{"id":"https://openalex.org/W4361017256","doi":"https://doi.org/10.1093/bioinformatics/btad155","title":"A framework for high-throughput sequence alignment using real processing-in-memory systems","display_name":"A framework for high-throughput sequence alignment using real processing-in-memory systems","publication_year":2023,"publication_date":"2023-03-27","ids":{"openalex":"https://openalex.org/W4361017256","doi":"https://doi.org/10.1093/bioinformatics/btad155","pmid":"https://pubmed.ncbi.nlm.nih.gov/36971586"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad155","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad155/49650358/btad155.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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad155/49650358/btad155.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077981231","display_name":"Safaa Diab","orcid":"https://orcid.org/0000-0002-6504-3461"},"institutions":[{"id":"https://openalex.org/I98635879","display_name":"American University of Beirut","ror":"https://ror.org/04pznsd21","country_code":"LB","type":"education","lineage":["https://openalex.org/I98635879"]}],"countries":["LB"],"is_corresponding":true,"raw_author_name":"Safaa Diab","raw_affiliation_strings":["Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon","institution_ids":["https://openalex.org/I98635879"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049680239","display_name":"Amir Nassereldine","orcid":"https://orcid.org/0009-0000-0173-5410"},"institutions":[{"id":"https://openalex.org/I98635879","display_name":"American University of Beirut","ror":"https://ror.org/04pznsd21","country_code":"LB","type":"education","lineage":["https://openalex.org/I98635879"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Amir Nassereldine","raw_affiliation_strings":["Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon","institution_ids":["https://openalex.org/I98635879"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081055664","display_name":"Mohammed Alser","orcid":"https://orcid.org/0000-0002-6117-3701"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mohammed Alser","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044416322","display_name":"Juan G\u00f3mez-Luna","orcid":"https://orcid.org/0000-0002-6514-1571"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Juan G\u00f3mez Luna","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050695684","display_name":"Onur Mutlu","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Onur Mutlu","raw_affiliation_strings":["Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering, ETH Z\u00fcrich , Gloriastrasse 35 , Z\u00fcrich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076404852","display_name":"Izzat El Hajj","orcid":"https://orcid.org/0000-0003-3356-6898"},"institutions":[{"id":"https://openalex.org/I98635879","display_name":"American University of Beirut","ror":"https://ror.org/04pznsd21","country_code":"LB","type":"education","lineage":["https://openalex.org/I98635879"]}],"countries":["LB"],"is_corresponding":true,"raw_author_name":"Izzat El Hajj","raw_affiliation_strings":["Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, American University of Beirut , Riad El-Solh , Beirut 1107 2020, Lebanon","institution_ids":["https://openalex.org/I98635879"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5050695684","https://openalex.org/A5076404852","https://openalex.org/A5077981231"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I98635879"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.9382,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.96819468,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"39","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9926999807357788,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9675999879837036,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.7647205591201782},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.763646125793457},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5720736384391785},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5373603105545044},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47839581966400146},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.38427650928497314},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3642805218696594},{"id":"https://openalex.org/keywords/real-time-computing","display_name":"Real-time computing","score":0.3522135317325592},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3393233120441437},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23726585507392883},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06850963830947876}],"concepts":[{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.7647205591201782},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.763646125793457},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5720736384391785},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5373603105545044},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47839581966400146},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.38427650928497314},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3642805218696594},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3522135317325592},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3393233120441437},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23726585507392883},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06850963830947876},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad155","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad155/49650358/btad155.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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36971586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36971586","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:10159653","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10159653","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10159653/pdf/btad155.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad155","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad155","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad155/49650358/btad155.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/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2342797219","display_name":null,"funder_award_id":"101047160","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4051374864","display_name":null,"funder_award_id":"101047","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4338567859","display_name":null,"funder_award_id":"104107","funder_id":"https://openalex.org/F4320309999","funder_display_name":"American University of Beirut"},{"id":"https://openalex.org/G490593687","display_name":null,"funder_award_id":"Intel","funder_id":"https://openalex.org/F4320306087","funder_display_name":"Semiconductor Research Corporation"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320306087","display_name":"Semiconductor Research Corporation","ror":"https://ror.org/047z4n946"},{"id":"https://openalex.org/F4320309999","display_name":"American University of Beirut","ror":"https://ror.org/04pznsd21"},{"id":"https://openalex.org/F4320316785","display_name":"VMware","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4361017256.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1828154403","https://openalex.org/W1981409766","https://openalex.org/W1998048394","https://openalex.org/W2001496424","https://openalex.org/W2025516544","https://openalex.org/W2045821558","https://openalex.org/W2055666215","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2092138236","https://openalex.org/W2108215151","https://openalex.org/W2121716038","https://openalex.org/W2128524432","https://openalex.org/W2260037449","https://openalex.org/W2560228154","https://openalex.org/W2789843538","https://openalex.org/W2790091177","https://openalex.org/W2921796727","https://openalex.org/W2923143097","https://openalex.org/W2953174564","https://openalex.org/W3046494740","https://openalex.org/W3086678357","https://openalex.org/W3086684206","https://openalex.org/W3101704407","https://openalex.org/W3103269557","https://openalex.org/W3111187134","https://openalex.org/W3193844559","https://openalex.org/W4214546858","https://openalex.org/W4214734582","https://openalex.org/W4254502766","https://openalex.org/W4285121610","https://openalex.org/W4292240213","https://openalex.org/W4319334382","https://openalex.org/W4388801332","https://openalex.org/W4394655901","https://openalex.org/W6638564077","https://openalex.org/W6740813679","https://openalex.org/W6783123973","https://openalex.org/W6783374065","https://openalex.org/W6786164786"],"related_works":["https://openalex.org/W2136583354","https://openalex.org/W2111238207","https://openalex.org/W2760721665","https://openalex.org/W330130819","https://openalex.org/W2288610023","https://openalex.org/W2112044895","https://openalex.org/W3121416282","https://openalex.org/W2281389338","https://openalex.org/W2037453743","https://openalex.org/W4312222450"],"abstract_inverted_index":{"Our":[0],"code":[1],"is":[2],"available":[3],"at":[4],"https://github.com/safaad/aim.":[5]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":10}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
