{"id":"https://openalex.org/W1922070671","doi":"https://doi.org/10.1093/bib/bbv073","title":"Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond","display_name":"Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond","publication_year":2015,"publication_date":"2015-09-01","ids":{"openalex":"https://openalex.org/W1922070671","doi":"https://doi.org/10.1093/bib/bbv073","mag":"1922070671","pmid":"https://pubmed.ncbi.nlm.nih.gov/26330577"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv073","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/713/6686308/bbv073.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/4/713/6686308/bbv073.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100708048","display_name":"Sungmin Lee","orcid":"https://orcid.org/0000-0002-4901-5794"},"institutions":[{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sungmin Lee","raw_affiliation_strings":["Sungmin Lee is a PhD Candidate at Department of Electrical and Computer Engineering, Seoul National University, Korea. His research areas include bioinformatics algorithms and biomedical imaging"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sungmin Lee is a PhD Candidate at Department of Electrical and Computer Engineering, Seoul National University, Korea. His research areas include bioinformatics algorithms and biomedical imaging","institution_ids":["https://openalex.org/I4210157667"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101764096","display_name":"Hyeyoung Min","orcid":"https://orcid.org/0000-0002-7964-2924"},"institutions":[{"id":"https://openalex.org/I4210123907","display_name":"National University College","ror":"https://ror.org/02hs8e066","country_code":"PR","type":"education","lineage":["https://openalex.org/I4210123907"]}],"countries":["PR"],"is_corresponding":false,"raw_author_name":"Hyeyoung Min","raw_affiliation_strings":["Hyeyoung Min is an Associate professor at College of Pharmacy, Chung-Ang University, Seoul, Korea. She earned her PhD in Cellular and Molecular Pathology from University of California, Los Angeles, USA and MS in Statistics from Stanford University. Her research interests include bioinformatics, and RNA biology, especially small noncoding RNA such as microRNAs and competitive endogenous RNAs"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hyeyoung Min is an Associate professor at College of Pharmacy, Chung-Ang University, Seoul, Korea. She earned her PhD in Cellular and Molecular Pathology from University of California, Los Angeles, USA and MS in Statistics from Stanford University. Her research interests include bioinformatics, and RNA biology, especially small noncoding RNA such as microRNAs and competitive endogenous RNAs","institution_ids":["https://openalex.org/I4210123907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086877012","display_name":"Sungroh Yoon","orcid":"https://orcid.org/0000-0002-2367-197X"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN","KR"],"is_corresponding":false,"raw_author_name":"Sungroh Yoon","raw_affiliation_strings":["Sungroh Yoon is an Associate professor at Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea. He received his PhD and postdoctoral training from Stanford University, Stanford, USA. His research interests include RNA bioinformatics, machine learning in bioinformatics and high-performance bioinformatics","Seoul National Univ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sungroh Yoon is an Associate professor at Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea. He received his PhD and postdoctoral training from Stanford University, Stanford, USA. His research interests include RNA bioinformatics, machine learning in bioinformatics and high-performance bioinformatics","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Seoul National Univ","institution_ids":["https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.1345,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.89128158,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"17","issue":"4","first_page":"713","last_page":"727"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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":0.9818999767303467,"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":0.9722999930381775,"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":0.8062677383422852},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6663680672645569},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.6286340951919556},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5226445198059082},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.4233718812465668},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33926963806152344},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3303806781768799},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3088398575782776},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12560555338859558}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8062677383422852},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6663680672645569},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.6286340951919556},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5226445198059082},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.4233718812465668},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33926963806152344},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3303806781768799},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3088398575782776},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12560555338859558},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbv073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv073","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/713/6686308/bbv073.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26330577","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26330577","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bib:17/4/713","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/4/713","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv073","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv073","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/713/6686308/bbv073.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1922070671.pdf"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W301287984","https://openalex.org/W1555915743","https://openalex.org/W1867995571","https://openalex.org/W1957591766","https://openalex.org/W1966822396","https://openalex.org/W1981029608","https://openalex.org/W1995541084","https://openalex.org/W2000875411","https://openalex.org/W2021341670","https://openalex.org/W2022642059","https://openalex.org/W2037953066","https://openalex.org/W2048466306","https://openalex.org/W2053841991","https://openalex.org/W2055030646","https://openalex.org/W2055043387","https://openalex.org/W2089083615","https://openalex.org/W2097065948","https://openalex.org/W2099173493","https://openalex.org/W2101731563","https://openalex.org/W2103441770","https://openalex.org/W2106308757","https://openalex.org/W2106882534","https://openalex.org/W2108234281","https://openalex.org/W2109701112","https://openalex.org/W2112113834","https://openalex.org/W2112491476","https://openalex.org/W2118526609","https://openalex.org/W2119180969","https://openalex.org/W2119745866","https://openalex.org/W2127768708","https://openalex.org/W2134533400","https://openalex.org/W2136145671","https://openalex.org/W2141249441","https://openalex.org/W2141408320","https://openalex.org/W2145091349","https://openalex.org/W2151370125","https://openalex.org/W2153562609","https://openalex.org/W2154431984","https://openalex.org/W2155871507","https://openalex.org/W2159081928","https://openalex.org/W2168104108","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2173213060","https://openalex.org/W2772934464","https://openalex.org/W2885727518","https://openalex.org/W4211208250","https://openalex.org/W4235064662","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W1980160788","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W4287182096","https://openalex.org/W27867058","https://openalex.org/W3160031511"],"abstract_inverted_index":{"A":[0],"wide":[1],"variety":[2],"of":[3,18,33,45,55,93,111,118,124,140,148,185,260],"large-scale":[4,41],"data":[5,21],"have":[6,58],"been":[7,23,115],"produced":[8],"in":[9,72,100],"bioinformatics.":[10],"In":[11,86],"response,":[12],"the":[13,30,69,104,152,227],"need":[14],"for":[15,40,209],"efficient":[16],"handling":[17],"biomedical":[19],"big":[20],"has":[22,114],"partly":[24],"met":[25],"by":[26,50,97,202,226],"parallel":[27,84],"computing.":[28],"However,":[29],"time":[31],"demand":[32],"many":[34],"bioinformatics":[35,128,143,168,220,251],"programs":[36,144,177],"still":[37],"remains":[38],"high":[39],"practical":[42],"uses":[43],"because":[44],"factors":[46],"that":[47,81,239,255],"hinder":[48],"acceleration":[49,79,201],"parallelization.":[51],"Recently,":[52],"new":[53,258],"generations":[54,259],"storage":[56,262],"devices":[57],"emerged,":[59],"such":[60,187,222],"as":[61,188,223],"NAND":[62],"flash-based":[63],"solid-state":[64],"drives":[65,96],"(SSDs),":[66],"and":[67,107,121,138,166,170,182,196,212,231,246],"with":[68,207],"renewed":[70],"interest":[71],"near-data":[73],"processing,":[74],"they":[75],"are":[76],"increasingly":[77],"becoming":[78],"methods":[80],"can":[82,204,217,242],"accompany":[83,249],"processing.":[85],"certain":[87],"cases,":[88],"a":[89],"simple":[90],"drop-in":[91],"replacement":[92],"hard":[94],"disk":[95],"SSDs":[98,208,216],"results":[99],"dramatic":[101],"speedup.":[102],"Despite":[103],"various":[105],"advantages":[106],"continuous":[108],"cost":[109],"reduction":[110],"SSDs,":[112],"there":[113],"little":[116],"review":[117,241],"SSD-based":[119],"profiling":[120,137],"performance":[122,211],"exploration":[123],"important":[125,219],"but":[126],"time-consuming":[127],"programs.":[129],"For":[130],"an":[131],"informative":[132],"review,":[133],"we":[134,154,159,178],"perform":[135],"in-depth":[136],"analysis":[139,233],"23":[141],"key":[142],"using":[145,215,234],"multiple":[146],"types":[147],"devices.":[149,263],"Based":[150],"on":[151],"insight":[153],"obtain":[155],"from":[156],"this":[157,240],"research,":[158],"further":[160],"discuss":[161],"issues":[162],"related":[163],"to":[164,172,248],"design":[165,253],"optimize":[167],"algorithms":[169],"pipelines":[171],"fully":[173],"exploit":[174],"SSDs.":[175],"The":[176],"profile":[179],"cover":[180],"traditional":[181],"emerging":[183],"areas":[184],"importance,":[186],"alignment,":[189],"assembly,":[190],"mapping,":[191],"expression":[192],"analysis,":[193],"variant":[194,224],"calling":[195,225],"metagenomics.":[197],"We":[198,237],"explain":[199],"how":[200,214],"parallelization":[203],"be":[205],"combined":[206],"improved":[210],"also":[213],"expedite":[218],"pipelines,":[221],"Genome":[228],"Analysis":[229],"Toolkit":[230],"transcriptome":[232],"RNA":[235],"sequencing.":[236],"hope":[238],"provide":[243],"useful":[244],"directions":[245],"tips":[247],"future":[250],"algorithm":[252],"procedures":[254],"properly":[256],"consider":[257],"powerful":[261]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
