display_name":"DNA sequence comparison","score":0.42399999499320984}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5228265523910522},{"id":"https://openalex.org/C84148353","wikidata":"https://www.wikidata.org/wiki/Q863908","display_name":"Nucleic acid sequence","level":3,"score":0.46718886494636536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46251004934310913},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.44203120470046997},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.43778687715530396},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.4159959554672241},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2598375678062439},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24813151359558105},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2364773154258728},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18916848301887512},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14610210061073303},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002877","descriptor_name":"Chromosomes, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/embc.2013.6609568","doi":"https://doi.org/10.1109/embc.2013.6609568","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc.2013.6609568","pdf_url":null,"source":{"id":"https://openalex.org/S4363608786","display_name":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","issn_l":"2375-7477","issn":["2375-7477"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["doyens","jufo-1","ki-jl-1","medline","russia-white-list-3"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:24109755","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24109755","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,"listed_in":[],"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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2896729","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3909563","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3909563","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3909563/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Conf Proc IEEE Eng Med Biol Soc","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:2896729","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3909563","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2566442100","display_name":"iDASH: Integrating Data for Analysis, Anonymization, and Sharing","funder_award_id":"U54HL108460","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3562438863","display_name":"San Diego Clinical and Translational Research Institute","funder_award_id":"UL1TR000100","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4437105622","display_name":"Protection of Records: Privacy (PReP) Technology for Medical Research","funder_award_id":"K99LM011392","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G5075328969","display_name":"SCANNER: SCALABLE NATIONAL NETWORK FOR EFFECTIVENESS RESEARCH","funder_award_id":"R01HS019913","funder_id":"https://openalex.org/F4320332177","funder_display_name":"Agency for Healthcare Research and Quality"},{"id":"https://openalex.org/G6447849018","display_name":null,"funder_award_id":"UL1TR00010003","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G7712304226","display_name":"Phenotype Discovery in NHLBI Genomic Studies (PhD)","funder_award_id":"UH2HL108785","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332177","display_name":"Agency for Healthcare Research and Quality","ror":"https://ror.org/03jmfdf59"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1527917680","https://openalex.org/W1980397590","https://openalex.org/W1981558336","https://openalex.org/W1983008863","https://openalex.org/W1985948328","https://openalex.org/W2011289056","https://openalex.org/W2043365501","https://openalex.org/W2072576946","https://openalex.org/W2090044421","https://openalex.org/W2090511351","https://openalex.org/W2090705041","https://openalex.org/W2097341408","https://openalex.org/W2098816661","https://openalex.org/W2100495679","https://openalex.org/W2103441770","https://openalex.org/W2106882534","https://openalex.org/W2107248520","https://openalex.org/W2112132489","https://openalex.org/W2123179625","https://openalex.org/W2132926880","https://openalex.org/W2137813581","https://openalex.org/W2160979406","https://openalex.org/W2165686834","https://openalex.org/W7095603021"],"related_works":["https://openalex.org/W1965229078","https://openalex.org/W3170129293","https://openalex.org/W2032682947","https://openalex.org/W2762331921","https://openalex.org/W1497946259","https://openalex.org/W2535667775","https://openalex.org/W2352762766","https://openalex.org/W4416237846","https://openalex.org/W2118767738","https://openalex.org/W1532450218"],"abstract_inverted_index":{"Advances":[0],"in":[1],"DNA":[2],"information":[3,24],"extraction":[4],"techniques":[5],"have":[6],"led":[7],"to":[8,51,74,90,103,111],"huge":[9],"sequenced":[10],"genomes":[11],"from":[12],"organisms":[13],"spanning":[14],"the":[15,30,53,56,61,98],"tree":[16],"of":[17,22,29,55,63,78],"life.":[18],"This":[19],"increasing":[20],"amount":[21],"genomic":[23],"requires":[25],"tools":[26],"for":[27],"comparison":[28],"nucleotide":[31,40,57,65,106],"sequences.":[32,58],"In":[33],"this":[34],"paper,":[35],"we":[36,70],"propose":[37],"a":[38,76],"novel":[39],"sequence":[41],"alignment":[42],"method":[43],"based":[44],"on":[45],"sparse":[46,72],"coding":[47,73],"and":[48,68,108,114],"belief":[49,85],"propagation":[50,86],"compare":[52],"similarity":[54],"We":[59],"used":[60],"neighbors":[62],"each":[64],"as":[66],"features,":[67],"then":[69],"employed":[71],"find":[75],"set":[77],"candidate":[79,92],"nucleotides.":[80,93],"To":[81],"select":[82],"optimum":[83],"matches,":[84],"was":[87],"subsequently":[88],"applied":[89],"these":[91],"Experimental":[94],"results":[95],"show":[96],"that":[97],"proposed":[99],"approach":[100],"is":[101,109],"able":[102],"robustly":[104],"align":[105],"sequences":[107],"competitive":[110],"SOAPaligner":[112],"[1]":[113],"BWA":[115],"[2].":[116]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}