{"id":"https://openalex.org/W2766890412","doi":"https://doi.org/10.1186/s12864-018-4460-0","title":"GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies","display_name":"GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies","publication_year":2018,"publication_date":"2018-05-01","ids":{"openalex":"https://openalex.org/W2766890412","doi":"https://doi.org/10.1186/s12864-018-4460-0","mag":"2766890412","pmid":"https://pubmed.ncbi.nlm.nih.gov/29764378"},"language":"en","primary_location":{"id":"doi:10.1186/s12864-018-4460-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12864-018-4460-0","pdf_url":"https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4460-0","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4460-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jeremie S. Kim","orcid":null},"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"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["CH","US"],"is_corresponding":true,"raw_author_name":"Jeremie S. Kim","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland. jeremiekim123@gmail.com","Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. jeremiekim123@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland. jeremiekim123@gmail.com","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. jeremiekim123@gmail.com","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Damla Senol Cali","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Damla Senol Cali","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hongyi Xin","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyi Xin","raw_affiliation_strings":["Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Donghyuk Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donghyuk Lee","raw_affiliation_strings":["NVIDIA Research, Austin, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NVIDIA Research, Austin, TX, USA","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Saugata Ghose","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saugata Ghose","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mohammed Alser","orcid":null},"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":"Mohammed Alser","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hasan Hassan","orcid":null},"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":"Hasan Hassan","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Oguz Ergin","orcid":null},"institutions":[{"id":"https://openalex.org/I13236232","display_name":"TOBB University of Economics and Technology","ror":"https://ror.org/03ewx7v96","country_code":"TR","type":"education","lineage":["https://openalex.org/I13236232"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Oguz Ergin","raw_affiliation_strings":["Department of Computer Engineering, TOBB University of Economics and Technology, Sogutozu, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, TOBB University of Economics and Technology, Sogutozu, Ankara, Turkey","institution_ids":["https://openalex.org/I13236232"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Can Alkan","orcid":null},"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, Bilkent, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Bilkent, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":null,"display_name":"Onur Mutlu","orcid":null},"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"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Onur Mutlu","raw_affiliation_strings":["Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland. omutlu@gmail.com","Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. omutlu@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Z\u00fcrich, Z\u00fcrich, CH, Switzerland. omutlu@gmail.com","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. omutlu@gmail.com","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I74973139"],"apc_list":{"value":1570,"currency":"GBP","value_usd":1925},"apc_paid":{"value":1570,"currency":"GBP","value_usd":1925},"fwci":4.6398,"has_fulltext":true,"cited_by_count":127,"citation_normalized_percentile":{"value":0.95851302,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"19","issue":"S2","first_page":"89","last_page":"89"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8027999997138977,"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":0.8027999997138977,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.19339999556541443,"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/T12029","display_name":"DNA and Biological Computing","score":0.14000000059604645,"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/bottleneck","display_name":"Bottleneck","score":0.892300009727478},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.7035999894142151},{"id":"https://openalex.org/keywords/bandwidth","display_name":"Bandwidth (computing)","score":0.546999990940094},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.45840001106262207},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.39750000834465027},{"id":"https://openalex.org/keywords/emerging-technologies","display_name":"Emerging technologies","score":0.3855000138282776}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.892300009727478},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.7035999894142151},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6837999820709229},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"score":0.546999990940094},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.45840001106262207},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.39750000834465027},{"id":"https://openalex.org/C207267971","wikidata":"https://www.wikidata.org/wiki/Q120208","display_name":"Emerging technologies","level":2,"score":0.3855000138282776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3612000048160553},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.35019999742507935},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3116999864578247},{"id":"https://openalex.org/C188045654","wikidata":"https://www.wikidata.org/wiki/Q17148339","display_name":"Memory bandwidth","level":2,"score":0.3003000020980835},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2816999852657318},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.27489998936653137},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2655999958515167},{"id":"https://openalex.org/C104267543","wikidata":"https://www.wikidata.org/wiki/Q208163","display_name":"Signal processing","level":3,"score":0.259799987077713},{"id":"https://openalex.org/C82687282","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Auxiliary memory","level":2,"score":0.25529998540878296},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25119999051094055},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.25110000371932983}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12864-018-4460-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12864-018-4460-0","pdf_url":"https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4460-0","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},{"id":"pmid:29764378","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29764378","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":"BMC genomics","raw_type":null},{"id":"pmh:oai:arXiv.org:1711.01177","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1711.01177","pdf_url":"https://arxiv.org/pdf/1711.01177","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:0c114fee79d948bbbce02af311133723","is_oa":false,"landing_page_url":"https://doaj.org/article/0c114fee79d948bbbce02af311133723","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Genomics, Vol 19, Iss S2, Pp 23-40 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4877578","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5954284","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,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5954284","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5954284","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":"BMC Genomics","raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/50359","is_oa":true,"landing_page_url":"http://hdl.handle.net/11693/50359","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Genomics","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12864-018-4460-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12864-018-4460-0","pdf_url":"https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4460-0","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4539561046","display_name":null,"funder_award_id":"HG006004","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306087","display_name":"Semiconductor Research Corporation","ror":"https://ror.org/047z4n946"},{"id":"https://openalex.org/F4320316785","display_name":"VMware","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332195","display_name":"Samsung","ror":"https://ror.org/04w3jy968"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2766890412.pdf","grobid_xml":"https://content.openalex.org/works/W2766890412.grobid-xml"},"referenced_works_count":78,"referenced_works":["https://openalex.org/W240706956","https://openalex.org/W755906292","https://openalex.org/W1534435001","https://openalex.org/W1828154403","https://openalex.org/W1897953244","https://openalex.org/W1970426108","https://openalex.org/W1974307224","https://openalex.org/W1975237352","https://openalex.org/W1985681048","https://openalex.org/W1992487929","https://openalex.org/W2009475335","https://openalex.org/W2011652244","https://openalex.org/W2013435193","https://openalex.org/W2015831381","https://openalex.org/W2024818089","https://openalex.org/W2030407693","https://openalex.org/W2034798008","https://openalex.org/W2034861439","https://openalex.org/W2045431893","https://openalex.org/W2062949766","https://openalex.org/W2074079408","https://openalex.org/W2091193685","https://openalex.org/W2096791516","https://openalex.org/W2103184242","https://openalex.org/W2105194472","https://openalex.org/W2112893969","https://openalex.org/W2117683095","https://openalex.org/W2119305840","https://openalex.org/W2121716038","https://openalex.org/W2129991978","https://openalex.org/W2132269953","https://openalex.org/W2135965542","https://openalex.org/W2139747296","https://openalex.org/W2140673900","https://openalex.org/W2145186114","https://openalex.org/W2146496959","https://openalex.org/W2153527981","https://openalex.org/W2157474903","https://openalex.org/W2158319074","https://openalex.org/W2158620667","https://openalex.org/W2161129061","https://openalex.org/W2168303240","https://openalex.org/W2168622264","https://openalex.org/W2170257519","https://openalex.org/W2218392081","https://openalex.org/W2233523872","https://openalex.org/W2293640271","https://openalex.org/W2331766458","https://openalex.org/W2332254524","https://openalex.org/W2335240678","https://openalex.org/W2414912620","https://openalex.org/W2513721464","https://openalex.org/W2514454343","https://openalex.org/W2517869808","https://openalex.org/W2545376626","https://openalex.org/W2556232283","https://openalex.org/W2556370608","https://openalex.org/W2560228154","https://openalex.org/W2607477256","https://openalex.org/W2612835180","https://openalex.org/W2623880136","https://openalex.org/W2736517506","https://openalex.org/W2766489088","https://openalex.org/W2766890412","https://openalex.org/W2998041822","https://openalex.org/W3005783121","https://openalex.org/W3139689176","https://openalex.org/W3146736181","https://openalex.org/W3147501999","https://openalex.org/W4233386150","https://openalex.org/W4234059142","https://openalex.org/W4235631643","https://openalex.org/W4236382111","https://openalex.org/W4243233609","https://openalex.org/W4244600229","https://openalex.org/W4245276998","https://openalex.org/W4245654632","https://openalex.org/W4247053599"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Seed":[1],"location":[2,90,110,137,238,261,281],"filtering":[3,138,214,239],"is":[4,124,277],"critical":[5],"in":[6,259],"DNA":[7,15],"read":[8,36,68,188,222,231,274,289],"mapping,":[9],"a":[10,20,25,75,104,134,151,170,199,229,272,278],"process":[11],"where":[12],"billions":[13],"of":[14,32,58,85,173,176,204,213,225,251,271,309],"fragments":[16],"(reads)":[17],"sampled":[18],"from":[19],"donor":[21],"are":[22],"mapped":[23],"onto":[24],"reference":[26,54,72,178],"genome":[27],"to":[28,81,119,142,158,186,228,253,287,301],"identify":[29,187],"genomic":[30],"variants":[31],"the":[33,59,83,86,177,209,234,248,255,269],"donor.":[34],"State-of-the-art":[35],"mappers":[37],"1)":[38,168,207],"quickly":[39,163],"generate":[40],"possible":[41],"mapping":[42,60],"locations":[43,99,117,166],"for":[44,198,298],"seeds":[45],"(i.e.,":[46,78],"smaller":[47],"segments)":[48],"within":[49,150,190],"each":[50,57,67,191],"read,":[51],"2)":[52,181,218],"extract":[53],"sequences":[55,73],"at":[56],"locations,":[61],"and":[62,69,180,217,312],"3)":[63],"check":[64],"similarity":[65],"between":[66],"its":[70],"associated":[71],"with":[74],"computationally-expensive":[76],"algorithm":[77],"sequence":[79,200],"alignment)":[80],"determine":[82],"origin":[84],"read.":[87],"A":[88],"seed":[89,98,109,136,165,237,260,280],"filter":[91,111,282],"comes":[92],"into":[93],"play":[94],"before":[95],"alignment,":[96],"discarding":[97],"that":[100,122,147,197,265,283,293,306],"alignment":[101,120,201],"would":[102,112],"deem":[103],"poor":[105,115],"match.":[106],"The":[107],"ideal":[108],"discard":[113],"all":[114],"match":[116],"prior":[118],"such":[121,316],"there":[123],"no":[125],"wasted":[126],"computation":[127,149],"on":[128],"unnecessary":[129],"alignments.":[130],"RESULTS:":[131],"We":[132,263,291],"propose":[133],"novel":[135],"algorithm,":[139],"GRIM-Filter,":[140],"optimized":[141],"exploit":[143],"3D-stacked":[144,244,320],"memory":[145,156,256,321],"systems":[146],"integrate":[148],"logic":[152],"layer":[153],"stacked":[154],"under":[155],"layers,":[157],"perform":[159],"processing-in-memory":[160,318],"(PIM).":[161],"GRIM-Filter":[162,206,242,266,276],"filters":[164],"by":[167,215],"introducing":[169],"new":[171,299,313],"representation":[172],"coarse-grained":[174,192],"segments":[175],"genome,":[179],"using":[182,319],"massively-parallel":[183],"in-memory":[184],"operations":[185],"presence":[189],"segment.":[193],"Our":[194],"evaluations":[195],"show":[196,264],"error":[202],"tolerance":[203],"0.05,":[205],"reduces":[208],"false":[210],"negative":[211],"rate":[212],"5.59x-6.41x,":[216],"provides":[219],"an":[220],"end-to-end":[221],"mapper":[223,232],"speedup":[224],"1.81x-3.65x,":[226],"compared":[227],"state-of-the-art":[230,273],"employing":[233],"best":[235],"previous":[236],"algorithm.":[240],"CONCLUSION:":[241],"exploits":[243],"memory,":[245],"which":[246],"enables":[247],"efficient":[249],"use":[250],"processing-in-memory,":[252],"overcome":[254],"bandwidth":[257],"bottleneck":[258],"filtering.":[262],"significantly":[267],"improves":[268],"performance":[270],"mapper.":[275,290],"universal":[279],"can":[284],"be":[285],"applied":[286],"any":[288],"hope":[292],"our":[294],"results":[295],"provide":[296],"inspiration":[297],"works":[300],"design":[302],"other":[303],"bioinformatics":[304],"algorithms":[305],"take":[307],"advantage":[308],"emerging":[310],"technologies":[311],"processing":[314],"paradigms,":[315],"as":[317],"devices.":[322]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":25},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":6}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2017-11-10T00:00:00"}
