{"id":"https://openalex.org/W4404571009","doi":"https://doi.org/10.1109/tcbbio.2026.3657252","title":"gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs","display_name":"gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs","publication_year":2026,"publication_date":"2026-01-23","ids":{"openalex":"https://openalex.org/W4404571009","doi":"https://doi.org/10.1109/tcbbio.2026.3657252","pmid":"https://pubmed.ncbi.nlm.nih.gov/41576120"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3657252","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3657252","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2411.11547","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2597-8331","affiliations":[{"raw_affiliation_string":"Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075168236","display_name":"Felix Kallenborn","orcid":"https://orcid.org/0000-0003-4516-6357"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Felix Kallenborn","raw_affiliation_strings":["Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4516-6357","affiliations":[{"raw_affiliation_string":"Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054938143","display_name":"Alexander Wichmann","orcid":"https://orcid.org/0000-0002-6138-6475"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander Wichmann","raw_affiliation_strings":["Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6138-6475","affiliations":[{"raw_affiliation_string":"Insitute of Computer Science, Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072699100","display_name":"Alejandro Chac\u00f3n","orcid":"https://orcid.org/0000-0001-8851-7618"},"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":"Alejandro Chacon","raw_affiliation_strings":["NVIDIA Corporation, Santa Clara, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-8851-7618","affiliations":[{"raw_affiliation_string":"NVIDIA Corporation, Santa Clara, CA, USA","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027561629","display_name":"Christian Hundt","orcid":"https://orcid.org/0000-0002-7995-1858"},"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":"Christian Hundt","raw_affiliation_strings":["NVIDIA Corporation, Santa Clara, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-7995-1858","affiliations":[{"raw_affiliation_string":"NVIDIA Corporation, Santa Clara, CA, USA","institution_ids":["https://openalex.org/I4210127875"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.9847,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.86148328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"23","issue":"2","first_page":"788","last_page":"794"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9835000038146973,"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/T12029","display_name":"DNA and Biological Computing","score":0.9835000038146973,"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":0.9684000015258789,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9667999744415283,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.6226598620414734},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5830459594726562},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5375008583068848},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.461590051651001},{"id":"https://openalex.org/keywords/speech-recognition","display_name":"Speech recognition","score":0.2577221989631653}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6226598620414734},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5830459594726562},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5375008583068848},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.461590051651001},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.2577221989631653}],"mesh":[{"descriptor_ui":"D000098436","descriptor_name":"Parallel Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098436","descriptor_name":"Parallel Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098436","descriptor_name":"Parallel Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098436","descriptor_name":"Parallel 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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbbio.2026.3657252","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3657252","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41576120","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41576120","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2411.11547","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2411.11547","pdf_url":"https://arxiv.org/pdf/2411.11547","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2411.11547","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2411.11547","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2411.11547","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2411.11547","pdf_url":"https://arxiv.org/pdf/2411.11547","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4404571009.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2053269318","https://openalex.org/W2364370872","https://openalex.org/W2097963413","https://openalex.org/W2294335174","https://openalex.org/W2025614924","https://openalex.org/W2051487156","https://openalex.org/W3145575561"],"abstract_inverted_index":{"The":[0],"continually":[1],"increasing":[2],"volume":[3],"of":[4,17,21,62,80,144,166],"DNA":[5,37],"sequence":[6],"data":[7],"has":[8],"resulted":[9],"in":[10,36],"a":[11,33,106,164],"growing":[12],"demand":[13],"for":[14,94,111],"fast":[15],"implementations":[16,157],"core":[18],"algorithms.":[19],"Computation":[20],"pairwise":[22],"alignments":[23],"between":[24],"candidate":[25],"haplotypes":[26],"and":[27,58,121,131,161,171],"sequencing":[28],"reads":[29],"using":[30,74],"Pair-HMMs":[31],"is":[32],"key":[34],"component":[35],"variant":[38],"calling":[39],"tools":[40],"such":[41],"as":[42],"the":[43,59,75,92,112],"GATK":[44],"HaplotypeCaller":[45],"but":[46],"can":[47],"be":[48,65],"highly":[49],"time":[50,56],"consuming":[51],"due":[52],"to":[53,64,70],"its":[54],"quadratic":[55],"complexity":[57],"large":[60],"number":[61],"pairs":[63],"aligned.":[66],"Unfortunately,":[67],"previous":[68],"approaches":[69],"accelerate":[71],"this":[72,100],"task":[73],"massively":[76],"parallel":[77],"processing":[78],"capabilities":[79],"modern":[81,145],"GPUs":[82,147],"are":[83],"limited":[84],"by":[85,102,126,163],"inefficient":[86],"memory":[87,129],"access":[88],"schemes.":[89],"This":[90],"established":[91],"need":[93,101],"significantly":[95],"faster":[96],"solutions.":[97],"We":[98,133],"address":[99],"presenting":[103],"gpuPairHMM":[104],"-":[105],"novel":[107],"GPU-based":[108],"parallelization":[109],"scheme":[110],"dynamic-programming":[113],"based":[114,118],"Pair-HMM":[115],"forward":[116],"algorithm":[117],"on":[119,141,158],"wavefronts":[120],"warp-shuffles.":[122],"It":[123,153],"gains":[124],"efficiency":[125],"minimizing":[127],"both":[128],"accesses":[130],"instructions.":[132],"show":[134],"that":[135],"our":[136],"approach":[137],"achieves":[138],"close-to-peak":[139],"performance":[140],"several":[142],"generations":[143],"CUDA-enabled":[146],"(Volta,":[148],"Ampere,":[149],"Ada,":[150],"Hopper,":[151],"Blackwell).":[152],"also":[154],"outperforms":[155],"prior":[156],"GPUs,":[159],"CPUs,":[160],"FPGAs":[162],"factor":[165],"at":[167],"least":[168],"11.7,":[169],"14.2,":[170],"19.8,":[172],"respectively.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2024-11-21T00:00:00"}