{"id":"https://openalex.org/W4382198841","doi":"https://doi.org/10.1093/bioinformatics/btad404","title":"Accelerating open modification spectral library searching on tensor core in high-dimensional space","display_name":"Accelerating open modification spectral library searching on tensor core in high-dimensional space","publication_year":2023,"publication_date":"2023-06-27","ids":{"openalex":"https://openalex.org/W4382198841","doi":"https://doi.org/10.1093/bioinformatics/btad404","pmid":"https://pubmed.ncbi.nlm.nih.gov/37369033"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad404","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad404/50725390/btad404.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad404/50725390/btad404.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072579616","display_name":"Jaeyoung Kang","orcid":"https://orcid.org/0000-0003-1048-1285"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaeyoung Kang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California San Diego, San Diego , CA 92093, United States"],"raw_orcid":"https://orcid.org/0000-0003-1048-1285","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California San Diego, San Diego , CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039571679","display_name":"Weihong Xu","orcid":"https://orcid.org/0000-0003-3766-3353"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weihong Xu","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053271927","display_name":"Wout Bittremieux","orcid":"https://orcid.org/0000-0002-3105-1359"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210119540","display_name":"Province of Antwerp","ror":"https://ror.org/022v8s261","country_code":"BE","type":"government","lineage":["https://openalex.org/I4210119540"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Wout Bittremieux","raw_affiliation_strings":["Department of Computer Science, University of Antwerp , Antwerpen 2020, Belgium","Department of Computer Science, University of Antwerp, Antwerpen, 2020, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-3105-1359","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Antwerp , Antwerpen 2020, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210119540"]},{"raw_affiliation_string":"Department of Computer Science, University of Antwerp, Antwerpen, 2020, Belgium","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008998282","display_name":"Niema Moshiri","orcid":"https://orcid.org/0000-0003-2209-8128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niema Moshiri","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States"],"raw_orcid":"https://orcid.org/0000-0003-2209-8128","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112841571","display_name":"Tajana Rosing","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tajana Rosing","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California San Diego, San Diego , CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5112841571"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6454,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.82022472,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.5077000260353088,"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":0.5077000260353088,"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/T12808","display_name":"Ferroelectric and Negative Capacitance Devices","score":0.15219999849796295,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.020999999716877937,"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":0.8027775883674622},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6715309619903564},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.585143506526947},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.481202632188797},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.47851765155792236},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.46555736660957336},{"id":"https://openalex.org/keywords/tensor","display_name":"Tensor (intrinsic definition)","score":0.46166542172431946},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45106369256973267},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.43712905049324036},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4367212653160095},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4175931513309479},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11578533053398132},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09585598111152649}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8027775883674622},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6715309619903564},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.585143506526947},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.481202632188797},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.47851765155792236},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.46555736660957336},{"id":"https://openalex.org/C155281189","wikidata":"https://www.wikidata.org/wiki/Q3518150","display_name":"Tensor (intrinsic definition)","level":2,"score":0.46166542172431946},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45106369256973267},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.43712905049324036},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4367212653160095},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4175931513309479},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11578533053398132},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09585598111152649},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad404","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad404/50725390/btad404.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37369033","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37369033","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6800p770","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6800p770","pdf_url":"https://escholarship.org/content/qt6800p770/qt6800p770.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 39, iss 7","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10323168","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10323168","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10323168/pdf/btad404.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:ark:/13030/qt6800p770","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:c:irua:198272","is_oa":false,"landing_page_url":"https://hdl.handle.net/10067/1982720151162165141","pdf_url":null,"source":{"id":"https://openalex.org/S4306401849","display_name":"Institutional Repository University of Antwerp (University of Antwerp)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149213910","host_organization_name":"University of Antwerp","host_organization_lineage":["https://openalex.org/I149213910"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad404","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad404","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad404/50725390/btad404.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4300000071525574}],"awards":[{"id":"https://openalex.org/G317115702","display_name":"FET: Small: Brain-Inspired Hyperdimensional Computing for IoT Applications","funder_award_id":"1911095","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3744848179","display_name":"AI Institute for Learning-Enabled Optimization at Scale (TILOS)","funder_award_id":"2112665","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G502606643","display_name":"CC* NPEO: Toward the National Research Platform","funder_award_id":"1826967","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5665456810","display_name":"CCRI: ABR: Cognitive Hardware and Software Ecosystem Community Infrastructure (CHASE-CI)","funder_award_id":"2100237","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6003409357","display_name":"Category II: A Prototype National Research Platform","funder_award_id":"2112167","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6026952011","display_name":"IUCRC Phase I University of California, San Diego: Center for Power Management Integration (PMIC)","funder_award_id":"2052809","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7539330175","display_name":null,"funder_award_id":"2112167","funder_id":"https://openalex.org/F4320306087","funder_display_name":"Semiconductor Research Corporation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306087","display_name":"Semiconductor Research Corporation","ror":"https://ror.org/047z4n946"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382198841.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1480858518","https://openalex.org/W1573706465","https://openalex.org/W1973495005","https://openalex.org/W1993941153","https://openalex.org/W2013589890","https://openalex.org/W2013955377","https://openalex.org/W2021613526","https://openalex.org/W2053573662","https://openalex.org/W2057761395","https://openalex.org/W2059651000","https://openalex.org/W2070862086","https://openalex.org/W2073637473","https://openalex.org/W2096057003","https://openalex.org/W2098354599","https://openalex.org/W2109204063","https://openalex.org/W2179747797","https://openalex.org/W2289616942","https://openalex.org/W2314880009","https://openalex.org/W2465480251","https://openalex.org/W2478131123","https://openalex.org/W2607310450","https://openalex.org/W2789457189","https://openalex.org/W2888985586","https://openalex.org/W2894727674","https://openalex.org/W2930099314","https://openalex.org/W2949278902","https://openalex.org/W2970104449","https://openalex.org/W2993327327","https://openalex.org/W3021560762","https://openalex.org/W3108954960","https://openalex.org/W3138817412","https://openalex.org/W3192003864","https://openalex.org/W4285146458"],"related_works":["https://openalex.org/W2220968517","https://openalex.org/W2163816448","https://openalex.org/W2327123731","https://openalex.org/W2009665355","https://openalex.org/W185782823","https://openalex.org/W2095734710","https://openalex.org/W2060611139","https://openalex.org/W1965860946","https://openalex.org/W2168586703","https://openalex.org/W2027201655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Driven":[1],"by":[2,17,36],"technological":[3],"advances,":[4],"the":[5,59,116,137,154,194,216,252],"throughput":[6],"and":[7,108,192,212,236],"cost":[8],"of":[9,19,42,120,140,156,186],"mass":[10,34,161],"spectrometry":[11],"(MS)":[12],"proteomics":[13,122],"experiments":[14],"have":[15],"improved":[16],"orders":[18],"magnitude":[20],"in":[21,58,136,190,215],"recent":[22,217],"decades.":[23],"Spectral":[24],"library":[25,61,142],"searching":[26,81],"is":[27,53,83,112,179,210,227,248],"a":[28,146],"common":[29],"approach":[30,87],"to":[31,46,88,103,159,164,240],"annotating":[32],"experimental":[33],"spectra":[35,44,197],"matching":[37],"them":[38],"against":[39,96],"large":[40,105],"libraries":[41],"reference":[43],"corresponding":[45],"known":[47],"peptides.":[48],"An":[49],"important":[50],"disadvantage,":[51],"however,":[52],"that":[54,132,225],"only":[55],"peptides":[56,91],"included":[57],"spectral":[60,141,162],"can":[62,172],"be":[63,173],"found,":[64],"whereas":[65],"novel":[66],"peptides,":[67],"such":[68],"as":[69,256],"those":[70],"with":[71],"unexpected":[72],"post-translational":[73],"modifications":[74],"(PTMs),":[75],"will":[76],"remain":[77],"unknown.":[78],"Open":[79],"modification":[80],"(OMS)":[82],"an":[84,127,257],"increasingly":[85],"popular":[86],"annotate":[89],"modified":[90],"based":[92,152],"on":[93,153,204,230],"partial":[94],"matches":[95],"their":[97],"unmodified":[98],"counterparts.":[99],"Unfortunately,":[100],"this":[101],"leads":[102],"very":[104],"search":[106,189,234,242],"spaces":[107],"excessive":[109],"runtimes,":[110],"which":[111,209],"especially":[113],"problematic":[114],"considering":[115,199],"continuously":[117],"increasing":[118],"sizes":[119],"MS":[121],"datasets.":[123],"RESULTS:":[124],"We":[125,144,201],"propose":[126],"OMS":[128],"algorithm,":[129],"called":[130],"HOMS-TC,":[131],"fully":[133],"exploits":[134],"parallelism":[135],"entire":[138],"pipeline":[139],"searching.":[143],"designed":[145],"new":[147],"highly":[148],"parallel":[149,191],"encoding":[150],"method":[151],"principle":[155],"hyperdimensional":[157],"computing":[158],"encode":[160],"data":[163],"hypervectors":[165],"while":[166,198],"minimizing":[167],"information":[168],"loss.":[169],"This":[170],"process":[171],"easily":[174],"parallelized":[175],"since":[176],"each":[177],"dimension":[178],"calculated":[180],"independently.":[181],"HOMS-TC":[182,203,226,247],"processes":[183],"two":[184],"stages":[185],"existing":[187],"cascade":[188],"selects":[193],"most":[195],"similar":[196],"PTMs.":[200],"accelerate":[202],"NVIDIA's":[205],"tensor":[206],"core":[207],"units,":[208],"emerging":[211],"readily":[213],"available":[214,250],"graphics":[218],"processing":[219],"unit":[220],"(GPU).":[221],"Our":[222],"evaluation":[223],"shows":[224],"31\u00d7":[228],"faster":[229],"average":[231],"than":[232],"alternative":[233],"engines":[235],"provides":[237],"comparable":[238],"accuracy":[239],"competing":[241],"tools.":[243],"AVAILABILITY":[244],"AND":[245],"IMPLEMENTATION:":[246],"freely":[249],"under":[251],"Apache":[253],"2.0":[254],"license":[255],"open-source":[258],"software":[259],"project":[260],"at":[261],"https://github.com/tycheyoung/homs-tc.":[262]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
