{"id":"https://openalex.org/W7166704285","doi":"https://doi.org/10.1145/3774895.3815153","title":"In-depth data movement characterization of DNA read mapping algorithms","display_name":"In-depth data movement characterization of DNA read mapping algorithms","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7166704285","doi":"https://doi.org/10.1145/3774895.3815153"},"language":"en","primary_location":{"id":"doi:10.1145/3774895.3815153","doi":"https://doi.org/10.1145/3774895.3815153","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3774895.3815153","pdf_url":null,"source":{"id":"https://openalex.org/S4306419857","display_name":"International Conference on Supercomputing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM International Conference on Supercomputing - Workshops","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1145/3774895.3815153","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077634611","display_name":"Berkan \u015eahin","orcid":"https://orcid.org/0000-0003-4699-3418","observed_orcids":["https://orcid.org/0000-0003-4699-3418","https://orcid.org/0009-0002-5151-2973"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Berkan \u015eahin","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye"],"raw_orcid":"https://orcid.org/0009-0002-5151-2973","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005039914","display_name":"Ecem \u0130lg\u00fcn","orcid":"https://orcid.org/0000-0001-6496-6224","observed_orcids":["https://orcid.org/0000-0001-6496-6224"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ecem \u0130lg\u00fcn","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye"],"raw_orcid":"https://orcid.org/0000-0001-6496-6224","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119381425","display_name":"Klea Zambaku","orcid":"https://orcid.org/0000-0001-7951-7720","observed_orcids":["https://orcid.org/0000-0001-7951-7720"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Klea Zambaku","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye"],"raw_orcid":"https://orcid.org/0000-0001-7951-7720","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074885623","display_name":"Can Alkan","orcid":"https://orcid.org/0000-0002-5443-0706","observed_orcids":["https://orcid.org/0000-0002-5443-0706"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Can Alkan","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye"],"raw_orcid":"https://orcid.org/0000-0002-5443-0706","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara, ANKARA, Turkiye","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.42160052,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"82","last_page":"83"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.975600004196167,"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"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.975600004196167,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.006099999882280827,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.005400000140070915,"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/workload-analysis","display_name":"workload characterization","score":0.8190000057220459},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"hardware acceleration","score":0.9620000123977661},{"id":"https://openalex.org/keywords/sequencing-technologies","display_name":"sequencing technologies","score":0.8510000109672546},{"id":"https://openalex.org/keywords/performance-optimization","display_name":"performance optimization","score":0.46700000762939453}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6908000111579895},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5139999985694885},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.5037000179290771},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4952999949455261},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.44339999556541443},{"id":"https://openalex.org/C2780226923","wikidata":"https://www.wikidata.org/wiki/Q929848","display_name":"Movement (music)","level":2,"score":0.37689998745918274},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.36320000886917114},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3614000082015991},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.31380000710487366},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.2930999994277954},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.2874999940395355},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.27889999747276306},{"id":"https://openalex.org/C106516650","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm design","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C2987595161","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Optimization algorithm","level":2,"score":0.2732999920845032},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2718999981880188},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.25200000405311584}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3774895.3815153","doi":"https://doi.org/10.1145/3774895.3815153","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3774895.3815153","pdf_url":null,"source":{"id":"https://openalex.org/S4306419857","display_name":"International Conference on Supercomputing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM International Conference on Supercomputing - Workshops","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3774895.3815153","doi":"https://doi.org/10.1145/3774895.3815153","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3774895.3815153","pdf_url":null,"source":{"id":"https://openalex.org/S4306419857","display_name":"International Conference on Supercomputing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 40th ACM International Conference on Supercomputing - Workshops","raw_type":"proceedings-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G8860033530","display_name":"Processing-in-memory architectures and programming libraries for bioinformatics algorithms","funder_award_id":"101047160","funder_id":"https://openalex.org/F4320338448","funder_display_name":"HORIZON EUROPE European Innovation Council"}],"funders":[{"id":"https://openalex.org/F4320338448","display_name":"HORIZON EUROPE European Innovation Council","ror":"https://ror.org/05cx8cy07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2170551349","https://openalex.org/W2789843538","https://openalex.org/W2950121474","https://openalex.org/W3102863871","https://openalex.org/W3177485564","https://openalex.org/W3196818429"],"related_works":["https://openalex.org/W3046494740","https://openalex.org/W7042477067","https://openalex.org/W7214159215","https://openalex.org/W7056134548","https://openalex.org/W7165114180","https://openalex.org/W2133212095","https://openalex.org/W4404370287","https://openalex.org/W3110777056","https://openalex.org/W2102231818","https://openalex.org/W7095842900"],"abstract_inverted_index":{"We":[0],"present":[1],"an":[2],"extensive":[3],"workload":[4],"characterization":[5],"of":[6],"leading":[7],"read-mapping":[8],"algorithms":[9],"across":[10],"diverse":[11],"sequencing":[12],"technologies":[13],"to":[14],"understand":[15],"hardware":[16],"acceleration":[17],"and":[18,25],"optimization":[19],"opportunities,":[20],"using":[21],"Intel":[22],"VTune":[23],"profiler":[24],"DAMOV-SIM":[26],"for":[27],"specific":[28],"memory-bound":[29],"functions.":[30]},"counts_by_year":[],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2026-07-01T00:00:00"}