{"id":"https://openalex.org/W4309667336","doi":"https://doi.org/10.1371/journal.pcbi.1010665","title":"HELIOS: High-speed sequence alignment in optics","display_name":"HELIOS: High-speed sequence alignment in optics","publication_year":2022,"publication_date":"2022-11-21","ids":{"openalex":"https://openalex.org/W4309667336","doi":"https://doi.org/10.1371/journal.pcbi.1010665","pmid":"https://pubmed.ncbi.nlm.nih.gov/36409684"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010665","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010665","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010665&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010665&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086844964","display_name":"Ehsan Maleki","orcid":"https://orcid.org/0000-0002-1613-3508"},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Ehsan Maleki","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran"],"raw_orcid":"https://orcid.org/0000-0002-1613-3508","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I133529467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083830539","display_name":"Saeedeh Akbari Rokn Abadi","orcid":"https://orcid.org/0000-0001-7564-4204"},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Saeedeh Akbari Rokn Abadi","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran"],"raw_orcid":"https://orcid.org/0000-0001-7564-4204","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I133529467"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051811846","display_name":"Somayyeh Koohi","orcid":"https://orcid.org/0000-0002-3105-2511"},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Somayyeh Koohi","raw_affiliation_strings":["Department of Computer Engineering, Sharif University of Technology, Tehran, Iran"],"raw_orcid":"https://orcid.org/0000-0002-3105-2511","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Sharif University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I133529467"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051811846"],"corresponding_institution_ids":["https://openalex.org/I133529467"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.2604,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.53103283,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"18","issue":"11","first_page":"e1010665","last_page":"e1010665"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9771999716758728,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9739999771118164,"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":0.7414963841438293},{"id":"https://openalex.org/keywords/optical-engineering","display_name":"Optical engineering","score":0.5221564769744873},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.45112860202789307},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4206226170063019},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3571380376815796},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.22200411558151245},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.20065847039222717},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1162138283252716}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7414963841438293},{"id":"https://openalex.org/C151857401","wikidata":"https://www.wikidata.org/wiki/Q640621","display_name":"Optical engineering","level":2,"score":0.5221564769744873},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.45112860202789307},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4206226170063019},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3571380376815796},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.22200411558151245},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.20065847039222717},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1162138283252716}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010665","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010665","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010665&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36409684","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36409684","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:888c6e5e66cb42709a7f1836aa49d87b","is_oa":true,"landing_page_url":"https://doaj.org/article/888c6e5e66cb42709a7f1836aa49d87b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 11, p e1010665 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9678324","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9678324","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010665","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010665","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010665&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309667336.pdf","grobid_xml":"https://content.openalex.org/works/W4309667336.grobid-xml"},"referenced_works_count":89,"referenced_works":["https://openalex.org/W137864573","https://openalex.org/W317936557","https://openalex.org/W364444290","https://openalex.org/W589188476","https://openalex.org/W657798510","https://openalex.org/W1494075612","https://openalex.org/W1544691147","https://openalex.org/W1594728070","https://openalex.org/W1689369637","https://openalex.org/W1786896381","https://openalex.org/W1964145490","https://openalex.org/W1964733653","https://openalex.org/W1976731339","https://openalex.org/W1982597966","https://openalex.org/W1991330646","https://openalex.org/W1996112765","https://openalex.org/W2015377140","https://openalex.org/W2032764796","https://openalex.org/W2041384744","https://openalex.org/W2042316630","https://openalex.org/W2044250973","https://openalex.org/W2047458684","https://openalex.org/W2054557660","https://openalex.org/W2061871196","https://openalex.org/W2070050178","https://openalex.org/W2075436975","https://openalex.org/W2095439426","https://openalex.org/W2098023402","https://openalex.org/W2098235894","https://openalex.org/W2103441770","https://openalex.org/W2108187446","https://openalex.org/W2110145781","https://openalex.org/W2132926880","https://openalex.org/W2137759177","https://openalex.org/W2144362290","https://openalex.org/W2149248356","https://openalex.org/W2170551349","https://openalex.org/W2172191413","https://openalex.org/W2178845774","https://openalex.org/W2239421650","https://openalex.org/W2247766769","https://openalex.org/W2297084330","https://openalex.org/W2306772473","https://openalex.org/W2342363273","https://openalex.org/W2479194908","https://openalex.org/W2492325248","https://openalex.org/W2515732101","https://openalex.org/W2560077904","https://openalex.org/W2581735288","https://openalex.org/W2596261101","https://openalex.org/W2604585222","https://openalex.org/W2605168792","https://openalex.org/W2678953459","https://openalex.org/W2730968108","https://openalex.org/W2749116339","https://openalex.org/W2750791471","https://openalex.org/W2784788330","https://openalex.org/W2795392197","https://openalex.org/W2811248537","https://openalex.org/W2888832887","https://openalex.org/W2891819987","https://openalex.org/W2898461763","https://openalex.org/W2902846450","https://openalex.org/W2916121437","https://openalex.org/W2944021648","https://openalex.org/W2952870794","https://openalex.org/W2953263404","https://openalex.org/W2963963068","https://openalex.org/W2965789171","https://openalex.org/W2967236067","https://openalex.org/W2970789359","https://openalex.org/W2982461819","https://openalex.org/W2990912493","https://openalex.org/W3006645647","https://openalex.org/W3046771501","https://openalex.org/W3081014042","https://openalex.org/W3082507982","https://openalex.org/W3096245870","https://openalex.org/W3124086993","https://openalex.org/W3134980377","https://openalex.org/W3135189979","https://openalex.org/W3200404547","https://openalex.org/W4223473937","https://openalex.org/W4231434847","https://openalex.org/W4236900451","https://openalex.org/W4299908858","https://openalex.org/W4301506839","https://openalex.org/W4386771353","https://openalex.org/W6644266896"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810"],"abstract_inverted_index":{"In":[0],"response":[1],"to":[2,34,68,155,169,224],"the":[3,12,86,89,111,116,142,173,202,209,225,232],"imperfections":[4],"of":[5,106,115,150,157,186,211],"current":[6],"sequence":[7],"alignment":[8,149],"methods,":[9],"originated":[10],"from":[11,39],"inherent":[13],"serialism":[14],"within":[15,81],"their":[16,35,40],"corresponding":[17],"electrical":[18,180,226],"systems,":[19],"a":[20,47,146],"few":[21],"optical":[22,91,107,124,175,182,199,228,236],"approaches":[23],"for":[24,52,240],"biological":[25,83],"data":[26],"comparison":[27],"have":[28],"been":[29],"proposed":[30],"recently.":[31],"However,":[32],"due":[33],"low":[36],"performance,":[37],"raised":[38],"inefficient":[41],"coding":[42,205],"scheme,":[43],"this":[44],"paper":[45],"presents":[46],"novel":[48],"all-optical":[49],"high-throughput":[50],"method":[51,63,118,144,197,234],"aligning":[53],"DNA,":[54],"RNA,":[55],"and":[56,76,96,104,113,123,130,166,181,189,198,214,220,227,235],"protein":[57],"sequences,":[58,152],"named":[59],"HELIOS.":[60],"The":[61,137],"HELIOS":[62,90,117,143,174,233],"employs":[64],"highly":[65,153,195,207,238],"sophisticated":[66,196],"operations":[67],"locate":[69],"character":[70],"matches,":[71],"single":[72,77],"or":[73,78],"multiple":[74,79],"mutations,":[75],"indels":[80],"various":[82],"sequences.":[84],"On":[85],"other":[87],"hand,":[88],"architecture":[92,176,237],"exploits":[93],"high-speed":[94],"processing":[95,187],"operational":[97],"parallelism":[98],"in":[99,184],"optics,":[100],"by":[101],"adopting":[102],"wavelength":[103],"polarization":[105],"beams.":[108],"For":[109],"evaluation,":[110],"functionality":[112],"accuracy":[114,138],"are":[119,132],"approved":[120],"through":[121,134],"behavioral":[122],"simulation":[125],"studies,":[126],"while":[127],"its":[128,194],"complexity":[129],"performance":[131,171],"estimated":[133],"analytical":[135],"computation.":[136],"evaluations":[139],"indicate":[140],"that":[141],"achieves":[145],"precise":[147],"pairwise":[148],"two":[151],"similar":[154],"those":[156],"Smith-Waterman,":[158],"Needleman-Wunsch,":[159],"BLAST,":[160],"MUSCLE,":[161],"ClustalW,":[162],"Clustal\u03a9,":[163],"T-Coffee,":[164],"Kalign,":[165],"MAFFT.":[167],"According":[168],"our":[170],"evaluations,":[172],"outperforms":[177],"all":[178],"alternative":[179],"algorithms":[183],"terms":[185],"time":[188,219],"memory":[190],"requirement,":[191],"relying":[192],"on":[193],"architecture.":[200],"Moreover,":[201],"employed":[203],"compact":[204],"scheme":[206],"escalates":[208],"number":[210],"input":[212],"characters,":[213],"hence,":[215],"it":[216],"offers":[217],"reduced":[218],"space":[221],"complexities,":[222],"compared":[223],"alternatives.":[229],"It":[230],"makes":[231],"applicable":[239],"biomedical":[241],"applications.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
