{"id":"https://openalex.org/W2903863343","doi":"https://doi.org/10.1186/s12859-018-2559-6","title":"Accelerating a cross-correlation score function to search modifications using a single GPU","display_name":"Accelerating a cross-correlation score function to search modifications using a single GPU","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2903863343","doi":"https://doi.org/10.1186/s12859-018-2559-6","mag":"2903863343","pmid":"https://pubmed.ncbi.nlm.nih.gov/30541430"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2559-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2559-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2559-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2559-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100330183","display_name":"Hyunwoo Kim","orcid":"https://orcid.org/0000-0001-6785-7760"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Hyunwoo Kim","raw_affiliation_strings":["Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea. pardess@kisti.re.kr","Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea. pardess@kisti.re.kr","institution_ids":[]},{"raw_affiliation_string":"Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea","institution_ids":["https://openalex.org/I878022262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110734557","display_name":"Sunggeun Han","orcid":null},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sunggeun Han","raw_affiliation_strings":["KISTI Scientific Data School, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"KISTI Scientific Data School, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea","institution_ids":["https://openalex.org/I878022262"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077982415","display_name":"Jung-Ho Um","orcid":"https://orcid.org/0000-0002-8301-8753"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jung-Ho Um","raw_affiliation_strings":["Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea","institution_ids":["https://openalex.org/I878022262"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003111778","display_name":"Kyongseok Park","orcid":"https://orcid.org/0000-0001-5164-7099"},"institutions":[{"id":"https://openalex.org/I878022262","display_name":"Korea Institute of Science & Technology Information","ror":"https://ror.org/01k4yrm29","country_code":"KR","type":"facility","lineage":["https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I878022262"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyongseok Park","raw_affiliation_strings":["Super Computing Cloud Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Super Computing Cloud Center, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea","institution_ids":["https://openalex.org/I878022262"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100330183"],"corresponding_institution_ids":["https://openalex.org/I878022262"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4056,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.58814171,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"1","first_page":"480","last_page":"480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9986000061035156,"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":0.7254135012626648},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.6508983969688416},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.6000512838363647},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.49309632182121277},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.49116989970207214},{"id":"https://openalex.org/keywords/comet","display_name":"Comet","score":0.48110121488571167},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4493171274662018},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3440518379211426},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23159268498420715},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.19759562611579895},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.11668169498443604},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09929749369621277},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09651607275009155},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08622899651527405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07577520608901978}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7254135012626648},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.6508983969688416},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.6000512838363647},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.49309632182121277},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.49116989970207214},{"id":"https://openalex.org/C94081185","wikidata":"https://www.wikidata.org/wiki/Q3559","display_name":"Comet","level":2,"score":0.48110121488571167},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4493171274662018},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3440518379211426},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23159268498420715},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.19759562611579895},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.11668169498443604},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09929749369621277},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09651607275009155},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08622899651527405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07577520608901978},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2559-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2559-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2559-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30541430","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30541430","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 bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:b19cc4d6aaa845f99c4764a2bd968c7b","is_oa":true,"landing_page_url":"https://doaj.org/article/b19cc4d6aaa845f99c4764a2bd968c7b","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-5 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5265277","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6291950","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:6291950","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6291950","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2559-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2559-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2559-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322091","display_name":"Korea Institute of Science and Technology","ror":"https://ror.org/05kzfa883"},{"id":"https://openalex.org/F4320322105","display_name":"Korea Institute of Science and Technology Information","ror":"https://ror.org/01k4yrm29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2903863343.pdf","grobid_xml":"https://content.openalex.org/works/W2903863343.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1480858518","https://openalex.org/W1964194772","https://openalex.org/W1968044788","https://openalex.org/W1973333402","https://openalex.org/W1979231364","https://openalex.org/W2026465178","https://openalex.org/W2089273345","https://openalex.org/W2091375086","https://openalex.org/W2099515044","https://openalex.org/W2788106874"],"related_works":["https://openalex.org/W3049149308","https://openalex.org/W3036339064","https://openalex.org/W3132686465","https://openalex.org/W3080418168","https://openalex.org/W3031501629","https://openalex.org/W2985497073","https://openalex.org/W3017696152","https://openalex.org/W3006542304","https://openalex.org/W3017046140","https://openalex.org/W4229906614"],"abstract_inverted_index":{"We":[0],"propose":[1],"the":[2],"accelerating":[3],"score":[4],"function":[5],"to":[6],"search":[7],"modifications":[8],"using":[9],"a":[10],"single":[11],"GPU.":[12],"The":[13],"software":[14],"is":[15],"available":[16],"at":[17],"https://github.com/Tide-for-PTM-search/Tide-for-PTM-search":[18],".":[19]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
