{"id":"https://openalex.org/W3193770395","doi":"https://doi.org/10.1038/s43588-021-00113-z","title":"High performance computing framework for tera-scale database search of mass spectrometry data","display_name":"High performance computing framework for tera-scale database search of mass spectrometry data","publication_year":2021,"publication_date":"2021-08-20","ids":{"openalex":"https://openalex.org/W3193770395","doi":"https://doi.org/10.1038/s43588-021-00113-z","mag":"3193770395","pmid":"https://pubmed.ncbi.nlm.nih.gov/34723198"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-021-00113-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-021-00113-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8554525","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082182788","display_name":"Muhammad Haseeb","orcid":"https://orcid.org/0000-0002-0697-6894"},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Muhammad Haseeb","raw_affiliation_strings":["Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-0697-6894","affiliations":[{"raw_affiliation_string":"Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102729196","display_name":"Fahad Saeed","orcid":"https://orcid.org/0000-0002-3410-9552"},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fahad Saeed","raw_affiliation_strings":["Biomolecular Sciences Institute (BSI), Florida International University, Miami, FL, USA","Department of Human and Molecular Genetics, Herbert Wertheim School of Medicine, Florida International University, Miami, FL, USA","Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-3410-9552","affiliations":[{"raw_affiliation_string":"Biomolecular Sciences Institute (BSI), Florida International University, Miami, FL, USA","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"Department of Human and Molecular Genetics, Herbert Wertheim School of Medicine, Florida International University, Miami, FL, USA","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA","institution_ids":["https://openalex.org/I19700959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082182788"],"corresponding_institution_ids":["https://openalex.org/I19700959"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":1.4783,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.8119811,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"1","issue":"8","first_page":"550","last_page":"561"},"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":0.9991000294685364,"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":0.9908000230789185,"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":0.8138105869293213},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.6214706897735596},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6020697951316833},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.546511709690094},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.48466283082962036},{"id":"https://openalex.org/keywords/parallel-database","display_name":"Parallel database","score":0.457069993019104},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4560201168060303},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4279767870903015},{"id":"https://openalex.org/keywords/tera","display_name":"Tera-","score":0.42350947856903076},{"id":"https://openalex.org/keywords/symmetric-multiprocessor-system","display_name":"Symmetric multiprocessor system","score":0.42285650968551636},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.42126861214637756},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.40771862864494324},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1462148129940033}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8138105869293213},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6214706897735596},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6020697951316833},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.546511709690094},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.48466283082962036},{"id":"https://openalex.org/C2777541480","wikidata":"https://www.wikidata.org/wiki/Q2051600","display_name":"Parallel database","level":2,"score":0.457069993019104},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4560201168060303},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4279767870903015},{"id":"https://openalex.org/C2775904623","wikidata":"https://www.wikidata.org/wiki/Q108529","display_name":"Tera-","level":2,"score":0.42350947856903076},{"id":"https://openalex.org/C172430144","wikidata":"https://www.wikidata.org/wiki/Q17111997","display_name":"Symmetric multiprocessor system","level":2,"score":0.42285650968551636},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.42126861214637756},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.40771862864494324},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1462148129940033}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1038/s43588-021-00113-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-021-00113-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:34723198","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34723198","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:digitalcommons.fiu.edu:cs_fac-1027","is_oa":false,"landing_page_url":"https://digitalcommons.fiu.edu/cs_fac/28","pdf_url":null,"source":{"id":"https://openalex.org/S4306401637","display_name":"Florida International University Digital Commons (Florida International University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I19700959","host_organization_name":"Florida International University","host_organization_lineage":["https://openalex.org/I19700959"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"School of Computing and Information Sciences","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8554525","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8554525","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Comput Sci","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8554525","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8554525","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Comput Sci","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4555316915","display_name":null,"funder_award_id":"R01GM134384","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6706628490","display_name":null,"funder_award_id":"OAC-1925960","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1577446317","https://openalex.org/W1964194772","https://openalex.org/W1973333402","https://openalex.org/W1977180164","https://openalex.org/W1986060649","https://openalex.org/W1991502938","https://openalex.org/W1999751815","https://openalex.org/W2002555321","https://openalex.org/W2004515150","https://openalex.org/W2007176869","https://openalex.org/W2008117982","https://openalex.org/W2011354186","https://openalex.org/W2023655541","https://openalex.org/W2024668145","https://openalex.org/W2026465178","https://openalex.org/W2028673251","https://openalex.org/W2043701535","https://openalex.org/W2045271686","https://openalex.org/W2047275456","https://openalex.org/W2068016108","https://openalex.org/W2081930221","https://openalex.org/W2082006641","https://openalex.org/W2089273345","https://openalex.org/W2118294504","https://openalex.org/W2118544454","https://openalex.org/W2130706354","https://openalex.org/W2131806062","https://openalex.org/W2135078307","https://openalex.org/W2139096442","https://openalex.org/W2163078532","https://openalex.org/W2607310450","https://openalex.org/W2768087917","https://openalex.org/W2800303481","https://openalex.org/W2807827558","https://openalex.org/W2893957366","https://openalex.org/W2894727674","https://openalex.org/W2907043693","https://openalex.org/W2918401251","https://openalex.org/W2930099314","https://openalex.org/W2942957989","https://openalex.org/W2955234727","https://openalex.org/W2959428074","https://openalex.org/W2960326819","https://openalex.org/W2965249465","https://openalex.org/W2965474513","https://openalex.org/W2970571774","https://openalex.org/W2996870404","https://openalex.org/W3002735604","https://openalex.org/W3004571255","https://openalex.org/W3005653329","https://openalex.org/W3034583809","https://openalex.org/W3193770395","https://openalex.org/W4206366216","https://openalex.org/W6893888850","https://openalex.org/W6968478131"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W4389191251","https://openalex.org/W1919398273","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2319262638","https://openalex.org/W2783386063"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
